The NMDC Ontology (NMDCO) is used by the National Micrbiome Data Collaborative (NMDC, https://microbiomedata.org) to annotate multi-omic microbiome metadata. It merges a number of ontologies relevant to the NMDC (such as the plant and environment ontologies) into a single ontology. It is maintained using Github at https://github.com/microbiomedata/nmdc-ontology. Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
editor preferred term~editor preferred label
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Add as annotation triples in the granting ontology
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
tooth SubClassOf 'never in taxon' value 'Aves'
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Class: ?X DisjointWith: RO_0002162 some ?Y
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . }
mutually spatially disjoint with
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
ambiguous for taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
dubious for taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
present in taxon
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
annotation property cardinality
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
brain always_present_in_taxon 'Vertebrata'
forelimb always_present_in_taxon Euarchontoglires
S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
temporal logical macro assertion on a class
Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
Count of number of days intervening between the start of the stage and the time of coitum.
For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
Count of number of days intervening between the end of the stage and the time of coitum.
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
is asymmetric relational form of process class
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
is symmetric relational form of process class
R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
A shortcut relationship that holds between two entities based on their identity criteria
logical macro assertion involving identity
A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
in approximate one to one relationship with
x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
evidential logical macro assertion on an axiom
A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
is representative IRI for equivalence set
OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.
nominally disjoint with
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
valid_for_go_annotation_extension
valid_for_go_gp2term
valid_for_go_ontology
valid_for_gocam
A is disconnected_from B if they have no parts in common.
Relational slim: types of quality that require an additional entity in order to exist
Term used for mosses, liverworts, and/or hornworts
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x proximal to y iff x is closer to the point of attachment with the body than y.
The elbow is proximal to the hand, but distal to the shoulder.
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
x immediately deep to y iff x deep_to y and x is contiguous with y.
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
X intersects median plane of iff X crosses the midine plane of Y.
x immediately superficial to y iff x superficial to y and x is contiguous with y.
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x
Definition modified from 'surrounded by'.
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
derives from part of
A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities.
This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen.
Afforestation results in the expansion of a forest.
A process, p, results in the expansion of a material entity, m, if the spatial extent of m is increased as a result of participating in p.
A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process.
A derives_by_manipulation_from B means: A is a type of in vitro plant structure, and every instance of A exists at a point in time later than some instance of B from which it was created through human manipulation, and every instance of A inherited a biologically significant portion of its matter from the instance of B from which it was derived.
The derives_by_manipulation_from relation, is a special case of the RO relation derives_from. Derives_from implies an instance level derivation that holds between two distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Likewise, derives_by_manipulation_from joins two plant structures before and after some manipulation. Specifically, derives_by_manipulation_from is used to describe the relation between an in vitro plant structure and the in vivo plant structure that is its temporal precursor.
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is allergic trigger for
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has allergic trigger
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has autoimmune trigger
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
surface of
2D boundary of
May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
aligned with
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
A relation that holds between two neurons that are electrically coupled via gap junctions.
The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
tracheates
innervated_by
has synaptic terminal of
X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y
x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
A part of relation that applies only between occurrents.
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
in register with
Primitive instance level timing relation between events
before or simultaneous with
x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
starts before
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and a material anatomical entity that its soma is part of.
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
(forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
fasciculates with
Relation between a neuron and some structure its axon forms (chemical) synapses in.
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
axon synapses in
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
synapsed by
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Ib_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_Is_bouton_to
A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_II_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_II_bouton
Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Ib_bouton
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapsed in
http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
has postsynaptic terminal in
releases neurotransmitter
Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_Is_bouton
synapses in
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has presynaptic terminal in
A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
synapsed_via_type_III_bouton_to
Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
synapsed_by_via_type_III_bouton
Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
synapsed to
Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
dendrite synapsed in
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has synaptic terminal in
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
has fasciculating component
(forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
has fasciculating neuron projection
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
(forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
partially overlaps
d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
Consider obsoleting and merging with child relation, 'in homology relationship with'
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
has phenotype
phenotype of
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
David Osumi-Sutherland
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
gene product of
every HOTAIR lncRNA is the gene product of some HOXC gene
every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
has gene product
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
A parasite that kills or sterilizes its host
directly develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
has prototype
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
develops in
A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)
A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)
A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.
X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.
This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.
has component participant
A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
A broad relationship between an exposure event or process and the course takes from the source to the target.
Any relationship between an exposure event or process and any other entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
Any portion of roundup 'has active ingredient' some glyphosate
A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
developmentally induced by
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
X developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p.
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
developmentally replaces
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
ubiquitously expressed in
y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses
ubiquitously expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
results in formation of anatomical entity
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
results in maturation of
foramen ovale closure SubClassOf results in disappearance of foramen ovale
results in disappearance of
every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
results in developmental regression of
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
evolutionary variant of
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
transports or maintains localization of
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
results in acquisition of features of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
confers advantage in
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
colocalizes with
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
regulates levels of
enabled by
regulated by
negatively regulated by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
has target end location
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
imports
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
results in transport across
'pollen tube growth' results_in growth_of some 'pollen tube'
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
results in transport to from or in
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
exports
an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
results in commitment to
p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
results in determination of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
formed as result of
A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
results in structural organization of
The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
results in specification of
p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
results in developmental induction of
has dendrite location
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
has muscle origin
We need to import uberon muscle to create a stricter domain constraint
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
has muscle insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.
derived from ancestral fusion of
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary of
Deschutes River distributary_of Little Lava Lake
x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
distributary of
x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
anabranch of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
branching part of
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
main stem of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
proper distributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
proper tributary of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
'protein catabolic process' SubClassOf has_direct_input some protein
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
directly provides input for (process to process)
provides input for
transitive form of directly_provides_input_for
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
transitively provides input for (process to process)
transitively provides input for
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
differs in
differs in attribute of
differs in attribute
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
An interaction relationship in which the partners are related via a feeding relationship.
A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
is subject of predation interaction with
A biotic interaction in which the two organisms live together in more or less intimate association.
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
This relation groups a pair of inverse relations, parasite of and parasitized by
interacts with via parasite-host interaction
Pediculus humanus capitis parasite of human
A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
participates in a abiotic-biotic interaction with
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
all dengue disease transmitted by some mosquito
A relationship that holds between a disease and organism
A relation that holds between a disease or an organism and a phenotype
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
is subject of pollination interaction with
is target of pollination interaction with
Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
ABal nucleus child nucleus of ABa nucleus (in C elegans)
c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
A child nucleus relationship in which the cells are part of a hermaphroditic organism
A child nucleus relationship in which the cells are part of a male organism
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
x is transcribed from y if and only if x is synthesized from template y
x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
A relation that holds between two entities that have the property of being sequences or having sequences.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
Every UTR is adjacent to a CDS of the same transcript
Two consecutive DNA residues are sequentially adjacent
Two exons on a processed transcript that were previously connected by an intron are adjacent
x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
Every CDS has as a start sequence the start codon for that transcript
x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
In the SO paper, this was defined as an instance-type relation
Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
x has subsequence y iff all of the sequence parts of y are sequence parts of x
x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
is immediately downstream of sequence of
A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y
x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
A relation that holds between an attribute or a qualifier and another attribute.
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
participates in a biotic-biotic interaction with
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
capable of inhibiting or preventing pathological process
Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
capable of upregulating or causing pathological process
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
In the Gene Ontology association model, this corresponds to the With/From field
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite
A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
inverse of intercellular endoparasite of
A sub-relation of endoparasite-of in which the parasite inhabits host cells.
inverse of intracellular endoparasite of
Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
co-roosts with
An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts.
An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
is used to study
The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.
has role in modeling
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
causes condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
contributes to severity of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
contributes to frequency of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
ameliorates condition
A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
correlated with condition
A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
exacerbates condition
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
condition ameliorated by
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
condition exacerbated by
Do not use this relation directly. It is intended as a grouping for a more specific relations
has material basis in gain of function germline mutation in
has material basis in loss of function germline mutation in
has material basis in germline mutation in
has material basis in somatic mutation in
has partial material basis in germline mutation in
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
is causal gain of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
is causal loss of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
is causal germline mutation partially giving rise to
A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
disease has basis in dysfunction of (disease to anatomical structure)
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
disease has basis in disruption of (disease to process)
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
causal relationship with disease as subject
A relationship between a disease and a process where the disease process disrupts the execution of the process.
disease causes disruption of (disease to process)
disease causes dysfunction of (disease to anatomical entity)
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
TODO: complete range axiom once more of CARO has been mireoted in to this ontology
This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.
disease arises from alteration in structure
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.
A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.
An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.
An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.
An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.
Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.
has roost
muffin 'has substance added' some 'baking soda'
"has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
has substance added
'egg white' 'has substance removed' some 'egg yolk'
"has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
has substance removed
sardines 'immersed in' some 'oil and mustard'
"immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
immersed in
sardine has consumer some homo sapiens
'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
has consumer
bread 'has primary substance added' some 'flour'
'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
has primary substance added
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
indirectly regulates activity of
The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
The entity A has an activity that directly positively regulates the quantity of B.
directly positively regulates quantity of
The entity A has an activity that directly negatively regulates the quantity of B.
directly negatively regulates quantity of
The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
indirectly positively regulates activity of
AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
indirectly negatively regulates activity of
The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
indirectly negatively regulates quantity of
The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
indirectly positively regulates quantity of
a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
has small molecule regulator
a relation between a process and a continuant, in which the process is activated by the small molecule continuant
has small molecule activator
a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
has small molecule inhibitor
p acts on population of c iff c' is a collection, has members of type c, and p has participant c
acts on population of
a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
is small molecule regulator of
a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
is small molecule activator of
a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
is small molecule inhibitor of
The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
results in adhesion of
results in fusion of
p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
constitutively upstream of
p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
removes input for
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
positively regulates in another organism
x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
negatively regulates in another organism
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
has synaptic IO in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
receives synaptic input in region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
sends synaptic output to region
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
has synaptic IO throughout
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
receives synaptic input throughout
A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
sends synaptic output throughout
Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
has sensory dendrite in
A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
receives synaptic input from neuron
A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.
sends synaptic output to cell
A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
This relation is not meant to capture the relation between occurrents and data.
A relation between a group and another group it is part of but does not fully constitute.
X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics.
'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
A relation between entities in which one increases or decreases as the other does the same.
directly correlated with
positively correlated with
A relation between entities in which one increases as the other decreases.
inversely correlated with
negatively correlated with
anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
A relation between a container and measurement datum that specifies the actual amount of material in the container.
contains measured amount
Helper relation for OWL definition of RO:0018002 myristoylates
A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input
mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor
pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level
tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical.
pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.
neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.
(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
is tautomer of
carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.
is substitutent group from
hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
has functional parent
dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
is enantiomer of
pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.
has parent hydride
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.
brachial artery vessel supplies blood to brachialis muscle
x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
cystic vein vessel drains blood from gallbladder
x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
alveolar capillary directly supplies and drains some alveolus
x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.
This relation groups relations between diseases and any other kind of entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
p has anatomical participant c iff p has participant c, and c is an anatomical entity
results in changes to anatomical or cellular structure
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
Similarity that results from common evolutionary origin.
This broad definition encompasses all the working definitions proposed so far in the literature.
Similarity that results from independent evolution.
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
Homoplasy that involves different underlying mechanisms or structures.
Convergence usually implies a notion of adaptation.
Homoplasy that involves homologous underlying mechanisms or structures.
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
Homology that is defined by similarity with regard to selected structural parameters.
in structural homology relationship with
Homology that is defined by common descent.
in historical homology relationship with
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
in biological homology relationship with
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
Structural homology that is detected by similarity in content and organization between chromosomes.
Historical homology that involves genes that diverged after a duplication event.
Paralogy that involves sets of syntenic blocks.
Syntenic homology that involves chromosomes of different species.
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
in protein structural homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
in non functional homology relationship with
Historical homology that involves genes that diverged after a speciation event.
The term is sometimes also used for anatomical structures.
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
Historical homology that involves two members sharing no other homologs in the lineages considered.
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
Paralogy that results from a whole genome duplication event.
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
Paralogy that results from a duplication preceding a given speciation event.
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
Iterative homology that involves structures arranged along the main body axis.
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
in heterochronous homology relationship with
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
Paedomorphosis that is produced by a retardation of somatic development.
Convergence that results from co-evolution usually involving an evolutionary arms race.
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
in 1 to many orthology relationship with
Historical homology that involves two members of a larger set of homologs.
in many to many homology relationship with
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
Historical homology that is based on distant shared ancestry.
This term is usually contrasted to apomorphy.
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
Used for structures in distantly related taxa.
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
in chromosomal homology relationship with
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
in many to many orthology relationship with
Paralogy that involves genes from the same species.
in within-species paralogy relationship with
Paralogy that involves genes from different species.
The genes have diverged before a speciation event.
in between-species paralogy relationship with
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
Peramorphosis that is produced by a delay in the offset of development.
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
Orthology that involves functional equivalent genes with retention of the ancestral function.
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
Used for structures in closely related taxa.
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
These genes may come out as paralogs in a single-genome analysis.
Historical homology that involves functional equivalent genes with retention of the ancestral function.
This may include examples of orthology, paralogy and xenology.
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
Similarity that is characterized by interchangeability in function.
in functional equivalence relationship with
Biological homology that involves parts of the same organism.
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
This phenomenon is usually due to gene conversion process.
Structural homology that involves structures with the same or similar relative positions.
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
Biological homology that involves an ectopic structure and the normally positioned structure.
Synology that results from allopolyploidy.
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
has increased age-specific mortality rate
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
temporal region
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
characteristic
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
fiat object
fiat object part
object aggregate
site
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
process boundary
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
one-dimensional continuant fiat boundary
two-dimensional continuant fiat boundary
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
dicarboxylic acids and O-substituted derivatives
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3.
Any steroid that has beta-configuration at position 5.
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.
A simple monocarboxylic acid containing two carbons.
Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals.
A peptide containing ten or more amino acid residues.
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.
A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells.
A naturally occurring polypeptide synthesized at the ribosome.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position.
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid
2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid
2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
A compound in which a carbohydrate component is covalently bound to a protein component.
An aldohexose used as a source of energy and metabolic intermediate.
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
Any polysaccharide containing a substantial proportion of aminomonosaccharide residues.
Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose).
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
An iron group element atom that has atomic number 26.
That part of DNA or RNA that may be involved in pairing.
A phosphate ion that is the conjugate base of hydrogenphosphate.
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
A sodium salt of the conjugate of any bile acid with either glycine or taurine.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond.
Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position.
Any compound containing an indole skeleton.
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
A salt is an assembly of cations and anions.
A molecular entity having a net electric charge.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
mitochondrial respiratory-chain inhibitor
A molecule all atoms of which have the same atomic number.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan.
An oxoacid containing a single carboxy group.
An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.
Any organic ion with a net negative charge.
Any organic ion with a net positive charge.
Compounds of the general formula SO3HOR where R is an organyl group
An oxide is a chemical compound of oxygen with other chemical elements.
Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine.
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
Any alkali metal salt having sodium(1+) as the cation.
An ester of an alcohol and sulfuric acid.
A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom.
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
Tryptamine and its substitution derivatives.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
A polydisperse, highly branched glucan composed of chains of D-glucopyranose residues in alpha(1->4) glycosidic linkage, joined together by alpha(1->6) glycosidic linkages. A small number of alpha(1->3) glycosidic linkages and some cumulative alpha(1->6) links also may occur. The branches in glycogen typically contain 8 to 12 glucose residues.
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
A primary amino compound that is the 5-hydroxy derivative of tryptamine.
An onium cation obtained by protonation of ammonia.
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A monoatomic monocation obtained from sodium.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid.
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
A monoatomic entity is a molecular entity consisting of a single atom.
An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
An agrochemical is a substance that is used in agriculture or horticulture.
A fertilizer is any substance that is added to soil or water to assist the growth of plants.
A molecular entity containing one or more atoms of an alkali metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.
A molecular entity containing one or more atoms of a transition element.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
Any compound containing an o-diphenol component.
4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.
A catecholamine in which C-1 of the aminoethyl side-chain is hydroxy-substituted.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A molecule that features two fused rings.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A cation consisting of more than one atom.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
A hexose with a (potential) aldehyde group at one end.
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
An ammonium ion that is the conjugate acid of serotonin; major species at pH 7.3.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
A substance that diminishes the rate of a chemical reaction.
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups.
A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc).
A choline ester formed from choline and a carboxylic acid.
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A substance that reduces or suppresses inflammation.
A drug that mimics the effects of stimulating postganglionic adrenergic sympathetic nerves. Included in this class are drugs that directly stimulate adrenergic receptors and drugs that act indirectly by provoking the release of adrenergic transmitters.
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
An agent that selectively binds to and activates alpha-adrenergic receptors.
A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n.
A drug used to cause dilation of the blood vessels.
Any carboxylic acid containing two carboxy groups.
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
A steroid acid that consists of cholane having a carboxy group in place of the methyl group at position 24.
(5beta,17beta)-gamma-methylandrostane-17-butanoic acid
Members of the class of cholanic acids based on a 5beta-cholane skeleton.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
saturated organic heteromonocyclic parent
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
Compounds based on a biladiene skeleton.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A polysaccharide composed of glucose residues.
Glycans composed of a single type of monosaccharide residue. They are named by replacing the ending '-ose' of the sugar by '-an'.
Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid.
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
An agent that selectively binds to and activates adrenergic receptors.
Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter.
A compound composed of two or more pyrrole units.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons.
Any drug that binds to and activates cholinergic receptors.
Any drug that binds to and activates a muscarinic cholinergic receptor.
muscarinic acetylcholine receptor agonist
Any dianion containing at least one carboxy group.
An alkaloid containing an indole skeleton.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.
A phosphate ion that is the conjugate base of dihydrogenphosphate.
In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Any carboxylic ester where the carboxylic acid component is acetic acid.
Any steroid substituted by at least one carboxy group.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
Any drug that acts on an alpha-adrenergic receptor.
Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Any anion formed by loss of a proton from a steroid acid.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
proteinogenic amino-acid side-chain group
Drug used to cause constriction of the blood vessels.
Any molecular entity that contains carbon.
A role is particular behaviour which a material entity may exhibit.
A poison that interferes with the functions of the nervous system.
A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group.
A role played by the molecular entity or part thereof within a chemical context.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
An organic group that consists of a closed ring. It may be a substituent or a skeleton.
The biological role played by a material entity when bound by a receptor of the adaptive immune system. Specific site on an antigen to which an antibody binds.
envoPlastics
A polymer carrying multiple negative charges.
A macromolecule containing ionic groups.
A 29-amino acid peptide hormone consisting of His, Ser, Gln, Gly, Thr, Phe, Thr, Ser, Asp, Tyr, Ser, Lys, Tyr, Leu, Asp, Ser, Arg, Arg, Ala, Gln, Asp, Phe, Val, Gln, Trp, Leu, Met, Asn and Thr residues joined in sequence.
A cyclic compound having as ring members atoms of at least two different elements.
An ammonium ion that is the conjugate acid of tryptamine arising from protonation of the primary amino group; major species at pH 7.3.
A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3.
straight-chain saturated fatty acid anion
An organic anion of general formula RS(=O)2O(-) where R is an organyl group.
An organic anion arising from deprotonation of a acyclic tetrapyrrole compound.
Compounds containing one or more phosphoric acid units.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..
An ionic polymer is a polymer, composed of ionic macromolecules.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
Any compound that has a nucleobase as a part.
nucleobase-containing molecular entities
A polymer, composed of polyanion macromolecules.
A substance that removes electrons from another reactant in a redox reaction.
Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
A carbohydrate derivative that is formally obtained from a carbohydrate acid.
An aralylamino compound which contains one amino group connected to an aromatic ring by a two-carbon chain. Monoamines are derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by the action of aromatic amino acid decarboxylase enzymes.
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative.
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents.
An organic amino compound in which an aminoalkyl group is linked to an arene.
A fourteen-membered heterodetic cyclic peptide comprising the sequence Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys cyclised by a disulfide bridge between the two Cys residues at positions 3 and 14.
L-alanylglycyl-L-cysteinyl-L-lysyl-L-asparaginyl-L-phenylalanyl-L-phenylalanyl-L-tryptophyl-L-lysyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-cysteine cyclic (3-14) disulfide
Synthetic growth hormone release-inhibiting hormone
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
A carbohydrate derivative that is any derivative of a polysaccharide.
Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.
A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299).
An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3.
Any compound that has anti-inflammatory effects.
An organic cation that is the conjugate acid of (R)-noradrenaline, obtained by protonation of the priamry amino group; major species at pH 7.3.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment.
A mancude heterobicyclic organic group consisting of a benzene ring fused to a pyrrole ring.
A bicyclic organic group that contains both carbon and hetero atoms.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Saccharomyces cerevisiae secondary metabolites
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
Any metabolite produced by metabolism of a xenobiotic compound.
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
EC 1.14.14.1 (unspecific monooxygenase) inhibitor
Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms.
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any human metabolite produced by metabolism of a xenobiotic compound in humans.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container.
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
carbohydrates and carbohydrate derivatives
Any metabolite produced by all living cells.
Any inorganic anion with a valency of three.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill.
A Daphnia metabolite produced by the species Daphnia magna.
A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia
Any member of the class of indoles carrying at least one hydroxy group.
Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A material entity that has a plasma membrane and results from cellular division.
CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
cell
Any fibroblast that is deriived from the neural crest.
A cell found in the embryo before the formation of all the gem layers is complete.
Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
A stem cell that is the precursor of gametes.
Female germ cell is a germ cell that supports female gamete production.
A stem cell that is the precursor of female gametes.
A female germ cell that has entered meiosis.
An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization.
A smooth muscle cell derived from the neural crest.
A cell that will develop into a neuron often after a migration phase.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.
A stem cell that self-renews as well as give rise to a single mature cell type.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
A progenitor cell committed to the erythroid lineage.
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
Originally this term had some plant germ line cell children.
A stem cell that can give rise to multiple lineages of cells.
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).
A progenitor cell committed to the megakaryocyte and erythroid lineages.
colony forming unit erythroid megakaryocyte
MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
A stem cell from which all cells of the body can form.
A precursor cell with a limited number of potential fates.
define using PATO mulit-potent or oligopotent?
A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
A cell that has a filiform extrusion of the cell surface.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
An epithelial cell that is part of a duct.
An endothelial cell that lines the vasculature.
cuboidal endothelial cell of vascular tree
A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
A cell found predominately in the blood.
A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).
Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
A neuron whose cell body is within an autonomic ganglion.
A neuron that uses acetylcholine as a vesicular neurotransmitter.
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
A pigment cell is a cell that contains pigment granules.
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
A cell that specializes in controlled release of one or more substances.
A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
A cell that secretes glycosaminoglycans.
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
A neuron that is capable of some hormone secretion in response to neuronal signals.
The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.
A cell that secretes insulin and is located towards the center of the islets of Langerhans.
Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.
A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.
A cell whose primary function is to shorten.
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
A somatic cell located in skeletal muscle.
A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
A cell that is capable of detection of a stimulus involved in sensory perception.
A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
A cell specialized to detect and transduce light.
A cell whose function is determined by the generation or the reception of an electric signal.
A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
A cell whose primary function is to prevent the transport of stuff across compartments.
A cell that moves by its own activities.
A cell of the outer of the three germ layers of the embryo.
A cell of the middle germ layer of the embryo.
A cell of the inner of the three germ layers of the embryo.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.
A mature sexual reproductive cell having a single set of unpaired chromosomes.
Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
A cell that is specialised to accumulate a particular substance(s).
A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
A structural cell that is part of optic choroid.
A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface.
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).
A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.
A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
A smooth muscle cell associated with the vasculature.
An epithelial cell of the integument (the outer layer of an organism).
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
A cell whose function is determined by its response to an electric signal.
An interneuron that has its cell body in a central nervous system.
Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.
A cell that initiates an electrical signal and passes that signal to another cell.
A cell that contains more than two haploid sets of chromosomes.
A cell whose nucleus contains a single haploid genome.
A cell type that secretes 5-Hydroxytryptamine (serotonin).
A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
A photoreceptor cell that detects visible light.
A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
An endorphine cell that secretes enkephalin.
A peptide hormone secreting cell that secretes endorphin.
An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.
A peptide hormone secreting cell that secretes gastrin.
A precursor cell destined to differentiate into cardiac muscle cell.
A precursor cell destined to differentiate into smooth muscle myocytes.
A myoblast that differentiates into skeletal muscle fibers.
A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
A neuron which conveys sensory information centrally from the periphery.
A neuron which sends impulses peripherally to activate muscles or secretory cells.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.
A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
Megakaryocytes are reportedly CD181-positive and CD182-positive.
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
A mesenchymal stem cell capable of developing into blood vessel endothelium.
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
The reproductive cell in multicellular organisms.
A steroid hormone secreting cell that secretes androgen.
One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
A cell whose primary function is to support other cell types.
An extracellular matrix secreting cell that secretes collagen.
A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
A mature sexual reproductive cell of the female germline.
A non-terminally differentiated cell that is capable of developing into a muscle cell.
A cell that stores and secretes pancreatic polypeptide hormone.
Epithelial cells derived from neural plate and neural crest.
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
A stem cell that can give rise to cell types of the body other than those of the germ-line.
Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
A immature or mature cell in the lineage leading to and including erythrocytes.
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
A cell of the monocyte, granulocyte, or mast cell lineage.
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
hematopoietic multipotent progenitor cell
A progenitor cell restricted to the myeloid lineage.
Note that this is a class of cell types, not an identified single cell type.
myeloid lineage restricted progenitor cell
A leukocyte with a single non-segmented nucleus in the mature form.
A neuron that releases serotonin as a neurotransmitter.
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.
hematopoietic oligopotent progenitor cell, lineage-negative
A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
hematopoietic lineage restricted progenitor cell
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities.
This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060).
hematopoietic oligopotent progenitor cell
A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules.
An enteroendocrine cell that produces glucagon.
Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter.
A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery.
Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes.
The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides).
An epithelial cell derived from endoderm.
An epithelial cell derived from ectoderm.
Epithelial cell derived from mesoderm or mesenchyme.
Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH.
A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types.
A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart.
This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise.
Some argue this cell type is of mesenchymal origin.
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
A cell in the hilum of the ovary that produces androgens.
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
cubodial endothelial cell of vascular tree
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
An endothelial cell found in capillaries.
Epithelial cells derived from general body ectoderm and ectoderm placodes.
An epithelial cell found in the lining of the stomach.
A mucous cell in the epithelium of the stomach.
A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit.
A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes).
A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye.
A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth.
A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells.
smooth muscle fiber of sphincter of pupil
smooth muscle fibre of sphincter of pupil
smooth muscle cell of sphincter of pupil
A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells).
An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
An epithelial cell of the large intestine.
An epithelial cell of the small intestine.
An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver.
A type of enteroendocrine cell found in the stomach that secretes glucagon.
A PP cell located in the islets of the pancreas.
The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell.
A cell that is part of the nervous system.
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
An adipocyte derived from a neural crest cell.
An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin.
A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
A hematopoietic stem cell that exists during embryogenesis.
A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate.
An endo-epithelial cell of the respiratory tract.
A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.
A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles.
A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes.
A cell located in the heart, including both muscle and non muscle cells.
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc
An adipocyte that is part of subcutaneous adipose tissue.
An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes.
A mesenchymal stem cell that is part of the bone marrow.
mesenchymal stem cell of the bone marrow
An endothelial cell that is part of the vein.
An endothelial progenitor cell that participates in angiogenesis during development.
embryonic blood vessel endothelial progenitor cell
A mesenchymal stem cell of adipose tissue.
A mesenchymal stem cell of the vertebrae.
A blood vessel endothelial cell that is part of the retina.
A smooth muscle cell of the bachiocephalic vasculature.
smooth muscle cell of the brachiocephalic vasculature
A vascular associated smooth muscle cell of the brain vasculature.
smooth muscle cell of the brain vasculature
A smooth muscle of the pulmonary artery.
smooth muscle cell of the pulmonary artery
A smooth muscle cell of the subclavian artery.
smooth muscle cell of the subclavian artery
Smooth muscle cell of the carotid artery.
epithelial cell of lower respiratory tract
A glandular epithelial cell of the esophagus.
A glandular epithelial cell of the large intestine.
A glandular epithelial cell that is part of the stomach.
A myocardial endocrine cell that is part of the atrium.
A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart.
Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.
A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.
A neuroblast derived from a neural crest cell.
A CNS interneuron located in the spinal cord.
Is_a interneuron, part_of UBERON:0002240.
A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic.
somatomotor neuron
Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation.
hepatoblast
Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized).
Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)
Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells.
Any muscle cell in which the fibers are not organised into sarcomeres.
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
skeletal muscle fiber
A muscle cell that is part of some visceral muscle.
visceral muscle cell
A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods.
striated visceral muscle cell
A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods.
transversely striated visceral muscle cell
A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers.
The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins.
A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration.
A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves.
An endocrine cell that is part of the pancreas.
A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter.
Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation.
mural cell
microcirculation associated smooth muscle cell
A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord.
Any cell in the compound eye, a light sensing organ composed of ommatidia.
Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
An enteroendocrine cell that is located in the small intestine.
A stromal cell found in the lamina propria of the large intestine.
stromal cell of lamina propria of large intestine
A stromal cell found in the lamina propria of the small intestine.
stromal cell of lamina propria of small intestine
A mesothelial cell that is part of the small intestine.
A mesothelial cell that is part of the colon.
A stromal cell found in the lamina propria of the colon.
An enteroendocrine cell that is located in the colon.
A smooth muscle cell that is located in the anorectum.
A stromal cell found in the lamina propria of the anorectum.
stromal cell of anorectum lamina propria
An enteroendocrine cell that is located in the anorectum.
An endothelial cell that is part of a hepatic portal vein.
A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development.
A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen.
A stromal cell that is part_of a bone marrow.
A mononuclear cell that is part_of a bone marrow.
zygote
A neuron that has its soma in the heart.
This term is used in 3 GO terms that were created as part of the heart development focus project.
A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement.
A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites.
A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.
A mesothelial cell that is part of the epicardium.
A fibroblast that is part of upper back skin.
A fibroblast that is part of skin of back.
A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.
Any fibroblast that is part of skeletal muscle tissue.
Any microvascular endothelial cell that is part of the dermis.
Epithelial cell that is part of the colon epithelium.
A cell that, by division or terminal differentiation, can give rise to other cell types.
Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.
Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain.
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions.
A smooth muscle cell that is part of any blood vessel.
blood vessel smooth muscle cell
An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes.
extrahepatic cholangiocyte
An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid.
periportal hepatic sinusoidal endothelial cell
endothelial cell of periportal hepatic sinusoid
An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid.
central venous hepatic sinusoidal endothelial cell
endothelial cell of pericentral hepatic sinusoid
A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury.
A smooth muscle cell that is part of the small intestine.
non-striated muscle fiber of small intestine
A smooth muscle cell that is part of the duodenum.
A smooth muscle cell that is part of the large intestine.
non-striated muscle fiber of large intestine
A smooth muscle cell that is part of the colon.
A smooth muscle cell that is part of the cecum.
A smooth muscle cell that is part of the ascending colon.
non-striated muscle fiber of ascending colon
A smooth muscle cell that is part of the transverse colon.
non-striated muscle fiber of transverse colon
A smooth muscle cell that is part of the descending colon.
non-striated muscle fiber of descending colon
A smooth muscle cell that is part of the sigmoid colon.
non-striated muscle fiber of sigmoid colon
A smooth muscle cell that is part of the rectum.
A fibroblast that is part of the areolar connective tissue.
A fibroblast that is part of the tunica adventitia of artery.
fibroblast of tunica adventitia of artery
A fibroblast that is part of the dense regular elastic tissue.
fibroblast of dense regular elastic tissue
An adipocyte that is part of the epicardial fat.
An adipocyte that is part of the epicardial fat of right ventricle.
adipocyte of epicardial fat of right ventricle
An adipocyte that is part of the epicardial fat of left ventricle.
adipocyte of epicardial fat of left ventricle
A transitional myocyte that is part of the interatrial septum.
transitional myocyte of interatrial septum
A transitional myocyte that is part of the interventricular septum.
transitional myocyte of interventricular septum
A Purkinje myocyte that is part of the interventricular septum.
Purkinje myocyte of interventricular septum
An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates.
A muscle cell that is part of the sinoatrial node.
A muscle cell that is part of the atrioventricular node.
An endothelial cell that is part of the arteriole.
A blood vessel endothelial cell that is part of an arterial endothelium.
An endothelial cell that is part of the venule.
An epithelial cell that is part of the gallbladder.
A somatic stem cell that is part of the epidermis.
A smooth muscle cell that is part of the ciliary body.
A mesothelial cell that is part of the anterior chamber of eyeball.
mesothelial cell of anterior chamber of eye
A mesothelial cell that is part of the parietal peritoneum.
A mesothelial cell that is part of the visceral peritoneum.
A transitional myocyte that is part of the sinoatrial node.
A Purkinje myocyte that is part of the atrioventricular node.
Purkinje myocyte of atrioventricular node
A myocardial endocrine cell that is part of the interventricular septum.
myocardial endocrine cell of interventricular septum
An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts.
A mesothelial cell that is part of the peritoneum.
A mesothelial cell that is part of the pleura.
A mesothelial cell that is part of the parietal pleura.
A mesothelial cell that is part of the visceral pleura.
An epithelial cell of the exocrine pancreas.
The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract.
A vascular endothelial cell found in colon blood vessels.
oral cavity mucosa squamous epithelial cell
Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells.
Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell.
Glandular cell of gallbladder epithelium.
Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells.
A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) .
Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts.
Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.
A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
Any blood vessel endothelial cell that is part of a microvascular endothelium.
Any blood vessel endothelial cell that is part of a dermis.
Any skin fibroblast that is part of a skin of abdomen.
Any lung endothelial cell that is part of a microvascular endothelium.
Any photoreceptor cell that is part of a compound eye.
Any native cell that is part of a inner cell mass.
Any native cell that is part of a cardiac septum.
Any neuron that is part of a central nervous system.
A neuron that is part of a peripheral nervous system.
Any fibroblast that is part of a embryo.
Any microvascular endothelial cell that is part of a brain.
Any cardiac muscle cell that is part of a cardiac ventricle.
Any motor neuron that is part of a brainstem.
Any fibroblast that is part of a spleen.
Any endothelial cell that is part of a spleen.
Any fibroblast that is part of a female gonad.
Any epithelial cell that is part of a female gonad.
Any fibroblast that is part of a cardiac ventricle.
Any fibroblast that is part of a cardiac atrium.
Any fibroblast that is part of a pericardium.
Any fibroblast that is part of a gallbladder.
Any fibroblast that is part of a optic choroid.
Any microvascular endothelial cell that is part of a adipose tissue.
Any migratory neural crest cell that is part of a cardiac neural crest.
Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology.
Any mesenchymal stem cell of adipose tissue that is part of an abdomen.
mesenchymal stem cell of abdominal adipose
mesenchymal stem cell of abdominal adipose tissue
A ciliated epithelial cell of the esophagus.
A cell that is part of the brain vasculature.
A GABAergic inhibitory neuron that is derived from the midbrain.
A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli.
Any capillary endothelial cell that is part of a lung.
A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium.
A(n) vein endothelial cell that is part of a(n) respiratory system.
vein endothelial cell of respiratory system
A megakaryocyte that is resident in the lung connective tissue.
A neuron that releases catecholamine as a neurotransmitter.
Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis.
A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics.
An endothelial cell that is part of a central vein of liver.
endothelial cell of central vein of liver
Any mesenchymal stem cell of adipose tissue that is part of an orbital region.
orbital adipose-derived mesenchymal stem cell
mesenchymal stem cell of orbital adipose tissue
A process during which an organism comes into contact with another entity.
exposure of organism
An astrononmical body part which delimited by physical discontinuities with its surroundings.
This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.
A cavity developed along a bedding-plane and elongate in cross-section as a result.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
Mine tailings are the materials left over after the process of separating the valuable fraction from the uneconomic fraction (gangue) of an ore.
A primary administrative division of a country, such as a state in the United States.
A subdivision of a first-order administrative division.
A subdivision of a second-order administrative division.
A subdivision of a third-order administrative division.
A political association with effective dominion over a geographic area.
A construction which enables the movement of humans, their animals or their vehicles.
An enclosure for displaying selected plant or animal life.
A geographical feature associated with water.
A collection of caves interconnected by enterable passages or linked hydrologically or a cave with an extensive complex of chambers and passages.
Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation.
This class refers to the water contained in a canal channel, and not the channel itself.
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
A large expanse of saline water usually connected with an ocean.
A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L).
A lake whose water contains a considerable concentration of dissolved salts.
A body of water or other liquid of considerable size contained in a depression on a landmass.
A lake of whose water contains low concentrations of salts.
A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.
"There are no official definitions for the generic term river as applied to geographic features, although in some countries or communities a stream is defined by its size. Many names for small rivers are specific to geographic location; examples are "run" in some parts of the United States, "burn" in Scotland and northeast England, and "beck" in northern England. Sometimes a river is defined as being larger than a creek, but not always: the language is vague."
A watercourse which is linear and flows across the solid portion of a planetary surface.
streamlet
An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface.
A surface landform which provides an egress for groundwater or steam to flow out of the ground.
Springs are typically where an aquifer surface meets the ground surface or where there is a fissure.
A cave without streams or drips of water.
A valley or ravine, bounded by relatively steep banks, which in the rainy season becomes a watercourse.
The temporality of wadis is problematic in deciding whether they are watercourses or valleys.
An area of water bordered by land on three sides.
A body of water, usually of smaller size than a lake.
An area of broken, fast flowing water in a stream, where the slope of the bed increases (but without a prominent break of slope which might result in a waterfall), or where a gently dipping bar of harder rock outcrops.
A wetland ecosystem which includes communities of grasses, rushes, reeds, typhas, sedges, and other herbaceous plants (possibly with low-growing woody plants).
Artificial watercourse with no flow or a controlled flow used irrigation.
A small, human-made channel which has been dug for draining or irrigating the land.
A sheet of saline water separated from the open sea by sand or shingle banks. The sheet of water between an offshore reef, especially of coral and mainland. The sheet of water within a ring or horseshoe shaped atoll.
A long and narrow sea inlet with high steeply sloped walled sides. A fjord is a landform created during a period of glaciation.
A sudden descent of water over a step or ledge in the bed of a river.
A tidal water channel. Creeks may often dry to a muddy channel with little or no flow at low tide, but often with significant depth of water at high tide.
Artificial watercourse with no flow or a controlled flow used drainage.
An vegetated area which overlaps a wetland ecosystem.
A wetland ecosystem which accumulates acidic peat, a deposit of dead plant material.
A semi-enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea.
A dense growth of shrubbery planted as a fence or boundary.
Artificial watercourse with no flow or a controlled flow used navigation.
A hot spring that erupts periodically, ejecting a column of hot water and steam into the air.
A spring through which groundwater, heated by geothermal energy, flows.
A lake contained within a volcanic crater.
A marsh in which soils are saturated with water that contains low concentrations of salts.
A marsh whose water contains a considerable quantity of dissolved salts.
It would be more correct to say that this has_quality salty or has_part ((soil and water) and has_increased_levels_of salt.
A pond which is 1) shallow, 2) man-made, and 3) designed to produce salt from seawater through evaporation.
In such ponds, water is drawn out of seawater through natural evaporation which allows the salt to be subsequently harvested.
A pond or lake used for the artificial culture of fish.
A swamp which is located in tropical or subtropical environments and is determined by communities of trees and shrubs growing saline coastal environments.
A lake which is formed under the surface of the Earth. Such a lake may be associated with caves and aquifers and springs.
A river that is under the surface of the Earth.
A stream that is under the surface of the Earth.
A geographical feature associated with water that is under the surface of the earth.
This class should probably be replaced with a quality-like entity "underground" which can then be distributed to the subclasses, solving the double inheritance.
Place or area with clustered or scattered buildings and a permanent human population.
An accumulation of water of varying size.
The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.
An open way for the passage of vehicles, persons, or animals on land.
A permanent way having one or more rails which provides a track for cars.
Naturally formed, subterranean open area or chamber.
A stream that branches off and flows away from a main stream channel. They are a common feature of river deltas.
A construction that has been assembled by deliberate human effort.
"constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
A cave developed along a fault or fault zone, either by movement of the fault or by preferential solution along it.
Structure designed to transport water from a remote source, usually by gravity.
A permanent walled and roofed construction.
A barrier constructed across a watercourse to control the flow or raise the level of water.
A built structure erected over a depression or obstacle to carry traffic or some facility such as a pipeline.
An excavation in the Earth for the purpose of extracting earth materials.
As with other classes that are "features", the subclasses of this class are being moved to more informative locations. Their relation to agriculture will be modelled by something more akin to a quality or relation to an agricultural process.
An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.
An open artificial water channel, that leads water from a diversion dam or weir completely aside a natural flow, often an elevated box structure (typically wood) that follows the natural contours of the land.
A range of mounts which is dominated by mountains.
A landform that extends above the surrounding terrain in a limited area.
A mountain is generally steeper than a hill, but there is no universally accepted standard definition for the height of a mountain or a hill although a mountain usually has an identifiable summit. The USGS had previously defined mountains as localised elevations of more than 300 meters; however, the organisation has accepted there are no technical definitions in the US. In ENVO, we primarily use the UNEP-WCMC classification to be compliant with SDG monitoring, but we can host other classifications on request: http://www.fao.org/sustainable-development-goals/indicators/1542/en/
A range of mounts which is dominated by hills.
A rounded elevation of limited extent rising above the surrounding land with local relief of less than 300m.
A lower point that allows easier access through a mountain range. A pass has the general form of a saddle between two mountains.
A glacier contained in the site of a mountain valley.
We need to added classes such as "valley site" in order to fully axiomatize this class
A region of general uniform slope, comparatively level, and of considerable extent.
A slope which is part of a rocky elevation and which has a high degree of steepness.
A cliff that is a margin of a sea or ocean.
A cliff which is not adjacent to a major water body.
An area of flat, low-lying land adjacent to a coast and separated from the interior by other features.
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
A part of an astronomical body associated with a volcano - an opening, or rupture, in that body's surface or crust - which allows hot, molten rock, ash and gases to escape from deep below the surface.
A feature formed by the collapse of land following a volcanic eruption.
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
Area of dry or relatively dry land surrounded by water or low wetland.
A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate.
Valleys are typically located between hills our mountains.
A tract of alluvium formed at the mouth of a river where the deposition ofsome of its load exceeds its rate of removal, crossed by the divergent channels (distributaries) of the river.
A two-dimensional continuant fiat boundary which is used to demarcate the interior from the exterior of a cave.
cave exit
The term "cave entrance" is typically used when ingress or entry to the cave is desired. The same fiat bondary can serve as a cave exit, although that may be less feasible due to the shape or other physical properties of the cave.
An island formed of trees and shrubs that grow in saline coastal habitats in the tropics and subtropics.
A hydrographic feature which is located below the surface of a marine water body.
An area in which grasses (Graminae) are a significant component of the vegetation.
An upland moor or sandy area dominated by low shrubby vegetation including heather.
A grassland ecosystem which contains a variety of annual, biennial and perennial plants growing on rolling or flat terrain.
Typically, meadows have higher botanical biodiversity than other grasslands.
Land having a cover of trees, shrubs, or both.
A tunnel formed by the flow of molten lava, which has subsequently drained out.
These are usually classified as a sub-type of volcanic cave, rather than a tunnel.
An area with a high density of trees. A small forest may be called a wood.
The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome.
A vegetated area which is part of a tundra ecosystem.
A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.
An intentional planting of trees or shrubs maintained for food, typically fruit, production.
A place where grapes are grown for making wine, raisins or table grapes.
An intentional planting of a crop, on a large scale, usually for uses other than cereal production or pasture. The term is currently most often used for plantings of trees and shrubs. The term tends also to be used for plantings maintained on economic bases other than that of subsistence farming.
A forest that has been intentionally established by human intervention.
A channel of a watercource which has been constructed by humans or their technologies.
A geographical region whose affairs and population are administered by an authority.
A political entitity established by more than one state and with at least some influence over the affairs of its member states.
A spring which water contains a significant amount of dissolved minerals, that derive from the rocks through which the water flows.
A spring through which water with elevated levels of dissolved derivatives of sulfur flows.
An arid terrain with clay-rich soil that has been extensively eroded by wind and water.
A valley which no longer has water flowing or accumulating over its surface.
Typically found in either Karst (limestone) or chalk terrain.
A valley that contains, and has been formed by, a stream.
A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water.
A glacier which covers an area of greater than 50,000 square kilometers.
This is not always classified as a glacier in the cryosphere community.
An ice mass which is of sufficient mass that the action of gravity upon it overcomes the frictional forces holding it in place, causing it to deform and flow towards lower elevation.
The definition of glacier is highly variable. Two main issues exist: 1) Whether or not a mass of ice must currently show movement to be considered a glacier or not and 2) What is the relationship between ice sheets and glaciers (i.e., which is the parent in a parent/child relationship or whether they are distinct terms).
An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years.
Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.
A geographical region that serves the purpose of keeping two or more other areas (often, but not necessarily, countries) distant from one another, for whatever reason.
A geographical area, usually the frontier or boundary between two or more military powers (or alliances), where military activity is not permitted, usually by peace treaty, armistice or other bilateral or multilateral agreement.
A circular or round inlet with a narrow entrance.
A ditch that supplies water to surrounding land.
A ditch that collects water from the surrounding land.
The sloping margin of a watercourse, serving to confine it to its natural channel.
The sloping margin of a stream, serving to confine it to its natural channel.
The sloping margin of a river, serving to confine it to its natural channel.
A dome-shaped ice mass that covers less than 50,000 km2 of land area (usually covering a highland area).
A region of permanent snow in mountainous areas or high latitudes.
The region occupied by any more or less continuous, directed movement of ocean water that flows in one of the Earth's oceans. Ocean Currents are rivers of hot or cold water within the ocean. The currents are generated from the forces acting upon the water like the earth's rotation, the wind, the temperature and salinity differences and the gravitation of the moon. The depth contours, the shoreline and other movements influence the direction and strength of the movements of water that forms a given current.
Subclasses of this class are to be populated by inference. Definition modified from http://en.wikipedia.org/wiki/Ocean_current.
A shallow stretch of a river or stream, where the current is above the average stream velocity and where the water forms small rippled waves as a result. It often consists of a rocky bed of gravels or other small stones.
Chains of rocks or coral at or near the surface of water constructed by man.
A marine reef which is composed primarily of aragonite structures produced by living organisms, found in shallow, low-nutrient waters.
An alkaline flat, in the context of a marine environment.
A section of a river or stream that diverts from the main course and rejoins later.
The upper part of a river system, denoting the upper basin and source streams of a river.
An area of grassland or pasture beside a river, subject to seasonal flooding.
A depression which is semicircular or crescent-shaped, found towards the crest of a mountain, and formed by the erosional processes caused by the motion of a glacier.
A small, isolated, fertile or green area in a desert region, usually having a spring or well.
An artificial working of peatland to remove the peat.
A road or railway elevated by a bank, usually across a broad body of water or wetland.
A plantation which is used to grow Hevea brasiliensis or other species from which natural latex is harvested.
A lake formed of a natural deposit of alphalt, a black, highly viscous liquid or semi-solid composed of fossil hydrocarbons.
An oceanic island, often having a characteristic ring-like shape surrounding a lagoon. Atolls are formed when coral reef grows around a volcanic island that later subsides into the ocean.
A linear shoaling landform feature within a body of water. Bars tend to be long and narrow (linear) and develop where a current (or waves) promote deposition of granular material, resulting in localized shallowing (shoaling) of the water. Bars can appear in the sea, in a lake, or in a river. They are typically composed of sand, although could be of any granular matter that the moving water has access to and is capable of shifting around (for example, soil, silt, gravel, cobble, shingle, or even boulders). The grain size of the material comprising a bar is related: to the size of the waves or the strength of the currents moving the material, but the availability of material to be worked by waves and currents is also important.
A hole in coastal rock through which sea water is forced by a rising tide or waves and spurted through an outlet into the air.
Relatively narrow, deep depression with steep sides, the bottom of which generally has a continuous slope.
A hill of sand built by eolian processes.
A valley that contains, and has been formed by, a river.
A desert plain characterized by a surface veneer of sand.
There should be relation here to ENVO:sand, but it's more than "primarily composed of" and must call upon the idea of "ground surface" or layer.
A desert plain characterized by a surface veneer of rock.
There should be relation here to ENVO:rock, but it's more than "primarily composed of" and must call upon the idea of "ground surface" or layer.
Narrow section of land in a body of water connecting two larger land areas.
A surface landform which is formed by the dissolution of a soluble layer or layers of bedrock.
Karsts usually form in masses of carbonate rock such as limestone or dolomite. Karst landscapes display distinctive surface features and underground drainages, and in some examples there may be little or no surface drainage.
A landform elevated above the surrounding area.
elevation
An accumulation of boulders, stones, or other debris carried and deposited by a glacier.
An artificial slope or wall, usually earthen, which parallels the course of a river, built for the purpose of containing the river.
An elevated area of land with a flat top and sides that are usually steep cliffs. Mesas form in areas where horizontally layered rocks are uplifted by tectonic activity.
The exposed summit of a ridge, mountain, or peak not covered with ice or snow within an ice field or glacier. The term is typically used in areas where a permanent ice mass is present.
"peak" in the definition is understood as a synonym of mount, rather than of summit. Nunataks may also refer to areas of ridges. The definition and placement of this class may need to be revised.
An elevated and comparatively level expanse of land.
A desert plain characterized by a surface veneer of gravel or stones.
There should be relation here to ENVO:rock and ENVO:gravel, but it's more than "primarily composed of" and must call upon the idea of "ground surface" or layer.
A tributary valley with the floor at a higher relief than the main channel into which it flows. They are most commonly associated with U-shaped valleys when a tributary glacier flows into a glacier of larger volume.
Rain-fed, potentially deep peatlands occurring principally in lowland areas across much of Northern Europe, as well as in the former USSR, North America and parts of the southern hemisphere.
Flat or concave peatlands with a string-like pattern of hummocks (hence the name), found principally in northern Scandinavia but occurring in the western parts of the former USSR and in North America. A few examples exist in northern Britain.
Peatlands with a shallow peat layer, only about 500 mm thick, dominated by sedges and grasses. They form in permafrost areas, covering around 110,000 to 160,000 km2 in Alaska, Canada, and the former USSR.
Peatland typified by characteristic high mounds, each with a permanently frozen core, with wet depressions between the mounds.
These develop where the ground surface is frozen only for part of the year, and are common in the former USSR, Canada and parts of Scandinavia.
Forested peatlands including both rain- and groundwater-fed types, commonly recorded in tropical regions with high rainfall.
This type of peatland covers around 350,000 km2, primarily in south-east Asia but also occurring in the Everglades in Florida.
Feature on the ocean floor at a depth of 3500 - 6000 meters.
A part of an astronomical body which is primarily composed of solid material.
A wetland that forms when mud is deposited by the tides, rivers, sea or oceans.
Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders.
A natural depression or hole in the surface topography caused by the removal of soil or bedrock, often both, by water. Sinkholes may vary in size from less than a meter to several hundred meters both in diameter and depth, and vary in form from soil-lined bowls to bedrock-edged chasms.
A dry lakebed consisting of fine-grained sediments infused with alkali salts. Generally the shore or bed of an endorheic lake.
A lake from which there is no outflow of water, either on the surface as rivers, or underground by flow or diffusion through rock or permeable material.
A lake which has layers of water which do not intermix.
The deepest layer of water in such a lake typically does not contain any dissolved oxygen. The layers of sediment at the bottom of a meromictic lake remain relatively undisturbed because there are no living organisms to stir them up.
A lake, part of whose margin is formed by an ice mass, ice cap or glacier, the ice having obstructed the natural drainage of the land.
A lake in a glacially eroded valley, which has been eroded below sea level.
A lake which is formed when a wide meander from a stream or a river is cut off to form a lake. They are called oxbow lakes due to the distinctive curved shape that results from this process.
A lake which fills a depression that has formed as a result of subsidence along a a rift zone, an area of extensional tectonics in the continental crust.
A spring through which fluid intermittently flows.
The water mass of an ocean directly above a continental shelf.
The water mass of an ocean that is not above a continental shelf.
The zone of an ocean from the surface to where photosynthesis can occur, due to the penetration of light.
The zone of an ocean below 200m, in which photosynthesis cannot occur due to the lack of light.
The one of an ocean below the 10degC thermocline down to a temperature of 4degC.
The zone of the ocean below the bathypelagic zone, with its lowest boundary at about 6000m.
The zone of an ocean immediately below the photic zone down to a depth where the water temperature is 10degC (the thermocline).
The zone of an ocean in oceanic trenches, lying between 6000m and 10,000m.
A fissure in the Earths's surface from which geothermally heated water issues.
A hole in the Earth's crust from which steam and gases are emitted.
A hydrothermal vent found on the ocean floor. The vents are formed in fields hundreds of meters wide when superheated water from below the Earth's crust comes through the ocean floor. The superheated water is rich in dissolved minerals from the crust, most notably sulfides, which crystallize to create a chimney-like structure around each vent. When the superheated water in the vent comes in contact with the cold ocean water, many minerals are precipitated, creating the distinctive black color. The metal sulfides that are deposited can become massive sulfide ore deposits in time.
A sea that is not connected with an ocean.
A group of geographically or geologically associated islands.
An island that lies on a continental shelf.
An island that does not sit on a continental shelf, and is of volcanic origin.
A slope which a) extends the perimeter of a continent, b) is covered by a shallow marine water body during interglacial periods, c) has a low degree of steepness relative to a continental slope or rise.
The continental shelf is a gentle slope. This class refers to the geographical continental shelf and not the legal concept of the same name.
An estuary in which river output is less than the marine input, resulting in the mixing of the whole water column by current-induced turbulence, such that salinity varies more longitudinally rather than vertically.
An estuary whose river output and marine input are more even, with river flow still dominant; turbulence induces more mixing of salt water upward than the reverse.
An estuary in which river output greatly exceeds marine input, resulting in little mixing and thus a sharp contrast between fresh surface water and saline bottom water.
An estuary which is located in regions where evaporation greatly exceeds the inflow of fresh water, forming a zone of maximum salinity towards which both riverine and marine water masses flow, before sinking and spreading along the bottom in both seaward and landward directions.
An estuary which varies dramatically in its volume as a result of intermittent freshwater input, and is capable of changing from a wholly marine embayment to any other type of estuary.
A wetland ecosystem which overlaps both terrestrial and marine ecosystems.
A wetland found in upland areas, characterised by acidic soils.
A freshwater peat land with chemically basic (which roughly means alkaline) ground water.
A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions.
A small, slow-moving stream or creek; usually located in low-lying areas.
A fen which has developed to the point where it supports trees.
A class of complex shallow wetlands in central, southern and eastern Africa, particularly in Zambia and Zimbabwe. They are generally found in higher rainfall flat plateau areas, and have river-like branching forms which may be nowhere very large, but common enough to add up to a large area.
A palustrine wetland with deep, acidic, sandy, peat soils. Groundwater saturates the soil except during brief seasonal dry spells and during prolonged droughts. Pocosin soils are nutrient deficient (oligotrophic), especially in phosphorus.
A wetland ecosystem in which soil is saturated with saline water.
A level tract lying at a small depth below the surface of water, or alternately covered and left bare by the tide.
A wetland that forms when mud is deposited by a stream.
A wetland which is inundated with water that contains low concentrations of salts.
A flat or very gently sloping areas of the deep ocean basin floor.
A broad, low relief crater that results from a phreatic eruption or explosion caused by groundwater contact with hot lava or magma. The maar typically fills with water to form a relatively shallow crater lake.
A crater formed by a volcano, within which occurs a vent (or vents) from which magma erupts as gases, lava, and ejecta.
An opening, or rupture, in the Earth's surface or crust, which allows hot, molten rock, ash and gases to escape from deep below the surface.
A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section.
The parallel ridges of till deposited along the sides of an alglacier. The unconsolidated debris is deposited on top of the glacier by frost shattering of the valley walls and from tributary streams flowing into the valley. The till is carried along the glacial margin until the glacier melts.
A moriane formed when the inside lateral moraines of two glaciers merge together. They form a ridge down the center of the combined glaciers.
A till covered area with irregular topography and no ridges, often forming gently rolling hills or plains. Forms by the accumulation of till under the ice by lodgement, but may also be deposited as the glacier retreats.
Ridges of unconsolidated debris deposited at the snout or end of the glacier. They usually reflect the shape of the glacier's terminus.
A plain where a stream meanders across an area with a very low gradient, usually with a fairly continuous discharge. In addition to meanders, scroll plains are also characterised by many oxbow lakes.
An extensive flat plain of glacial till that forms when a sheet of ice becomes detached from the main body of a glacier and melts in place depositing the sediments it carried.
An area which is subject to periodic flooding.
The stream channel and adjacent areas that carry flood flows in a flood plain.
Area of a flood plane covered by the flood, but which does not experience a strong current.
A relatively flat and gently sloping landform found at the base of a range of hills or mountains, formed by the deposition of alluvial soil over a long period of time by one or more streams coming from the mountains.
A plain that originally formed in a lacustrine environment, that is, as the bed of a lake, but from which the water has disappeared, by natural drainage, evaporation or other geophysical processes.
An area of land of low topographic relief that historically supported grasses and herbs, with few trees, and having generally a mesic (moderate or temperate) climate. Dominated by tall grasses (contrast steppe).
A grassland of the tropics or subtropics with scattered trees.
A plain without trees (apart from those near rivers and lakes); it is similar to a prairie, although a prairie is generally considered as being dominated by tall grasses, while short grasses are said to be normal in the steppe. It may be semi-desert, or covered with grass or shrubs or both, depending on the season and latitude.
A narrow, vertical cave passage, often developed along a joint but not necessarily so. Usually due to solution but sometimes to tension.
A mountain rising from the ocean seafloor that does not reach to the water's surface (sea level), and thus is not an island. Typically formed from volcanoes that rise abruptly and are usually found rising from a seafloor of 1,000 - 4,000 meters depth. Independent features that rise to at least 1,000 meters above the seafloor.
A grassland ecosystem which is used for grazing of ungulate livestock as part of a farm or ranch.
A steep-sided valley on the sea floor of the continental slope. Many submarine canyons are found as extensions to large rivers; however there are many that have no such association. Canyons cutting the continental slopes have been found at depths greater than 2 km below sea level. Many submarine canyons continue as submarine channels across continental rise areas and may extend for hundreds of kilometers.
The ground surface that lies beneath a lake.
A continental island connected to its adjacent land by a natural feature, such as a causeway.
A pond that has formed as a consequence of the activities of beavers, building a beaver dam.
A dry (salt) lake in the Saharan area of Africa that stays dry in the summer, but receive some water in the winter. This water may come as a groundwater discharge.
The point where a tributary joins a more major river.
A slope which 1) is part of the seafloor and 2) extends from the end of the continental shelf (the shelf break) to the continental rise.
A slope which a) bridges, and thus lies between, a continental slope and an abyssal plain, b) is formed by the accumulation of sediments transported from a continental slope by processes including turbidity currents c) has a gradient less than a continental slope yet greater than a continental shelf.
On Earth, the gradient of the continental rise is on the order of 0.5-1. It may extend as far as 500 kilometers from the slope,
Hemispheric-scale long but narrow topographic depressions of the sea floor. They are the deepest parts of the ocean floor.
An elongated whale-shaped hill formed by glacial action. Its long axis is parallel with the movement of the ice, with the blunter end facing into the glacial movement. Drumlins are sometimes compared to kames, but their formation is distinctively different. A drumlin is not originally shaped by meltwater, but by the ice itself and has a quite regular shape. It occurs in fine grained material, such as clay or shale, not in sands and gravels. And drumlins usually have concentric layers of material, as the ice successively plasters new layers in its movement.
A lake that has either permanently or temporally lost its water.
Classes like this pose a logical problem. This probably shouldn't be a lake (water body) but a depression. Lakes which have temporarily lost water should be distinguished from permanently dry lakes.
A stream channel through which no water flows and which has dried, containing no appreciable accumulations of water.
A flat expanse of ground covered with salt and other minerals, usually shining white under the sun. A salt pan is formed where water pools. A saline pan would be a lake or a pond if it were located in a climate where the rate of water evaporation were not faster than the rate of water precipitation, i.e., if it were not in a desert. If the water is unable to drain into the ground, it remains on the surface until it evaporates, leaving behind whatever minerals were dissolved. Over thousands of years, the minerals (usually salts) accumulate on the surface.
A slope which separates different physiogeographic provinces that are typically composed of rocks of different age and compositoin.
An escarpment usually represents the line of erosional loss of the newer rock over the older.
A long, winding ridge of stratified sand and gravel which occur in glaciated and formerly glaciated regions of Europe and North America.
A long and narrow elevation with steep sides.
An open-pit mine from which rock or minerals are extracted.
A bed which is composed of quicksand forming a soft, shifting mass that yields easily to pressure.
An area reclaimed from the sea by diking and draining.
An isolated hill with steep sides and a small flat top, smaller than mesas and plateaus. Buttes are formed by erosion when a cap of hard rock, usually of volcanic origin, covers a layer of softer rock that is easily worn away. This hard rock avoids erosion while the rock around it wears down.
The raised fault block bounded by normal faults. The raised block is a portion of the Earth's crust that has remained stationary while the land has sunk on either side of it or has been crushed by a mountain range against it.
A depressed block of land bordered by parallel faults. A graben is the result of a block of land being downthrown producing a valley with a distinct scarp on each side. Grabens often occur side-by-side with horsts. Horst and graben structures are indicative of tensional forces and crustal stretching.
An extent or area of land where surface water from rain and melting snow or ice converges to a single point at lower elevation, usually the exit of the basin, where the waters join another waterbody.
The separation between neighbouring drainage basins (catchments). In hilly country, the divide lies along topographical peaks and ridges, but in flat country or on a high plateau (especially where the ground is marshy) the divide may be invisible - just a more or less notional line on the ground on either side of which falling raindrops will start a journey to different rivers, and even to different sides of a country or continent.
A watershed such that water falling on one side of the line eventually travels to one ocean or body of water, and water on the other side travels to another, generally on the opposite side of the continent.
A facility in which fish are raised commercially in tanks or enclosures, usually for food.
A hatchery in which the eggs of fish are hatched under artificial conditions.
A paddy field for the cultivation of rice.
A flooded parcel of arable land used for growing rice and other semiaquatic crops.
A large mass of detached land ice in the sea or stranded in shallow water.
A field of ice, formed in regions of perennial frost.
Ice mass may need to be resolved from ice field, the former referring simply to an accumulation of ice.
Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees.
A shrubland area found primarily in regions with a Mediterranean climate (mid, wet winters and hot dry summers) often shaped by wildfires.
A valley created by the formation of a rift, i.e. place where a planet's lithosphere is being pulled apart by tectonic forces.
The general region of indefinite width that extends from the sea inland to the first major change in terrain features.
That part of the land in immediate contact with a body of water including the area between high and low water lines.
A body of land jutting out into and nearly surrounded by water.
A deposition landform found off coasts. A spit is a type of bar or beach that develops where a re-entrant occurs, such as at a cove, bay, ria, or river mouth. Spits are formed by the movement of sediment (typically sand) along a shore by a process known as longshore drift. Where the direction of the shore turns inland (reenters) the longshore current spreads out or dissipates. No longer able to carry the full load, much of the sediment is dropped. This causes a bar to build out from the shore, eventually becoming a spit.
A portion of a glacier characterized by rapid flow, a chaotic crevassed surface, and a pronounced, at times vertical, slope.
Icefalls may be formed as glaciers flow through narrow openings in landmasses.
A landform sunken or depressed below the surrounding area.
Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486
depression
A crater caused by the impact of a meteor.
For the moment, no distinction is made between meteroids, lithometeors, or meteorites in this class. These can be added if needed.
A fluvioglacial landform occurring as the result of blocks of ice calving from the front of a receding glacier and becoming partially to wholly buried by glacial outwash. Glacial outwash is generated when sediment laden streams of meltwater flow away from the glacier and are deposited to form broad outwash plains called sandurs. When the ice blocks melt, holes are left in the sandur.
The plain formed by the large amounts of silt and sediment, picked up as a glacier erodes the underlying rocks as it moves slowly downhill, and at the snout of the glacier, meltwater can carry this sediment away from the glacier and deposit it on a broad plain. The material in the outwash plain is often size-sorted by the water runoff of the melting glacier with the finest materials, like silt, being the most distantly re-deposited, whereas larger boulders are the closest to the original terminus of the glacier.
A sandy depression in a sand dune ecosystem (psammosere) caused by the removal of sediments by wind.
A fan-shaped deposit formed where a fast flowing stream flattens, slows, and spreads typically at the exit of a canyon onto a flatter plain.
A convergence of neighboring alluvial fans into a single apron of deposits against a slope.
The area of the foreshore and seabed that is exposed to the air at low tide and submerged at high tide, i.e., the area between tide marks.
Very similar to the "marine eulittoral zone" class, but without reference to seasonal tide marks. Some sources make no distinction between these zones, thus, they are currently related synonyms.
Pools formed as a high tide comes in over a rocky shore. Water fills depressions in the ground, which turn into isolated pools as the tide retreats.
The tide zone that is flooded during high tide only, and is a highly saline environment.
The tidal zone that is mostly submerged, only being exposed at the point of low tide and for a longer period of time during extremely low tides.
A cavity developed along a joint and elongate in cross-section.
"Lave cave" is differentiated from "volcanic cave": the former is formed in volcanic rock, the latter is formed by volcanic processes.
A cave containing a stream or active speleothems.
A cave from which a stream flows or formerly did so and which cannot be followed upstream to the surface.
A large closed depression draining underground, with a flat floor across which there may be an intermittent or perennial stream and which may be liable to flood and become a lake. The floor makes a sharp break with parts of surrounding slopes.
A cave in present-day or emerged sea cliffs, formed by wave attack or solution.
A secondary mineral deposit formed in caves, most commonly calcite.
An interface layer which 1) is primarily composed of solid materials, 2) separates the land surface and phreatic zone, and 3) contains groundwater at atmospheric pressure.
If the vadose zone includes portions of soil, the water contained therein is termed soil moisture. In fine grained soils, capillary action can cause the pores of the soil to be fully saturated above the water table at a pressure less than atmospheric. In such soils, therefore, the unsaturated zone is the upper section of the vadose zone and not identical to it.
A compound astronomical body part which is located beneath the land surface and in which all interstices are filled with water that has a hydraulic head greater than atmospheric pressure due to the weight of overlying groundwater.
A speleothem projecting vertically upwards from a cave floor and formed by precipitation from drips.
A speleothem hanging downwards from a roof or wall, of cylindrical or conical form, usually with a central hollow tube.
A closed depression draining underground in karst, of simple but variable form, e.g. cylindrical, conical, bowl- or dish-shaped. From a few to many hundreds of metres in dimensions.
Karst developed in soluble beds underlying other rock formations; the surface may or may not be affected by the karst development.
Karst developed in eolian calcarenite when the development of karst features has taken place at the same time as the lithification of dune sand.
Karst completely pitted by closed depressions so that divides between them form a crudely polygonal network.
Karst dominated by closed depressions, chiefly dolines, perforating a simple surface.
A bodily fluid material which is composed primarily of vomit, a bodily fluid consisting of the expulsed contents of the stomach of an organism disgorged through the mouth or nose.
ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.
A mass of solid material which is composed primarily of rock.
A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand.
grain of sand
granule of sand
sand granule
In general, sand grains are larger than those of silt, but finer than those of gravel.
particle of sand
A piece of rock which is between two and 64 millimetres in length along its largest dimension.
Arguably, this could be placed in the "particle" hierarchy, but is usually considered too large in everyday semantics.
A comparatively elevated area on an icecap.
A particle which 1) is primarily composed of quartz or feldspar and 2) is or was part of a portion of silt.
grain of silt
granule of silt
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
A terrarium is a vivarium which simulates a terrestrial environment.
A volcanic caldera that has been partially filled by a new central cone.
This may be more a subclass of 'caldera'
A chain of volcanic islands or mountains formed by plate tectonics as an oceanic tectonic plate subducts under another tectonic plate and produces magma.
A volcanic arc formed by the subduction of oceanic crust below continental crust.
A volcanic arc formed by the subduction of oceanic crust other oceanic crust on an adjacent tectonic plate.
A geothermal field which is prone to localized volcanic activity.
A volcanic field of small, scattered volcanic vents. These volcanic fields, containing numerous monogenetic volcanoes, are noted for having only one short eruptive event. Monogenetic fields occur only where the magma supply to the volcano is low or where vents are not close enough or large enough to develop plumbing systems for continuous feeding of magma.
A cone made of material ejected from a volcano. The material can range from finest particles. In comparison, cinder cones are more uniform. They are usually found in or on larger features, such as stratovolcanoes, shield volcanoes and can be found inside calderas, however they can also be an independent feature. They can range from a few metres in height and are usually formed by a single eruption.
A device for raising and lowering boats between stretches of water of different levels on river and canal waterways. The distinguishing feature of a lock is a fixed chamber whose water level can be varied.
An area of land or of a body of water in which management practices, through legal or other effective means, prioritise the protection and maintenance of biological diversity, and of natural and associated cultural resources.
This class needs revision. Protected areas may be designated for multiple uses, and more clarity is needed. Further, the protections applied to the entities within the site may not prioritise biodiversity conservation. At a very general level, "protection" suggests that some forms of use are, in principle, excluded.
A natural environment which has been designated by a competent authority as having outstanding or unique value because of its rarity, aesthetic qualities, or cultural significance.
monument
The commemorative value may be associated with one or more components of the environment in question, such as a mountain, tree, or river.
A protected forest or woodland area in the United States. National forests are controlled by the federal government and managed by the United States Forest Service, under the direction of the United States Department of Agriculture.
A conservation designation denoting a protected area in the United Kingdom. SSSIs are the basic 'building block' of nature conservation legislation and most other legal nature/geological conservation designations are based upon them, including National Nature Reserves, Ramsar Sites, Special Protection Areas, and Special Areas of Conservation.
A protected area of the sea usually established to preserve a specific habitat and ensure the ecosystem is sustained for the organisms that exist there. Most marine parks are designated by governments, and organized like watery national parks.
A protected area of importance for wildlife, flora, fauna or features of geological or other special interest, which is reserved and managed for conservation and to provide special opportunities for study or research. Nature reserves may be designated by government institutions in some countries, such as the United Kingdom, or by private landowners, such as charities and research institutions, regardless of nationality.
A designation for certain protected areas of the United States managed by the United States Fish and Wildlife Service. The National Wildlife Refuge system is a network of lands and waters managed to protect wildlife and wildlife habitat.
A wetland protected by the terms of the Ramsar Convention (The Convention on Wetlands of International Importance, especially as Waterfowl Habitat).
An area of protected biodiversity which is of national significance for biological or Earth science interest.
Used as a designation in the United Kingdom.
area designated as a national nature reserve
An IUCN protected area which 1) primarily consists of ecosystems which are able to maintain their natural composition, structure, and function at a regional scale and which are deemed to be representative of a region's natural bio- and geodiversity, 2) is sufficiently large to allow its constituent ecosystems to function, develop, and recover from natural perturbations without human intervention, and 3) is managed to preserve natural ecosystem integrity and functioning at a regional scale, while allowing human access for the purposes of conservation, cultural and spiritural activities, research, education, tourism, subsistence use by indigenous communities, and recreation.
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. These areas often serve as migration corridors between other natural and semi-natural ecosystems and pools of biodiversity. They may have core zones that are similar to IUCN Protected Area classes Ia and Ib.
An island, usually the consequence of the activity of a submarine volcano, that only exists for a short period or short periods of time after its formation, then being eroded or otherwise disappearing beneath the surface of a body of water.
MERGED DEFINITION: TARGET DEFINITION: A large area of brine on the ocean basin near cold seep vents which release methane into the water. These pools are concentrations of water having an extremely high salinity as compared to the surrounding ocean, caused by the motion of large salt deposits through salt tectonics. -------------------- SOURCE DEFINITION: Marine brine pools are large areas of brine on the ocean basin. These pools are bodies of water that have a salinity three to five times greater than the surrounding ocean. For deep-sea brine pools the source of the salt is the dissolution of large salt deposits through salt tectonics. The brine often contains high concentrations of methane, providing energy to chemosynthetic animals that live near the pool.
A distinctive, flat-topped, steep-sided volcano formed when lava erupts through a thick glacier or ice sheet.
A volcano with more than one feature. They form because changes of their eruptive characteristics or the location of multiple vents in an area. Stratovolcanoes may form complex volcanoes, because they may overlap another from explosive eruptions, lava flows, pyroclastic flows and by repeated eruptions, to make multiple summits and vents. Stratovolcanoes could also form a large caldera that gets filled in by multiple small cinder cones, lava domes and craters may also develop on the caldera's rim.
A shield volcano that is formed mostly of pyroclastic and highly explosive eruptions rather than relatively fluid basaltic lava issuing from vents or fissures on the surface of the volcano. They typically display low-angle flank slopes and have little or no central collapse, although a shallow sag in the shield is commonly observed. Lava is commonly extruded after the cessation of explosive activity commonly superposes the vent region.
A protected area with the purpose of protecting and managing wild life.
A protected area that is a specific site (such as a forest, mountain, lake, desert, monument, building, complex, or city) that has been nominated and confirmed for inclusion on the list maintained by the international World Heritage Programme administered by the UNESCO World Heritage Committee.
An international conservation designation given by UNESCO under its Programme on Man and the Biosphere (MAB).
A reservoir constructed for the purpose of maintaining water levels in a canal or canals.
The disposition of an environmental system to be covered by liquid water.
inundation disposition
An ice mass which 1) is attached to the coast 2) at least 2 meters in thickness 3) forms where a glacier or ice mass flows down to a coastline and onto the ocean surface and 4) grows by annual snow accumulation or by the seaward extension of land glaciers.
An ice shelf may grow hundreds of miles out to sea. Usually of great horizontal extent and with a level or gently undulating surface. Nourished by annual snow accumulation and also by the seaward extension of land glaciers. Limited areas may be aground. Ice shelves are much thicker than sea ice often filling embayments in the coastline of an ice sheet.. Currently, nearly all ice shelves are in Antarctica, where most of the ice discharged into the ocean flows via ice shelves. The mass balance of an ice shelf may have significant components of both gain and loss at the base. The seaward edge is termed an ice front. The calving of an ice shelf forms tabular icebergs and ice islands.
A section of the Earths's crust that is demarcated by faults or flexures. In the movement of the crust, a massif tends to retain its internal structure while being displaced as a whole.
That part of the land in immediate contact with a lake.
The channel bottom of a stream; the physical confine of the normal water flow.
The channel bottom of a river; the physical confine of the normal water flow.
The place where a stream discharges into a lagoon, lake, or the sea.
The end of a stream where it enters a standing water body such as a lake, sea or ocean.
A depression which intermittently contains a lake.
This has been moved from the lake hierarchy.
A wetland ecosystem which is sometimes inundated or saturated by surface or ground water sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
In a strict sense, this class cannot always satisfy the subclass axiom of wetland, requiring soil to always have a wet quality. Perhaps this should be treated more like channel of an intermittent stream.
A spur which is part of a mountain.
An isthmus or other land connection between what at other times are separate land masses which allows animals and plants to cross and colonise new lands. Land bridges are commonly created by regression, in which sea levels fall exposing previously submerged sections of continental shelf. Land bridges are also formed by: (a) upthrust at the edge of continental plates; and (b) glacial retreat alleviating pressure on shallow marine formations.
A long and narrow sheet of ice projecting out from the coastline. An ice tongue forms when a valley glacier moves very rapidly out into the ocean or a lake.
A large sea or ocean inlet larger than a bay, deeper than a bight, wider than a fjord, or it may identify a narrow sea or ocean channel between two bodies of land.
A narrow channel of water that connects two larger bodies of water, and thus lies between two land masses.
A depressed landform which physically confines a river, slough or ocean strait, and which consists of a bed and banks.
We need a more general channel definition, the current is only for water course channels. We need to refactor the semantics of channels, tunnels and conduits, in a similar way to uberon anatomical channels http://purl.obolibrary.org/obo/UBERON_0004111. See https://github.com/EnvironmentOntology/envo/issues/147
A channel of a watercourse which contains marine water.
A channel of a watercourse which contains lake water.
Built by fragments (called ejecta) thrown up (ejected) from a volcanic vent, piling up around the vent in the shape of a cone with a central crater.
A cone that is composed of particles of silt to sand size. Explosive eruptions from a vent where the magma is interacting with groundwater or the sea (as in an eruption off the coast) produce steam and are called phreatic. The interaction between the magma, expanding steam, and volcanic gases results in the ejection of mostly small particles called ash. Fallen ash has the consistency of flour. The unconsolidated ash forms an ash cone which becomes a tuff cone or tuff ring once the ash consolidates.
A cone built almost entirely of loose volcanic fragments called cinders (pumice, pyroclastics, or tephra). They are built from particles and blobs of congealed lava ejected from a single vent. As the gas-charged lava is blown violently into the air, it breaks into small fragments that solidify and fall as cinders around the vent to form a circular or oval cone. Most cinder cones have a bowl-shaped crater at the summit.
A volcanic cone formed of molten lava ejected from a vent somewhat like taffy. Expanding gases in the lava fountains tear the liquid rock into irregular gobs that fall back to earth, forming a heap around the vent. The still partly liquid rock splashed down and over the sides of the developing mound is called spatter. Because spatter is not fully solid when it lands, the individual deposits are very irregular in shape and weld together as they cool, and in this way particularly differ from cinder and ash.
A volcano created by geologically excreted liquids and gases, although there are several different processes which may cause such activity. Temperatures are much cooler than igneous processes.
A large volcano with shallowly-sloping sides.
A tall, conical volcano composed of many layers of hardened lava, tephra, and volcanic ash. These volcanoes are characterized by a steep profile and periodic, explosive eruptions. The lava that flows from them is viscous, and cools and hardens before spreading very far. The source magma of this rock is classified as acidic, or high in silica to intermediate (rhyolite, dacite, or andesite).
An underwater mountain range, formed by plate tectonics. This uplifting of the ocean floor occurs when convection currents rise in the mantle beneath the oceanic crust and create magma where two tectonic plates meet at a divergent boundary. The mid-ocean ridges of the world are connected and form a single global mid-oceanic ridge system that is part of every ocean.
A volcano produced by subglacial eruptions or eruptions beneath the surface of a lake melted into a glacier or ice mass by the rising lava.
Something more specific than an adjacent_to relation would be better, especially considering the volcano in question may have melted nearby glacial mass.
A linear volcanic vent through which lava erupts, usually without any explosive activity. The vent is usually a few meters wide and may be many kilometers long. Fissure vents can cause large flood basalts and hannels. The volcano can usually be seen as a crack in the ground or on the ocean floor. Narrow fissures can be filled in with lava that hardens.
A large, swirling body of water produced by ocean tides.
An elevated area such as a hill, ridge or old lava dome inside or downslope from an area of active volcanism. New lava flows will cover the surrounding land, isolating the kipuka so that it appears as a (usually) forested island in a barren lava flow.
The shallow part of a stream which can be easily crossed.
A watercourse which has the intensity and direction of its flow primarily determined by the tides.
A mound of earth-covered ice found in the Arctic, subarctic, and Antarctica that can reach up to 70 metres in height and up to 2 kilometres in diameter.
Pingos may occur in cold-climate wetland areas, but are not necessarily wetlands themselves.
A natural formation where a rock arch forms, with a natural passageway through underneath.
A beach or wave cut platform raised above the shore line by a relative fall in the sea level.
A dune which is part of a coast.
A fertile low-lying raised beach found on the some of the coastlines of Ireland and Scotland, in particular in the Outer Hebrides.
A submergent coastal landform that forms where sea levels rise relative to the land either as a result of eustatic sea level change; where the global sea levels rise or isostatic sea level change; where the land sinks. When this happens valleys which were previously at sea level become submerged.
A geological landform consisting of a steep and often vertical column or columns of rock in the sea near a coast.
A deposition landform such as a spit or bar which forms a narrow piece of land between an island or offshore rock and a mainland shore, or between two islands or offshore rocks. They usually form because the island causes wave refraction, depositing sand and shingle moved by longshore drift in each direction around the island where the waves meet. Eustatic sea level rise may also contribute to accretion as material is pushed up with rising sea levels.
The narrow flat area often seen at the base of a sea cliff caused by the action of the waves.
A natural karst landform consisting of a flat, incised surface of exposed limestone that resembles artificial pavement.
seafloor
Seas are smaller than oceans and are usually located where the land and ocean meet. However, these two terms are often used interchangeably.
A bend in a stream. A stream flowing through a wide valley or flat plain will tend to form a meanders as it alternatively erodes and deposits sediments along its course.
A biome is an ecosystem which is undergoing climactic ecological succession.
In this definition, there is an assumption that no major perturbations are occurring or have occurred in a time frame affects the successional dynamics of the ecosystem. A "major" perturbation is one which disrupts the community's ability to restore its (near) equilibrium. Usually, pioneer or early secondary successional processes would be in effect in such scenarios.
A ridge which is jagged, narrow and separates glacier valleys or cirques.
The ridge frequently resembles the blade of a serrated knife. A French term referring to the bones in a fish backbone. Aretes are typically formed when two glaciers erode parallel U-shaped valleys. Aretes can also form when two glacial cirques erode towards one another, although frequently this results in a saddle-shaped pass, called a col.
A feature of a glacier, in which dirt, which has fallen into a hollow in the ice, forms a coating which insulates the ice below. The surrounding ice melts away, leaving the dirt cone.
A cluster of dozens to hundreds of similarly shaped, sized and oriented drumlins.
An isolated hill, knob, ridge, or small mountain that rises abruptly from a gently sloping or virtually level surrounding plain.
A fan-shaped body of sediments deposited by braided streams from a melting glacier.
A lake formed either by the damming action of a moraine or ice dam during the retreat of a melting glacier, or one formed by meltwater trapped against an ice mass due to isostatic depression of the crust around the ice.
A deep but narrow valley with a 'U' shaped cross-section and frequently a 'U' shaped plan which is usually found filled with glacial till. It is formed when the edge of an ice mass advances up a slope. Its length may be appropriately measured in centimetres or kilometres, depending on the circumstances of formation.
A steep-sided depression formed by the melting of permafrost; it may contain a lake.
A small wooded valley, either U- or V-shaped.
A shallow cave-like opening at the base of a bluff or cliff.
A ridge on a hillside formed when saturated soil particles expand, then contract as they dry, causing them to move slowly downhill.
A reservoir constructed for the purpose of containing a flood, an overflow of water from a body of water that sumerges land.
A tract of land which has few or no trees and is surrounded by more heavily wooded areas.
There should be a better superclass than "field" which should indicate that there are no woody plants in growth form "tree" around.
An aquaduct to transport water from one river basin to another one, to solve problems of hydrographic imbalance. It can decrease floods, moving the water to lands with droughts.
A biome which is primarily or completely situated on a landmass.
An aquatic biome which is determined by a marine water body.
This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt.
A reservoir constructed for the purpose of generating electricity.
A reservoir constructed for the purpose of providing drinking water.
A reservoir constructed for the purpose of providing water for irrigation.
A lake constructed, or modified, for the chief purpose of providing an amenity.
A lake that is long, narrow, and finger-shaped, usually found in a glacial trough. Its formation begins when a glacier moves over an area containing alternate bands of hard and soft bedrock. The sharp-edged boulders carried at the bottom of the glacier erode the softer rock more quickly by abrasion, thus creating a hollow called a rock basin. On either side of the rock basin, the more resistant rock is eroded less and these outcrops of harder rock are known as rock bars, which act as dams between which rainwater may accumulate after the retreat of the ice age, filling up the rock basin and creating a ribbon lake. A ribbon lake may also form behind a terminal or recessional moraine, both of which also act as dams, enabling water to accumulate behind them. A ribbon lake may also occur if a tributary glacier joins a main glacier. The increase in power can create a trough, which is filled with water from a river/meltwater to create a ribbon lake.
A lake or estuary that is formed at the mouth of a river where flow is blocked by a bar of sediments. It can be maritime (the bar being created by the current of a sea) or fluvial (the bar being created by the flow of a bigger river at the confluence).
A container of an intermittent lake unique to the limestone areas of Ireland, mostly west of the River Shannon. Most turloughs flood in the autumn, usually some time in October, and then dry up some time between April and July.
A mountain lake that is formed in a cirque excavated by a glacier. A moraine may form a natural dam below a tarn.
A glacier which terminates in a lake or the sea, with terminus either floating or grounded
The adjective indicates geographical setting, and not that tides play a role in the mass balance. Typically, tidewater glaciers calve ice to produce icebergs. There are currently issues in the community about the definition of this glacier type: It is undecided whether or not a) a tidewater glacier has to have a grounded terminus and b) whether glaciers terminating in a lake can be considered to be tidewater glaciers.
A glacier on a plateau or high area, smaller than an ice sheet.
A glacier which 1) flows for all or most of its length within the walls of a valley, in consequence having a distinct tongue and a well-defined outline and 2) descends from either high mountains, from an ice cap on a plateau, or from an ice sheet.
These glaciers typically flow down pre-existing valleys and have ice-free slopes overlooking the glacier surface.
A region of low topographic relief as a consequence of erosion by streams.
A volcanic landform which resembles a true volcanic crater, but differs in that it is not an actual vent from which lava has erupted. A pseudocrater is characterised by the absence of any magma conduit which connects below the surface of the earth. Pseudocraters are formed by steam explosions as flowing hot lava crosses over a wet surface, such as a swamp, a lake, or a pond. The explosive gases break through the lava surface in a manner similar to a phreatic eruption, and the tephra builds up crater-like forms which can appear very similar to real volcanic craters.
A volcanic field of scattered volcanic vents. These volcanic fields, containing numerous polygenetic volcanoes, are noted for having more than one eruptive event from the same vent(s), rather than the more common monogenetic volcanic field. Polygenetic volcanic fields generally occur where there is a high-level magma chamber. These volcanic fields may show lithological discontinuities due to major changes in magma chemistry, volcanotectonic events, or long erosional intervals, and may last >10 million year period.
A landform which provides shelter from atmospheric weather and marine currents, waves, and other dynamics.
harbor
Harbours are often used to store or shelter ships.
A harbor which is formed by a natural landform where a part of a body of water is protected and deep enough to furnish anchorage.
An area of land on which a college or university and related institutional buildings are situated.
A dam constructed for the purpose of generating electricity from the water stored behind it.
A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
A dam constructed for the purpose of holding water in a reservoir for irrigation.
A dam constructed for the purpose of controlling flooding.
An area of calm water unaffected by the current of a stream.
A quarry from which gravel is extracted.
An excavation of the Earth's surface to provide passage for a road, railway, canal, etc.
An opening of the sea into the land, or of a lake into its shore.
This is not placed under surface landform, as seamounts are also mounts and are submerged.
A field which includes at least two mounts connected by high ground and arranged in an approximately linear fashion.
The exit or point of discharge of a stream into another stream, lake or sea.
A tall, slender, spire-shaped rock projecting from a level or more gently sloping surface.
Meeresboden
fondale marino
fondo marino
ocean floor
seabed
海床
海底
A hollow eroded by the force of the falling water at the base of a waterfall, particularly by the eddying effect.
Problematic. Does this refer to the depression or the accumulated water?
A sea surface layer which is 1) not covered by ice and 2) laterally surrounded by either pack ice or land and pack ice.
Polyn'ya
A polynya is a Russian term for any non-linear shaped area of open water within the ice pack. Polynyas may contain brash ice and/or be covered with new ice, nilas or young ice; submariners refer to these as skylights. Sometimes the polynya is limited on one side by the coast and is called a shore polynya or by fast ice and is called a flaw polynya. If it recurs in the same position every year, e.g. off the mouths of big rivers, it is called a recurring polynya. A temporary small clearing in pack ice which consists of small floes and brash in continuous local movement is called an unstable polynya; an opening which is flanked by large floes and therefore appears to be relatively stable is called a stable polynya. Polynyas range in size from relatively small to enormous. The largest polynya observed in the Antarctic was the Weddell Polynya of 1975-77, covering an area of 2x105km2. The two main categories of polynya are sensible heat and latent heat, depending on the mechanism responsible for maintaining their presence. Latent heat polynyas are maintained by persistent katabatic winds that drain off the continent. Newly formed ice is advected away by the wind, leaving the surface ice-free and open to more ice formation. In this manner latent heat polynyas can be major sources of new ice production. Coastal polynyas are primarily of this type. Sensible heat polynyas are maintained by upwelling warm water that supplies a sufficiently large oceanic heat flux to the base of the ice to reduce its thickness, or melt it completely. These polynyas are not responsible for large quantities of new ice production. A polynya may also form by a combination of the sensible and latent heat processes. From the remote sensing/sea ice standpoint a polynya is a hole in the ice that ordinarily wouldn't be there - except that either the wind is creating it by pushing the ice away or there is something under the ice that is warmer than its surroundings and melting the ice that would otherwise be there.
Could be a subclass of a class that describes holes in solid material covering water or other liquids. Perhaps a class like "clearing". Logical def can include surrounded_by "ice mass".
That part of the land in immediate contact with a sea, including the intertidal zone.
A two-dimensional continuant fiat boundary which is located between a landmass and a water body.
Küstenlinie
linea costiera
línea costera
海岸線
1) this term is usually used for larger water bodies like lakes and oceans, 2) that the actual spatial extent of a shoreline, and the sharpness of its boundaries, is often arbitrarily or operationally defined, and 3) this term is for the physical shoreline, not the one- or two-dimensional representation of shorelines.
The distinction between shoreline and coastline needs more thought.
One of a series of glacial lakes connected by a single stream or a braided stream system.
A lake which is primarily composed of glacial meltwater and which fills a depression formed as a result of a glacial erosion process.
A frost heave which is formed as the result of a perennial ice lens forming under soil, pushing a roughly oval portion land surface upwards.
Palsas typically occur in areas with discontinuous permafrost, frequently peat bogs. A palsa consists, similarly to a pingo, of an ice core and overlying soil materials, in case of a palsa usually boggy soil. Palsas are characteristically found in areas with discontinuous permafrost and in such areas bay be the only reliable surface evidence of permafrost. A palsa needs large quantities of water for the formation of its ice core (i.e. ice lens), which is why they frequently emerge from and are bound by boggy soils, which can store enormous quantities of water in their pores. Palsas develop particularly in moorlands and are therefore also named palsamoors.
A stream whose course is a direct consequence of the original slope of the surface upon which it developed, i.e., a stream that follows the slope of the original land.
A stream whose course has been determined by selective headward erosion along weak strata. These streams have generally developed after the original stream. Subsequent streams developed independently of the original relief of the land and generally follow paths determined by the weak rock belts.
A stream whose course follows the original relief, but at a lower level than the original slope (e.g., flows down a course determined by the underlying strata in the same direction). These streams develop later and are generally a tributary to a subsequent stream.
A stream flowing in the opposite direction of the consequent drainage.
A stream that has an almost random drainage often forming dendritic patterns. These are typically tributaries and have developed by a headward erosion on a horizontally stratified belt or on homogeneous rocks. These streams follow courses that apparently were not controlled by the original slope of the surface, its structure or the type of rock.
A stream or river which flows into another river (a parent river) or body of water but which may not flow directly into the sea.
A narrow and shallow incision into soil resulting from erosion by overland flow that has been focused into a thin thread by soil surface roughness. Rilling, the process of rill formation, is common on agricultural land and unvegetated ground.
An intrusive igneous body. Its thickness is usually much smaller than its other two dimensions. Thickness can vary from sub-centimeter scale to many meters in thickness and the lateral dimensions can extend over many kilometers. A dike is an intrusion into a cross-cutting fissure, meaning a dike cuts across other pre-existing layers or bodies of rock, this means that a dike is always younger than the rocks that contain it. Dikes are usually high angle to near vertical in orientation, but subsequent tectonic deformation may rotate the sequence of strata through which the dike lies so that the latter becomes horizontal.
A linear structural depression that extends laterally over a distance, while being less steep than a trench. A trough can be a narrow basin or a geologic rift. There are various oceanic troughs, troughs found under oceans; examples include the rift along the mid-oceanic ridge and the Cayman Trough.
An obstruction in a stream constructed by a beaver.
The portion of the ground surface which lies below water.
A depression that is periodically filled with saline water, forming a saline lake.
container of an intermittent saline lake
A depression which is continous with one or more abandoned meander loops of a river channel.
A container of an intermittent water body which, when filled with water, has a well-illuminated surface layer, is subject to complete mixing of the water it holds, and is smaller than the container of a lake.
A gently inclined underground tunnel bringing water for irrigation from an aquifer.
A reservoir that is not permanently filled with water, at times being dry.
The lower terminus of a wadi where it widens into an adjoining floodplain, depression, or water body.
A step-like feature between higher and lower ground: a relatively flat or gently inclined shelf of earth, backed and fronted by steep slopes or manmade detaining walls.
A terrace which is located in a marine water body.
A landform which is the narrowest part of a meander.
A peatland whose development is mostly independent of basins or topographical features where water collects; it simply covers the landscape like a blanket. Peat develops due to a continuous supply of water from rainfall, maintaining waterlogged conditions on the ground. Blanket bogs are ombrotrophic or rain fed, and as a result their pH lies between 3.5 and 4.2.
The ground surface that lies beneath a pond.
The ground surface that lies beneath a reservoir.
A generally circular saucer or bowl-shaped depression caused by explosive action.
A patch of ground, distinct from and slightly above the surrounding plain or wetland. Often occurs in groups.
A surface stream that disappears into an underground channel, or dries up in an arid area.
The exit or point of discharge of a ditch.
A terrace which is used for agricultural activities.
A mound of earth material, at the base of a slope and the associated scoured area.
An irregular mass of fallen rock at the base of a cliff or steep slope.
A channel formed as a result of a stream cutting through a meander neck.
A former stream or distributary no longer carrying flowing water, but still evident due to lakes, wetland, topographic or vegetation patterns.
A stream that has been substantially ditched, diked, or straightened.
A deep narrow slot, notch, or groove in a cliff.
A relatively undissected upland between adjacent stream valleys.
A ridge of sand just inland and parallel to the beach, usually in series.
A gentle slope, with a generally smooth surface, particularly found around groups of islands and seamounts.
A depression which is part of an ice cap.
A depression which contains objects and materials discarded by humans or their technologies.
Deponie
discarica
garbage dump
rubbish dump
vertedero
垃圾掩埋場
churn hole
evorsion
kettle
pot
rock mill
eddy mill
giant's kettle
kolk
stream kettle
swirlhole
A depression which 1) has smooth surfaces, 2) has a bowl-like or cylindrical shape, 3) results from the erosion of the rocky bed of a watercourse.
A low obstruction built across the path of s stream to raise its level.
An annular depression that may not be continuous, located at the base of many seamounts, islands, and other isolated elevations.
A high altitude or high latitude bare, flat area covered with large angular rocks.
An undersea area of subdued corrugations.
The low part of a gap or saddle separating basins.
A lake which is primarily composed of brackish water, having a higher salinity than fresh water but a lower salinity than marine water.
A pond which is composed primarily of brackish water.
An irregularly shaped hill or mound composed of sorted or stratified sand and gravel that is deposited in contact with the glacial ice. It can have an irregular shape. Kames are often associated with kettles, and this is referred to as kame and kettle topography. When the ice retreats further, the delta kame often collapses. Kame terraces are frequently found along the side of a glacial valley and are the deposits of meltwater streams flowing between the ice and the adjacent valley side.
A depression which comprises a low tract of land, especially when moist or marshy.
The term can refer to a natural landscape feature or a human-created one. When created by humans, this open drain system is designed to manage water runoff.
A man-made watercourse, or makeshift aqueduct, often an artificial channel which supplies water to a watermill or its mill pond, collecting water from upstream of the mill so that the natural level of the driving water is above the level of the stream at the mill. Alternatively to may deliver water for mineral washing and concentration, irrigation or to a dye works.
A beach which is armoured with pebbles or small to medium sized cobbles.
Lake sediment is sediment which covers the bottom of a lake. Lake sediments are comprised mainly of clastic material (sediment of clay, silt, and sand sizes), organic debris, chemical precipitates, or combinations of these.
A pond, often temporary or seasonal, used as a drinking place by mammals and birds.
A field which is composed primarily of gravel.
A depression which is is periodically filled with water when water supply exceeds evapotranspiration and bed seepage.
Despite the relocation from its position under 'water body' and the rewording of the definition, the class was not obsoleted as the entity being referenced is effectively the same.
This was formerly represented as a water body, which would not be valid during dry periods. This class more properly refers to the container of the water body, thusfar always some depression, which periodically contains a water body.
A mountain range which is submerged under a marine water body.
A drainage basin from which there is no outflow of water, either on the surface as rivers, or underground by flow or diffusion through rock or permeable material.
An area of unfrozen ground surrounded by permafrost.
A dam constructed for more than one purpose.
An auxiliary dam constructed to confine the reservoir created by a primary dam either to permit a higher water elevation and storage or to limit the extent of a reservoir for increased efficiency.
A dam designed to reduce flow velocity and control soil erosion.
A dam that only partly restricts a waterway, creating a faster channel that resists the accumulation of sediment.
A dam designed to control flooding. It normally holds back no water and allows the channel to flow freely, except during periods of intense flow that would otherwise cause flooding downstream.
A dam designed to divert all or a portion of the flow of a river from its natural course.
A region at which weapons, typically military, are tested.
A weapons test site at which nuclear weapons are, or have been, tested.
A region in which military personnel train.
A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation.
A raised walkway over water, supported by piles or pillars.
A place (or group of physical sites) in which evidence of past activity is preserved (either prehistoric or historic or contemporary), and which is, has been, or may be, investigated using the discipline of archaeology.
A building or region where sports activities can be carried out.
The inclusion of "region" in this definition is problematic.
A sports facility constructed for skiing and allied sports that require snow and/or ice.
A deep valley with steep sides, typically of limestone, in part submerged by the sea.
An aquatic biome which is determined by a body of freshwater.
A freshwater river biome which is determined by a large river.
"Large" is ambiguous. For details on "Large rivers" (e.g. the Mekong river) see http://worldwildlife.org/biomes/large-river-ecosystems This class will be replaced with a less ambiguous class.
A freshwater river biome which is determined by the headwaters of a large river.
"Large" is ambiguous. For details on "Large river headwaters" (e.g. the Upper Amazon headwaters) see http://worldwildlife.org/biomes/large-river-headwater-ecosystems This class will be replaced with a less ambiguous class.
A freshwater river biome which is determined by the delta of a large river.
"Large" is ambiguous. For details on "Large river deltas" (e.g. the Niger river delta) see http://worldwildlife.org/biomes/large-river-delta-ecosystems This class will be replaced with a less ambiguous class.
A freshwater river biome which is determined by a small river.
"Small" is ambiguous. For details on "Small rivers" (e.g. the Salween river) see http://worldwildlife.org/biomes/small-river-ecosystems. This class will be replaced with a less ambiguous class.
A freshwater biome which is determined by a large lake.
"Large" is ambiguous. For details on "Large lakes" (e.g. African rift lakes) see http://worldwildlife.org/biomes/large-lake-ecosystems This class will be replaced with a less ambiguous class.
A freshwater lake biome which is determined by a small lake.
"Small" is ambiguous. For details on "Small lakes" (e.g. Cameroon crater lakes) see http://worldwildlife.org/biomes/small-lake-ecosystems. This class will be replaced with a less ambiguous class.
A biome which has little permanent surface water and a low relative abundance of springs.
The WWF definition is somewhat ambiguous, but workable.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
A lentic water body which is composed primarily of marine water.
A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land.
Water that has been adversely affected in quality by anthropogenic influence.
An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation.
This is distinct from classes such as http://purl.obolibrary.org/obo/UBERON_0001988 in that it refers to the environmental material composed primarily of feces rather than 'just' feces.
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
An environmental material primarily composed of dihydrogen oxide in its liquid form.
Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.
Sediment is typically deposited on the bed or bottom of a body of water or other liquid.
Particulate environmental material with diameters less than 500 micrometers.
Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
Dust occurs in and may be deposited from the atmosphere.
Water which contains a significant concentration of dissolved salts.
The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.
Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.
The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water.
Water which contains a highly increased concentration of dissolved salts, surpassing the average salinity of seawater.
We make no commitment to a particular threshold; this should be described on the data/information layer according to the norms of a discipline, accepted standard, or similar reference.
The average salinity of sea water is assumed to be around 35,000 ppm, equivalent to 35 grams of salt per one liter (or kilogram) of water.
An igneous rock that results from the crystallization of a magma below the surface of the Earth.
An igneous rock that results from magma reaching the surface either as lava or fragmental ejecta.
Due to the general suggestion that volcanic rock simply comes from a volcanic process, it's not immediately clear whether this is interchangeable with igneous rock.
A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis.
A rock formed by subjecting any rock type (including previously-formed metamorphic rock) to different temperature and pressure conditions than those in which the original rock was formed. These temperatures and pressures are always higher than those at the Earth's surface and must be sufficiently high so as to change the original minerals into other mineral types or else into other forms of the same minerals (e.g. by recrystallisation).
Wastewater that is contaminated with feces or urine,
Water which has a higher salinity than fresh water but a lower salinity than marine water.
A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water.
A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum.
A natural object originating in outer space that survives an impact with a planetary surface without being destroyed.
Water that is found on the surface of an astronomical object.
The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.
Sediment characterised by the absence of oxygen.
An excreta material which is composed primarily of urine, a liquid excreta containing water and waste products made by the kidneys, stored in the bladder, and leaves the body through the urethra.
A stony meteorite that have not been modified due to melting or differentiation of the parent body.
A stony meteorite that is made of material similar to terrestrial basalts or plutonic rocks.
A meteorite that consists of a mixture of iron-nickel metal and silicate minerals.
A meteorite that overwhelmingly of nickel-iron alloys.
A sedimentary rock which is composed primarily of calcium carbonate in the form of calcite or aragnoite.
An interesting reasoning error was generated when this class had "composed primariy of some CHEBI:calcium carbonate". As that was a CHEBI:mineral, and minerals are disjoint from ENVO:rock, it led to an unsatisfiable class. The current axiom works around this, but this is requires some sort of geological convention to diffferentiate between masses of minerals and rocks that are composed primarily of minerals.
Limestone which is soft, white, and porous.
A sedimentary rock composed mainly of sand-size mineral or rock grains.
A fine-grained sedimentary rock whose original constituents were clays or muds. It is characterized by thin laminae breaking with an irregular curving fracture, often splintery and usually parallel to the often-indistinguishable bedding plane.
A treated form of sludge, sometimes used as a fertilizer in agriculture.
A solid or gel in motor oil caused by the oil gelling or solidifying, usually at temperatures lower than 100deg C.
The result of the unintentional release of liquid petroleum hydrocarbon into the environment as a result of human activity.
The result of the release of natural hydrocarbons to the surface of the earth, including beneath the sea, by natural geological processes.
Mine drainage which is formed as a result of the mining of gold.
Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays.
Sediment which has increased levels of one or more chemical compounds.
Organically enriched sediment which has increased levels of petroleum.
A portion of contaminated soil is a portion of soil with elevated levels of some contaminant.
"contaminant" is more of a disposition - any material entity can be a contaminant in particular circumstances.
Soil which has elevated concentrations of creosote.
A alkaline spring through which groundwater, heated by geothermal energy, flows.
An acidic spring through which groundwater, heated by geothermal energy, flows.
acid hot spring
acidic hot spring
A saline lake which has a high pH.
The formation processes of these lakes would be an interesting project to develop.
The pH of alkaline lakes is typically between 9 and 12. They are characterized by high concentrations of carbonate salts, typically sodium carbonate (and related salt complexes), giving rise to their alkalinity. In addition, many soda lakes also contain high concentrations of sodium chloride and other dissolved salts, making them saline or hypersaline lakes as well. High pH and salinity often coincide, because of how soda lakes develop.
Mud which has elevated concentrations of arsenic.
A biomaterial containment unit which is capable of 1) containing a mass of environmental material which hosts an active collection of organisms and 2) maintaining conditions which are conducive to one or more metabolic activities of the organisms it contains.
A bioreactor in which the contained material is not oxygenated (i.e. void of biologically consequential free oxygen)
A device or system that supports a biologically active environment. A vessel in which is carried out a chemical process which involves organisms or biochemically active substances derived from such organisms. This process can either be aerobic or anaerobic.
A bioreactor in which the contained material is well-oxygenated.
Revise adjacent to. Consider sampled stream sediment. Dry stream sediment.
A sulfur spring through which water at a temperature optimal for the growth of mesophillic microorganism (approximately 20 to 45 degrees Celsius) flows.
The dense, bottom layer of water in a thermally-stratified lake. It is the layer that lies below the thermocline.
The top-most layer in a thermally stratified lake, occurring above the deeper hypolimnion. It is warmer and typically has a higher pH and dissolved oxygen concentration than the hypolimnion.
A cline which is part of a lake and across which temperature changes rapidly with depth.
Especially used in connection with meromictic lakes.
Mud which has no or neglible concentrations of dissolved oxygen.
An estuary which is composed primarily of brackish water.
A piece of rock which is derived from clastic rock and has a grain size of 4 to 64 millimeters.
The grain size classification is based on the Krumbein phi scale of sedimentology.
A piece of rock which has a grain size between 64 and 256 mm.
The liquid produced when water percolates through any permeable material. It can contain either dissolved or suspended material, or usually both.
A calcic spring through which groundwater, heated by geothermal energy, flows.
calcic hot spring
A solid surface layer which 1) forms part of the boundary between the cavity of a cave and its solid container and 2) is roughtly perpendicular to the cave floor.
Soil which has elevated concentrations of chromate.
Soil which has elevated concentrations of xylene.
Coal mine lake sediment is lake sediment which covers the bottom of a coal mine lake.
Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean.
When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class.
This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels.
Coastal sea water is sea water that is adjacent to a coast.
The limits of what qualifies as "adjacent to" vary greatly. This should be defined on a data level and is left intentionally fuzzy here. The label is "coastal sea water" rather than "coastal water" as some large lakes are often said to have coasts.
A bioreactor which captures and, through the biological processes maintained in the medium it contains, degrades pollutants.
A biofilter which contains compost and avails of the microbial communities within it to degrade pollutants.
A highly contaminated site designated by the United States of America's Comprehensive Environmental Response, Compensation, and Liability Act.
A solid environmental material which is formed by the replacement of organic substances (including those in soils and sediments) with mineral material.
Manure which has been derived from the aerobically decomposed remnants of organic materials.
A hospital is a building in which health care services are provided by specialized staff and equipment.
A zone within a portion of petroleum contaminated sediment within which iron-reducing processes occur.
iron-reducing zone of petroleum contaminated sediment
Organically enriched sediment which has increased levels of naphthalene.
A neutral spring through which groundwater, heated by geothermal energy, flows.
Organically enriched sediment which has increased levels of nitrobenzene.
A manufactured container within which oil or other petrochemical products are stored and which these products are usually transported to end users or further storage facilities.
Consider using http://purl.obolibrary.org/obo/OBI_0000967 as a super-class
sub-surface landform
underground physiographic feature
A landform which is located under the surface of a landmass.
A subsurface landform which contains fluid hydrocarbons in porous or fractured rock formations.
oil and gas reservoir
petroleum reservoir
Straw or other material strewn in an animal's enclosure (e.g. a stable) for it to sleep on and to absorb its faeces and urine.
Acid mine drainage which has elevated levels of pyritic acid.
An aquarium is a vivarium which simulates the submerged portions of an aquatic environment
A saline water aquarium is an aquarium which contains saline water as its primary ecological medium.
A fresh water aquarium is an aquarium which contains fresh water as its primary ecological medium.
A beach which is primarily composed of sand.
Water ice which has formed by the freezing of sea water.
Parse comment from GCW and new subclases where appropriate.
In the United States, NOAA sea ice operations does not include superstructure icing as being sea ice. In sea ice operations however, sea ice is any form of ice found at sea which has originated from the freezing of sea water. It presents the main kind of floating ice encountered at sea. Except where it forms ridges, sea ice is up to a few metres thick, in which respect it differs from shelf ice. Sea ice may be discontinuous pieces (ice floes) moved on the ocean surface by wind and currents (pack ice), or a motionless sheet attached to the coast (land-fast ice). In brief, it forms first as lolly ice (frazil crystals), thickens into sludge, and coagulates into sheet ice, pancake ice, or into floes of various shapes and sizes. Thereafter, sea ice may develop into pack ice and/or become a form of pressure ice. Sea ice less than one year old is called first-year ice. Perennial ice is sea ice that survives at least one summer. It may be subdivided into second-year ice and multi-year ice, where multiyear ice has survived at least two summers.
Organically enriched sediment which has increased levels of cis-dichloroethane.
cis-dichloroethane contaminated sediment
Chemically-enriched sediment which has increased levels of organic compounds.
Chemically-enriched sediment which has increased levels of inorganic compounds.
An anthropogenic geographic feature which has increased levels of contaminants in its consituent materials.
A dump which contains ammunition, or other material intended for use during combat, that still has the potential to explode.
Saline lake sediment is sediment which covers the bottom of a saline lake.
An aerobic bioreactive which contains microbial communities capable of sulfide oxidation.
An anaerobic biorector which uses elevated temperatures and appropriate chemical substrates to support the production of methane by microbial communities.
thermophilic anaerobic methanogenic reactor
An anaerobic bioreactor which is capable of treating wastewater through the action of methanogenic microbes which form a blanket of sludge due to the upward flow in the reactor.
This can be unpacked with some hierarchies of different bioreactors.
A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely.
A geothermal power plant is a power plant which uses heat generated by the decay of radioactive isotopes in the Earth's mantle and crust as well as primordial heat left over from the formation of the Earth to drive its generators.
A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods.
A shop in which a business offers food products for sale or trade.
Whether food is the primary product offered by the business or simply one of the products it offers is not specified in this class.
Water which has very low concentrations of nutrients.
Water with a nutrient level intermediate between eutrophic and oligotrophic.
A channel which is constructed by removing materials from land or submerged beds.
Arenosols are sandy soils, including both soils developed in residual sands after in situ weathering of usually quartz-rich sediments or rock, and soils developed in recently deposited sands such as dunes in deserts and beach lands.
Anthrosols comprise soils that have been modified profoundly through human activities, such as addition of organic materials or household wastes, irrigation and cultivation.
Alisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Alisols have a low base saturation at certain depths and high-activity clays throughout the argic horizon. They lack the albeluvic tonguing as in Albeluvisols. They occur predominantly in humid tropical, humid subtropical and warm temperate regions.
Andosols are soils that develop in volcanic ejecta or glasses under almost any climate (except under hyperarid climate conditions). However, Andosols may also develop in other silicate-rich materials under acid weathering in humid and perhumid climates.
Albeluvisols are soils that have, beginning within 1 m of the soil surface, a clay illuviation horizon with an irregular or broken upper boundary resulting in tonguing of bleached soil material into the illuviation horizon.
Acrisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Acrisols have in certain depths a low base saturation and low-activity clays.
Cambisols combine soils with at least an incipient subsurface soil formation. Transformation of parent material is evident from structure formation and mostly brownish discoloration, increasing clay percentage, and/or carbonate removal.
Cryosols comprise mineral soils formed in a permafrost environment. Where water is present, it occurs primarily in the form of ice. Cryogenic processes are the dominant soil-forming processes.
Chernozems are soils with a thick black surface layer that is rich in organic matter.
Durisols are associated mainly with old surfaces in arid and semi-arid environments and accommodate very shallow to moderately deep, moderately well- to well-drained soils that contain cemented secondary silica (SiO2) within 100 cm of the soil surface.
Calcisols are soils in which there is substantial secondary accumulation of lime. Calcisols are common in highly calcareous parent materials and widespread in arid and semi-arid environments.
Kastanozems are dry grassland soils, among them the zonal soils of the short-grass steppe belt, south of the Eurasian tall-grass steppe belt with Chernozems. Kastanozems have a similar profile to that of Chernozems but the humus-rich surface horizon is thinner and not as dark as that of the Chernozems and they show more prominent accumulation of secondary carbonates.
Leptosols are very shallow soils over continuous rock and soils that are extremely gravelly and/or stony. Leptosols are azonal soils and particularly common in mountainous regions.
Lixisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Lixisols have a high base saturation and low-activity clays at certain depths.
Histosols comprise soils formed in organic material. These vary from soils developed in predominantly moss peat in boreal, arctic and subarctic regions, via moss peat, reeds/ sedge peat (fen) and forest peat in temperate regions to mangrove peat and swamp forest peat in the humid tropics. Histosols are found at all altitudes, but the vast majority occurs in lowlands.
Gleysols are wetland soils that, unless drained, are saturated with groundwater for long enough periods to develop a characteristic gleyic colour pattern. This pattern is essentially made up of reddish, brownish or yellowish colours at ped surfaces and/or in the upper soil layer or layers, in combination with greyish/bluish colours inside the peds and/or deeper in the soil.
Gypsisols are soils with substantial secondary accumulation of gypsum (calcium sulfate). These soils are found in the driest parts of the arid climate zone.
Ferralsols represent the classical, deeply weathered, red or yellow soils of the humid tropics. These soils have diffuse horizon boundaries, a clay assemblage dominated by low-activity clays (mainly kaolinite) and a high content of sesquioxides.
Nitisols are deep, well-drained, red, tropical soils with diffuse horizon boundaries and a subsurface horizon with more than 30 percent clay and moderate to strong angular blocky structure elements that easily fall apart into characteristic shiny, polyhedric (nutty) elements. Weathering is relatively advanced but Nitisols are far more productive than most other red, tropical soils.
Luvisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Luvisols have high-activity clays throughout the argic horizon and a high base saturation at certain depths.
Phaeozems accommodate soils of relatively wet grassland and forest regions in moderately continental climates. Phaeozems are much like Chernozems and Kastanozems but are leached more intensively. Consequently, they have dark, humus rich surface horizons that, in comparison with Chernozems and Kastanozems, are less rich in bases. Phaeozems may or may not have secondary carbonates but have a high base saturation in the upper metre of the soil.
Plinthosols are soils with plinthite, petroplinthite or pisoliths. Plinthite is an Fe-rich (in some cases also Mn-rich), humus-poor mixture of kaolinitic clay (and other products of strong weathering such as gibbsite) with quartz and other constituents that changes irreversibly to a layer with hard nodules, a hardpan or irregular aggregates on exposure to repeated wetting and drying. Petroplinthite is a continuous, fractured or broken sheet of connected, strongly cemented to indurated nodules or mottles. Pisoliths are discrete strongly cemented to indurated nodules. Both petroplinthite and pisoliths develop from plinthite by hardening.
Planosols are soils with a light-coloured, surface horizon that shows signs of periodic water stagnation and abruptly overlies a dense, slowly permeable subsoil with significantly more clay than the surface horizon.
Solonchaks are soils that have a high concentration of soluble salts at some time in the year. Solonchaks are largely confined to the arid and semi-arid climate zones and to coastal regions in all climates.
Umbrisols are soils in which organic matter has accumulated within the mineral surface soil (in most cases with low base saturation) to the extent that it significantly affects the behaviour and utilization of the soil.
A soil in which there is a high content of expansive clay known as montmorillonite that forms deep cracks in drier seasons or years. Alternate shrinking and swelling causes self-mulching, where the soil material consistently mixes itself, causing vertisols to have an extremely deep A horizon and no B horizon.
Solonetz are soils with a dense, strongly structured, clayey subsurface horizon that has a high proportion of adsorbed Na and/or Mg ions. Solonetz that contain free soda (Na2CO3) are strongly alkaline (field pH > 8.5).
Regosols form a taxonomic remnant group containing all soils that could not be accommodated in any of the other RSGs. In practice, Regosols are very weakly developed mineral soils in unconsolidated materials that do not have a mollic or umbric horizon, are not very shallow or very rich in gravels (Leptosols), sandy (Arenosols) or with fluvic materials (Fluvisols). Regosols are extensive in eroding lands, particularly in arid and semi-arid areas and in mountainous terrain.
Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
A soil which is composed of approximately equal proportions of sand and silt, with a smaller proportion of clay.
Some authorities consider loam to be any soil material that contains 7 to 27% clay, 28 to 50% silt, and less than 52% sand.
Soil which is part of an ecosystem used for agricultural activities.
Soil which is part of some dune.
A portion of soil which is found in a forested area.
Soil which is primarily composed of clay.
A portion of soil which is found in a garden.
A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).
This seems more like a role than a material. Anything can be waste. Thus, a "waste" role or disposition will be created and this class can then be populated by inference: any environmental material which has [role,disposition] waste will be considered a waste material.
Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products.
This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with industrial entities.
A peatland dominated by species of the Bryophyte Sphagnum.
A cline across which temperature changes rapidly.
A cline across which the chemical composition of a fluid changes rapidly.
This cline is typically horizontal, with qualities varying with depth.
A nuclear power plant is a power plant which uses heat generated by a radioactive decay in a nuclear reactor to convert water into steam in order to drive turbines in electrical generators through pressure.
Fluvisols accommodate genetically young, azonal soils in alluvial deposits.
Stagnosols are soils with a perched water table showing redoximorphic features caused by surface water. Stagnosols are periodically wet and mottled in the topsoil and subsoil, with or without concretions and/or bleaching.
Technosols are soils whose properties and pedogenesis are dominated by their technical origin. They contain a significant amount of artefacts (something in the soil recognizably made or extracted from the earth by humans), or are sealed by technic hard rock (material created by humans, having properties unlike natural rock). They include soils from wastes (landfills, sludge, cinders, mine spoils and ashes), pavements with their underlying unconsolidated materials, soils with geomembranes and constructed soils in human-made materials.
This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with animal metabolism.
A depression in the sea floor that results from the collision of continental plates; the weight of the sinking plate causes the overlying plate to stretch and thin, causing a basin in the overlying plate. Sometimes, the Earth's crust in these basins stretches so much it cracks, allowing magma through from the mantle beneath. Hence, basins often contain active volcanoes and hydrothermal vents.
A structural basin that is below sea level.
This class is defined in its geological sense: https://en.wikipedia.org/wiki/ Hydrologically, an oceanic basin may be anywhere on Earth that is covered by seawater, but geologically ocean basins are large geologic basins that are below sea level. Geologically, there are other undersea geomorphological features such as the continental shelves, the deep ocean trenches, and the undersea mountain ranges (for example, the mid-Atlantic ridge) which are not considered to be part of the ocean basins; while hydrologically, oceanic basins include the flanking continental shelves and shallow, epeiric seas.
Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep.
A natural building material mode from sand, clay, water, and some kind of fibrous or organic material (sticks, straw, and/or manure).
Soil which has been eroded and influenced by flowing water and redeposited in a non-marine setting.
The biomass remaining after sugarcane stalks are crushed to extract their juice.
This should probably be merged with biological waste material.
A manufactuered product which is capable of removing heat and controlling the humidity of the air within a site.
A/C
A/C unit
air conditioner
Soil which has elevated concentrations of oil.
Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils.
An oil which 1) is liquid at room temperature (approximately 20 degrees Celsius) 2) is intended to be burned in a furnace or boiler for the generation of heat or used in an engine for the generation of power, 3) is obtained from petroleum distillation, either as a distillate or a residue, 4) composed of long hydrocarbon chains, particularly alkanes, cycloalkanes and aromatics.
Oils having a flash point of approximately 42 degrees Celsius and oils burned in cotton or wool-wick burners are not typically considered fuel oils. The term fuel oil is also used in a stricter sense to refer only to the heaviest commercial fuel that can be obtained from crude oil, i.e., heavier than gasoline and naphtha.
A naturally occurring flammable liquid consisting of a complex mixture of hydrocarbons of various molecular weights and other liquid organic compounds, that are found in geologic formations beneath the planetary surfaces.
A nonpolar, hydrophobic, and lipophilic material which is a viscous liquid at ambient temperatures (about 20 degrees Celsius) or slightly warmer.
A fermented, high-moisture forage that can be fed to ruminants.
Manure which is derived from the waste products of animals.
This is interesting in that the "role" aspect of "waste" is (or can be) replaced by another role "fertilizer". Thus, the positioning of "manure" under waste may not be totally correct.
A compost which generally consists of a combination of wheat straw, dried blood, horse manure and ground chalk, composted together and is the residual compost waste generated by industrial mushroom production.
A house used for sheltering non-human animals.
While humans are animals, this class does not refer to human houses.
An animal house which is used to shelter cows.
byre
cattle shed
cow barn
cow house
cowhouse
cowshed
milking shed
An animal house which is used to house pigs.
A waste treatment plant which equipped to treat sewage such that its potential for environmental contamination is reduced.
sewage treatment plant
sewage treatment works
Water saturated or nearly saturated with salt (NaCl).
It is used (now less popular than historically) to preserve vegetables, fish, and meat.
Drinking water is water which may be consumed by humans with no adverse effects on their health.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
A function realised by an environmental material when used to bind material entities together.
This sounds more like a role than a material, per se.
Soil which has elevated concentrations of metals.
A portion of enriched soil is a portion of soil with elevated levels of some material entity.
This could be demoted to an inferred class if issues with double inheritance arise.
A portion of sarcosine enriched soil is a portion of soil with elevated levels of sarcosine.
A portion of trimethylamine enriched soil is a portion of soil with elevated levels of trimethylamine.
A portion of skatole enriched soil is a portion of soil with elevated levels of skatole.
A portion of ethanol enriched soil is a portion of soil with elevated levels of ethanol.
A portion of acetamide enriched soil is a portion of soil with elevated levels of acetamide.
A portion of pantothenate enriched soil is a portion of soil with elevated levels of pantothenate.
A portion of testosterone enriched soil is a portion of soil with elevated levels of testosterone.
A portion of kynurenate enriched soil is a portion of soil with elevated levels of kynurenate.
A portion of threonine enriched soil is a portion of soil with elevated levels of threonine.
A portion of salicylate enriched soil is a portion of soil with elevated levels of salicylate.
A portion of poly-beta-hydroxybutyrate enriched soil is a portion of soil with elevated levels of poly-beta-hydroxybutyrate.
A portion of L-(+)-tartrate enriched soil is a portion of soil with elevated levels of L-(+)-tartrate.
A portion of quinate enriched soil is a portion of soil with elevated levels of quinate.
A tannery is a building in which the skins of animals are treated with chemicals to alter the structure of their constituent proteins, creating leather.
Manure which is primarily composed of pig feces.
An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered.
It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1.
A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption.
'Terminology differs between countries. For example, in the United States, the entire dairy farm is commonly called a "dairy." The building or farm area where milk is harvested from the cow is often called a "milking parlor" or "parlor." The farm area where milk is stored in bulk tanks is known as the farm's "milk house." Milk is then hauled (usually by truck) to a "dairy plant," also referred to as a "dairy", where raw milk is further processed and prepared for commercial sale of dairy products. In New Zealand, farm areas for milk harvesting are also called "milking parlours", and are historically known as "milking sheds."' https://en.wikipedia.org/wiki/Dairy
A food processing building is a building in which materials that contain or consist of essential body nutrients - such as carbohydrates, fats, proteins, vitamins, or minerals - and may be ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life are converted alternative forms.
The semantics of food are being handled by FOODON http://purl.obolibrary.org/obo/foodon.owl
A bakery is a building in which raw flour-based food is baked in an oven to produce food products such as bread, cakes, pastries, and pies. These products are often sold from the bakery itself.
A bakery is a food processing building and a 'food shop' at the same time. This needs to be resolved.
An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed.
A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery.
A manufactured product which has been formulated to modifying the appearance of external human anatomical parts.
A cosmetic product which has been formulated 2) to have a viscous, fatty, liquid consistency resembling the fat-rich component of milk and 2) to be applied to human facial skin to modify its appearance or functioning.
A product which is composed primarily of paper.
A paper product which is used as legal tender in economic or other monetary trasactions.
bank note
A sake brewery is a brewery which produces rice wine by fermenting rice which has been polished to remove the bran.
Soil which has increased levels of chalk.
A building or collection of co-located buildings constructed for the purpose of undertaking scientific research.
A layer of impurities that accumulates at the surface of a liquid (especially water or molten metal).
A warehouse is a building which is used for the storage of goods.
A tobacco warehouse is a warehouse used to store cured leaves of plants from the genus Nicotiana, primarily N. tabacum and N. rustica.
A creamery is a part of a dairy where cream is separated from whole milk.
An air filter is a device that removes some substance from air.
This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed.
Limestone which is deposited from the water of mineral springs or streams saturated with calcium carbonate.
A building within which logs are cut into lumber products.
A large flat plain in karst territory with areas usually 5 to 400 sqaure kilometres.
An environmental material which has the quality of a foam.
A foamy environmental material which 1) is created by the agitation of seawater, 2) whose stability depends on the content of the seawater.
The lifetime of sea foam can vary from only seconds to several hours or days. The longer-lasting foam are formed in particular when seawater contain higher concentration of dissolved organic matter that derived from sources such as algal blooms.
Soil which is part of a paddy field.
Soil which is part of an alpine environment.
Soil which is capable of supporting the growth of crops.
A portion of soil which is found in a roadside area.
Soil which is part of an allotment garden.
A garden which is made available for individual, non-commercial gardening or growing food plants.
allotment
community garden
Allotments gardens are so named as they are typically subdivisions (lots) of a larger piece of land.
A portion of soil which is found in a savanna.
Soil which has little to no water content and in which minerals and other soluble chemical entities have either bonded or become adsorbed to sold particles due to insufficient water availability.
A portion of soil which is part of a cropland or a rangeland biome.
A portion of soil which is found in a grassland.
Soil which is part of a densely forested area subject to tropical climate patterns.
Soil which is part of a sawah, a wet or irrigated rice field.
A portion of urea enriched soil is a portion of soil with elevated levels of urea.
Soil which has been amended with fertilizers.
Soil which is part of an agricultural field.
Soil which is formulated to promote the growth of grasses or other plants used to establish managed areas of vegetation.
A portion of bacteria enriched soil is a portion of soil with elevated bacterial abundance.
A portion of alluvial soil which is part of a swamp ecosystem.
Alluvial soil whichi is part of a paddy field.
Soil which has been transformed through a combustion process.
Soil which is part of a meadow.
A portion of chloropicrin enriched soil is a portion of soil with elevated levels of chloropicrin.
Soil which 1) has increased levels of humus, 2) has low pH levels, 3) has increased levels of mineral ash.
Soil which is adjacent to a pond.
Compost soil which is frozen.
Soil which has been amended with mineral additives to increase its pH.
Common liming agents include calcium- and magnesium-rich materials in various forms, including marl, chalk, limestone, burnt lime or hydrated lime. Liming often improves plant growth and increases the activity of soil bacteria, but oversupply may result in harm to plant life. Liming can also improve aggregate stability on clay soils. For this purpose structure lime, products containing calcium oxide (CaO) or hydroxide (Ca(OH)2) in mixes with calcium carbonate (CaCO3), are often used. Structure liming can reduce losses of clay and nutrients from soil aggregates.
Soil which has, as a part, a portion of either fresh or processed animal manure.
Soil which has properties to which plants in the Family Orchidaceae have adapted, including increased levels of aeration and drainage.
Soil which is part of a forest growing on a mountain.
Soil which is part of a forest whose communites of arborescent plants are dominated the genus Fagus.
Soil which is composed of a large proportion of mud, thus having properties resembling mud.
Soil in which trees from an orchard grow.
Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows.
A histosol which is formed by the decomposition of vegetation or organic matter.
turf
Soil which has elevated concentrations of sodium chloride.
Paddy field soil which has increased levels of peat.
A portion of soil which is found in a steppe.
Soil which is part of a tropical environment.
Garden soil which is part of a garden used for the cultivation of vegetables.
A portion of soil which is found in a greenhouse.
Soil which is has been heated such that its chemical, physical, or biological properties are destabilised.
Soil which is formed from avian fecal matter.
Soil which is part of a woodland dominated by leafy trees.
Soil which is part of a forest whose communites of arborescent plants are dominated the genus Picea.
Soil which is part of some elevated land.
Soil which is part of a forest whose communites of arborescent plants are dominated the genus Eucalyptus.
Soil which is part of a rubber plantation.
Bluegrass field soil is a soil which is found in a field of Kentucky Bluegrass (Poa pratensis).
Soil which has 1) low concentrations of nutrients and humus, 2) low water retention capacity, 3) textural variation from sand to clay, 4) a porous and friable structure, and 5) low concentrations of soluble salts.
Red soil typically derives from crystalline rock in warm, temperate, moist climates under deciduous or mixed forest. It has thin organic and organic-mineral layers, a black brown leached layer resting on an illuvium red layer. The majority of red soils have a loamy texture. Their chemical composition varies across regions, but often includes non-soluble material 90.47%, iron 3.61%, aluminium 2.92%, organic matter 1.01%, magnesium 0.70%, lime 0.56%, carbon dioxide 0.30%, potash 0.24%, soda 0.12%, phosphorus 0.09% and nitrogen 0.08%. On the uplands, they are thin, poor and gravelly, sandy, or stony and porous, light-colored soils on which food crops like bajra can be grown. In contrast, on the lower plains and valleys they are rich, deep, dark colored fertile loam on which, under irrigation, can produce excellent crops like cotton, wheat, pulses, tobacco, jowar, linseed, millet, potatoes and fruits.
Sterile water is water which does not contain lliving organisms.
Water which has physicochemical properties determined by processes which occur beneath the planetary crust.
This class references any water that's under a planetary surface. For water that is in an aquifer, see "groundwater" (ENVO:01001004). Previously, this class included both.
Mud which is part of a marine ecosystem.
Mud which constitutes the bed of a lake.
The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
Soil that is not penetrated by the root systems of plants.
The dwelling of an animal or group of similar animals.
This class represents habitations of non-human animals. This distinction may be removed in future releases.
A pile of earth, sand, pine needles, or clay or a composite of these and other materials that build up at the entrances of the subterranean dwellings of ant colonies as they are excavated. A colony is built and maintained by legions of worker ants, who carry tiny bits of dirt and pebbles in their mandibles and deposit them near the exit of the colony. They normally deposit the dirt or vegetation at the top of the hill to prevent it from sliding back into the colony, but in some species they actively sculpt the materials into specific shapes, and may create nest chambers within the mound.
A bird nest is the spot in which a bird lays and incubates its eggs and raises its young.
An ice rise is an elevation which is part of an ice shelf, typically dome shared, and formed by the ice shelf overriding an obstruction in the seabed. An ice rise may be adjacent only to an ice shelf, or to an ice shelf and a sea. For some features, properly ice rises, the term island has become established through usage.
A glacier covering a coastal strip of low-lying land backed by mountains, and sloping gently seaward over a distance up to 30km or more to terminate in ice cliffs or to merge with an ice shelf.
Fissure at the junction between an inland ice sheet, ice piedmont or ice rise and an ice shelf, the latter being subject to the rise and fall of the tide.
A volumetric density quality which inheres in soil by virtue of some influence exerted by the soil's mass on a given volume.
It is calculated as the dry weight of soil divided by its volume.
soil bulk density
A fomite is any inanimate object or substance capable of carrying infectious organisms (such as germs or parasites) and hence transferring them from one individual to another. A fomite can be anything such as a cloth or mop heads so when cleaning this is important to remember that this could aid when spreading pathogenic organisms.
A dump for domestic waste. A term used to describe any kind of feature containing waste products relating to day-to-day human life.
A material entity which other material entities in an environmental system are primarily or partially composed of.
Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water".
Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
Should connect to PATO as "quality of an aerosol"
A mixture of two immiscible (unblendable) substances. One substance (the dispersed phase) is dispersed in the other (the continuous phase).
A manufactured product which has been designed for use in one or more medical procedures.
A vivarium is an enclosure for keeping and raising organisms for observation or research. Often, a portion of the ecosystem for a particular species is simulated on a smaller scale, with controls for environmental conditions.
A sedimentary carbonate rock and a mineral, both composed of calcium magnesium carbonate CaMg(CO3)2 found in crystals.
A place where a wide variety of plants primarily categorized and documented for scientific purposes.
A facility in which animals are confined within enclosures and displayed to the public, and in which they may also be bred.
A research facility consisting of instruments that measure the properties of the oceans over time. Usually of at least approximately fixed location.
An underground layer of water-bearing permeable rock or unconsolidated materials (gravel, sand, silt, or clay) from which groundwater can be usefully extracted using a water well.
A cave which is part of a karst formation.
Anthropogenic material in or on which organisms may live.
This class will be depopulated and eventually deprecated. Convenience class.
This is quite odd and it probably should be obsoleted. Any material that is a participant in an agricultural process can be seen as an agricultural material.
A dry valley which was formed as a result of erosion due to stream formation and flow.
A dry stream valley which was formed as a result of erosion due to river formation and flow.
Organic matter in soil which has reached a point of stability, where it will break down no further and might, if conditions do not change, remain essentially as it is for centuries, or millennia.
An environmental material which is a liquid or semi-liquid mixture of water and some combination of soil, silt, and clay particles.
A well which provides access to groundwater held in an aquifer.
A well which has been drilled in order to extract petroleum oil from subterranean reservoirs and bring it to the surface.
The concentration basin mediterranean sea biome comprises expressions of the mediterranean sea biome that have higher salinity than bordering oceans due to evaporation. Water exchange consists of inflow of the fresher oceanic water in the upper layer and outflow of the saltier mediterranean water in the lower layer of the connecting channel.
concentration basin mediterranean sea biome
MERGED DEFINITION: TARGET DEFINITION: An oceanographic feature that involves wind-driven motion of dense, cooler, and usually nutrient-rich water towards the ocean surface, replacing the warmer, usually nutrient-deplete surface water. -------------------- SOURCE DEFINITION: A marine upwelling is a net flow of marine water to the surface of the water column from deeper regions. This is often a result of surface water displacement off continental coasts by wind action. Localised upwellings may also occur along divergent fronts around eddies and along some of the major oceanographic features. Deeper waters often have higher nutrient content; consequently blooms of primary producers, such as planktonic algae, are generally observed around upwelling zones.
This term is specific to marine upwellings.
An organic object which is formed as a result of the biological processes mediated by microbial assemblages.
A very generic class, intended to be populated by inference. Please avoid use in annotation, opting for a more descriptive term.
organic object formed through microbial activity
A multi-layered sheet of micro-organisms, mainly bacteria and archaea. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces but a few survive in deserts.
Particulate environmental material which is primarily composed of silt particles.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.
An environmental material which is composed primarily of pieces of gravel.
As with all size-based classifications, there is considerable variation in what is considered gravel.
A solid surface layer which 1) forms part of the boundary between the cavity of a cave and its solid container and 2) is the closest solid boundary to the gravitational centre of the astronomical body of which the cave is a part.
surface layer with role "walking substrate" or similar. Indicate it is some sort of "bottom"
Expressions of the estuarine biome occur at wide lower courses of a rivers where they flow into a sea. Estuaries experience tidal flows and their water is a changing mixture of fresh and salt.
The marine salt marsh biome comprises marshes that are transitional intertidals between land and salty or brackish marine water (e.g.: sloughs, bays, estuaries). It is dominated by halophytic (salt tolerant) herbaceous plants. The daily tidal surges bring in nutrients, which tend to settle in roots of the plants within the salt marsh. The natural chemical activity of salty (or brackish) water and the tendency of algae to bloom in the shallow unshaded water also allow for great biodiversity.
The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths.
The marine benthic biome (benthic meaning 'bottom') encompasses the seafloor and includes such areas as shores, littoral or intertidal areas, marine coral reefs, and the deep seabed.
The marine neritic zone biome comprises sea floor from the high tide mark to a continental shelf break. This zone generally extends to 200 m below average sea level.
The marine bathyal zone biome comprises regions of the marine benthic biome between approximately 200 m and 3000 m depth. This zone generally coincides with the continental slope.
The marine abyssal zone biome comprises regions of the marine benthic biome between approximately 2500 m and 6000 m depth. This zone generally coincides with the continental rise and the abyssal plain.
The marine hadal zone biome describes sea floor deeper than 6000 m such as that of the oceanic trenches.
A biome expressed by strips or ridges of rocks, sand, or coral that rises to or near the surface of a body of marine water.
The marine hydrothermal vent biome comprises regions of the marine benthic biome where heat generated due to tectonic activity, either at divergent plate boundaries or convergent ocean plates where back-arc spreading occurs, is released or 'vented' to the surface. The resultant high temperature water jets are laden with dissolved metals and minerals.
The neritic epipelagic zone biome comprises the marine water column above a continental shelf.
The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf.
The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
The oceanic epipelagic zone biome comprises regions of the marine water column that occur offshore, beyond a continental shelf. This biome extends from the surface of the ocean to a depth of ca. 200-250m. Throughout the zone the light field tends to be asymmetrical vertically, so that the direction and elevation of the sun can still be detected. The oceanic epipelagic zone biome encompasses the euphotic zone and, where and when it occurs, the seasonal thermocline.
The oceanic mesopelagic zone biome comprises regions of the marine water column that occur offshore, beyond a continental shelf. This biome extends through the water column from approximately 200-1000 m depth - the maximal depth of light penetration in all but the clearest oligotrophic ocean regions. In comparison to the epipelagic zone, dominant forms of pelagic organisms do not change very much; however, there are marked changes in species composition and the proportion of smaller-sized individuals decreases.
The bathypelagic zone biome comprises the marine water column below approximately 1000 m water depth - the maximum depth to which detectable daylight penetrates in all but the clearest oligotrophic waters - and extends to about 2500 - 2700 m water depth. In the temperate Atlantic, the beginning of the bathypelagic zone biome approximates to the deep oxygen minimum and the base of the permanent thermocline.
The abyssopelagic zone biome comprises the marine water column below the bathypelagic zone biome at approximately 2500 -2700 m and extends either to the hadal pelagic zone biome (at approximately 6000 m) or to the benthopelagic zone biome within ca. 100 m of the seafloor. The depth of 2700 m may be critical for physiological reasons as the change in hydrostatic pressure across this depth may preclude organism migration.
The oceanic hadal pelagic zone biome comprises the water column in oceanic trenches occurring at depths between 6000m and 10,000m.
The benthopelagic zone biome comprises regions of the marine water column which usually coincide with the benthic boundary layer (BBL) - the layer of isothermal and isohaline water contiguous to the sea floor. A general reversal in the declining gradient of pelagic biomass may be observed here, perhaps explained by viable nutrition on the sea floor being resuspended by bottom currents. This zone typically extends 100 m above the seafloor, but may reach upto1000 m during benthic storms.
The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
The neritic epipelagic zone biome comprises the marine water column that occurs above a continental shelf and extends from the surface of the ocean to a depth of ca. 200-250m. Throughout the zone the light field tends to be asymmetrical vertically, so that the direction and elevation of the sun can still be detected. The epipelagic zone encompasses the euphotic zone and, where and when it occurs, the seasonal thermocline.
The neritic mesopelagic zone biome comprises the marine column that occurs above a continental shelf and extends from approximately 200 to 1000 m depth - the maximal depth of light penetration in all but the clearest oligotrophic ocean regions. In comparison to the epipelagic zone, dominant forms of pelagic organisms do not change very much; however, there are marked changes in species composition and the proportion of smaller-sized individuals decreases.
The epeiric sea (also known as an epicontinental sea) biome comprises a shallow seas that extend over part of a continent. Epeiric seas are usually associated with the marine transgressions of the geologic past, which have variously been due to either global eustatic sea level changes, local tectonic deformation, or both, and are occasionally semi-cyclic.
The marginal sea biome comprises parts of an ocean partially enclosed by land such as islands, archipelagos, or peninsulas. Unlike mediterranean seas, marginal seas have ocean currents caused by ocean winds. Many marginal seas are enclosed by island arcs that were formed from the subduction of one oceanic plate beneath another.
The mediterranean sea biome comprises mostly enclosed seas that have limited exchange of deep water with outer oceans and where the water circulation is dominated by salinity and temperature differences rather than winds.
A marine biome which is determined by an ocean.
Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt.
The marine coral reef biome comprises constructional wave-resistant entities which are primarily built by corals and are often cemented together. The growth of these structures is aided by zooxanthellae, algae that are symbiotic with the reef-building corals.
The marine rocky subtidal reef biome comprises regions of the marine reef biome composed mainly of rock and which harbour abundant communities of algae and invertebrates. These reefs are often very patchy, with alterations of rocks dominated by rich invertebrate assemblages and turf-forming calcareous red algae.
A marine black smoker biome comprises regions of the marine hydrothermal vent biome characterised by a black vent plume. This black plume is a consequence of dissolved metals and minerals forming complexes with sulphide and indicates polymetallic sulphide mineral deposits beneath the surface.
A marine white smoker biome comprises regions of the marine hydrothermal vent biome characterised by lightly hued plumes, typically containing barium, calcium, and silicon. These vents tend to have lower temperature plumes when compared to black smoker environments.
A marine ultramafic hydrothermal vent biome comprises regions of themarine hydrothermal vent biome hosted on ultramafic (also referred to as ultrabasic) rocks. Ultramafic rocks are igneous and meta-igneous rocks with very low silica content (less than 45%), generally >18% MgO, high FeO, low potassium, and are composed of usually greater than 90% mafic minerals (dark colored, high magnesium and iron content). The Earth's mantle is composed of ultramafic rocks.
marine ultramafic hydrothermal vent biome
A marine basaltic hydrothermal vent biome comprises regions of the marine hydrothermal vent biome hosted on basaltic rocks. Basalt generally has a composition of 45 to 55 wt % SiO2, 2 to 6 wt % total alkalis, 0.5 to 2.0 wt % TiO2, 5 to 14 wt % FeO and 14 wt % or more Al2O3. Contents of CaO are commonly near 10 wt %, those of MgO commonly in the range 5 to 12 wt %.
A marine algal bloom is a rapid increase or accumulation in the population of algae in a marine system. Typically, only one or a small number of phytoplankton species are involved. Although there is no officially recognized threshold level, algae can be considered to be blooming at concentrations of hundreds to thousands of cells per milliliter, depending on the severity.
Kelp forests are underwater areas with a high density of kelp. They are recognized as one of the most productive and dynamic ecosystems on Earth. Smaller areas of anchored kelp are called kelp beds.
Kelp forests and beds may extend many meters above the sea floor, thus should not be considered a type of "bed".
A bed of a marine, saline water body which is covered by one or more speices of seagrass typically belonging to the families Posidoniaceae, Zosteraceae, Hydrocharitaceae, or Cymodoceaceae.
"Seagrass beds are highly diverse and productive ecosystems, and can harbor hundreds of associated species from all phyla, for example juvenile and adult fish, epiphytic and free-living macroalgae and microalgae, mollusks, bristle worms, and nematodes. Few species were originally considered to feed directly on seagrass leaves (partly because of their low nutritional content), but scientific reviews and improved working methods have shown that seagrass herbivory is a highly important link in the food chain, with hundreds of species feeding on seagrasses worldwide, including green turtles, dugongs, manatees, fish, geese, swans, sea urchins and crabs." https://en.wikipedia.org/wiki/Seagrass 2016-01-18
An environmental material which is composed primarily of particles.
Do not oversimplify this branch with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
particulate matter
particulate environmental material
The upper part of the marine water column with generally uniform properties resulting from wind-driven mixing.
Benthic storms are strong benthic (near bottom) currents transporting sediment, created by the input of energy (largely kinetic) to the seabed. In regions with high mesoscale eddy activity, benthic storms are frequent and can create isohaline and isothermal conditions extending as much as 1000m above the seafloor.
A portion of planktonic material is a portion of environmental material primarily composed of plankton.
See Issue #251. Awaiting class creation in PCO to attempt logical definitions.
planktonic material
A marine downwelling describes a net current of marine surface water towards deeper regions of the water column. Marine downwellings are usually caused by differences in the density (and hence, temperature and salinity) of seawater.
A marine water mass which is characterized by having much lower than normal dissolved oxygen concentrations persistently.
Low oxygen rates are typically due to the rate of respiration being greater than the rate of oxygen resupply, and are not necessarily due to anthropogenic activity.
Marine anoxic zones are areas of marine water that are depleted of dissolved oxygen. This condition is generally found in areas that have restricted water exchange. In most cases, oxygen is prevented from reaching the deeper levels by a physical barrier (sill) as well as by a pronounced density stratification. Anoxic conditions will occur if the rate of oxidation of organic matter by bacteria is greater than the supply of dissolved oxygen.
A water current which is maintained by a continuous, directed movement of marine water, generated by forces caused by breaking waves, wind, Coriolis force, temperature and salinity differences, and tides caused by the gravitational pull of astronomical bodies. Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength.
Marine streamers are tongues of cold water that extend > 100 km offshore from upwelling regions. Enhanced primary productivity may occur in these waters as they are typically more nutrient rich than marine surface waters.
Mesoscale marine eddies are characterized by currents which flow in a roughly circular motion around the center of the eddy. The sense of rotation of these currents may either be cyclonic or anticyclonic. Ocean eddies are also usually made of water masses that are different to those outside of the eddy. Marine mesoscale eddies are between about 10 and 500 km in diameter, and persist for periods of days to months. They may be formed when an ocean current develops an instability. This instability grows, causing the current to meander, and eventually an eddy is pinched off from the meander.
Sediment comprised of weathered continental rocks, wind blown dust, volcanic ash or other terrestrial material.
An oceanic front is a narrow zone of enhanced horizontal gradients of water properties (temperature, salinity, nutrients, etc.) that separates broader areas with different water masses or different vertical structure (stratification).
A marine Taylor column is a Taylor column that is formed in a marine body of water. Currents flowing over shoaling topography such as seamounts are accelerated and destabilised, resulting in Taylor columns. Eddies and internal waves are generated downstream of the topological feature and may extend 1000 m or so above them. This may result in a localised increase in primary production where the Taylor column reaches surface waters.
A marine water mass which is composed primarily of water with low concentrations of nutrients.
On Earth, the nutrients which are of low concentration in these water masses are typically phosphate, nitrate. and organic matter. The result is low primary productivity in such regions. These regions tend to have high dissolved oxygen levels due to a lack of respiration.
A gyre in oceanography is any large system of rotating ocean currents, particularly those involved with large wind movements. Gyres are caused by the Coriolis Effect; planetary vorticity along with horizontal and vertical friction, which determine the circulation patterns from the wind curl (torque).
A thermocline which is part of a marine water body.
Marine thermoclines are usually associated with rapid changes in water density and salinity.
A marine chemocline is a marine cline caused by a strong, vertical chemistry gradient within a body of marine water. Chemoclines most commonly occur where local conditions favor the formations of anoxic bottom water.
A pycnocline which is part of a marine water body and composed primarily of sea water.
Marine pycnoclines are usually associated with rapid changes in water temperature and salinity.
A nutricline which is part of a marine water body.
The marine lysocline denotes the depth in the ocean below which the rate of dissolution of calcite increases dramatically. As water column depth and therefore pressure increases, the corresponding calcite saturation of seawater decreases and the calcite begins dissolve.
A roughly planar, pelagic region characterised by equal water temperature.
A roughly planar, pelagic region characterised by equal salinity.
Biogenous sediment is derived from living organisms, typically planktonic organisms possessing shells, frustules or coccoliths.
A roughly planar, pelagic region characterised by equal water density.
A convergence front which is located in a region subject to subtropical climate patterns.
A marine current that generally occurs below the permanent thermocline (where it occurs) or below 400 m depth and that is driven by density and temperature gradients.
A marine current bordered by the surface of the water column and the permanent thermocline, where it occurs. Surface currents are mostly wind driven and mostly limited to the top 400 m of the water column. Ocean currents are driven by the circulation of wind above surface waters. Frictional stress at the interface between the ocean and the wind causes the water to move in the direction of the wind. Large ocean currents are a response of the atmosphere and ocean to the flow of energy from the tropics to polar regions. In some cases, currents are transient features and affect only a small area. Other ocean currents are essentially permanent and extend over large horizontal distances.
A marine surface current that flows along an oceanic front.
A warm water, narrow marine surface current flowing from the equator to high latitudes at speeds between 40 and 120 kilometers per day. Western boundary currents are the deepest ocean surface flows, usually extending 1000 meters below the ocean surface.
A cold water, broad marine surface current flowing from high latitudes to the equator at speeds between 3 and 7 kilometers per day.
A marine thermocline which separates the marine cold-water sphere from the marine warm-water sphere and which does not dissipate seasonally.
The permanent marine thermocline is typically found in temperate to tropical latitudes,
A marine thermocline which is present below the marine wind mixed layer.
The marine cold-water sphere describes a water mass extending from the polar seas and across low latitudes at depths of ca. 800 to 1000 m, which is separated from the marine warm-water sphere by the permanent marine thermocline
The marine warm-water sphere describes a water mass extending to depths of ca. 800 to 1000 m in low and middle latitudes. It is separated from the marine cold-water sphere by the permanent marine thermocline
Hydrogenous sediment is derived from solutes that precipitate out of sea water by a variety of chemical reactions. These are typically less abundant than other sediment types.
Cosmogenous sediment is derived from extraterrestrial dust and debris in the form of meteorites and similar entities.
Polymetallic nodules, also called manganese nodules, are rock concretions on the sea bottom formed of concentric layers of iron and manganese hydroxides around a core. Nodules vary in size from tiny particles visible only under a microscope to large pellets more than 20 centimetres (8 in) across. However, most nodules are between 5 and 10 cm in diameter.
Suspended sediment, or suspended load, is the term for the particles settle slowly enough to be carried in flowing water (such as a stream or coastal area) either without touching the bed or while only intermittently touching it. These particles are generally of the fine sand, silt and clay size, although larger particles may be carried as well depending on the intensity of the flow.
Sediment characterised by an average particle diameter greater than 256 mm.
Sediment characterised by an average particle diameter between 64 and 256 mm.
Sediment characterised by an average particle diameter between 4 and 32 mm.
Sediment characterised by an average particle diameter between 2 and 4 mm.
Sediment characterised by an average particle diameter between 62.5 micrometers and 2 mm.
Sediment characterised by an average particle diameter between 3.9 and 62.5 micrometers.
Sediment characterised by an average particle diameter between 1 and 3.9 micrometers.
Sediment characterised by an average particle diameter below 1 micrometer.
Note that by the particle-size-based definition used here, colloidal sediment need not actually be a colloid. If that is the case, please use "suspended colloidal sediment".
A marine hydrothermal vent is a marine benthic feature where heat generated due to tectonic activity, either at divergent plate boundaries or convergent ocean plates where back-arc spreading occurs, is released or 'vented' to the surface. The resultant high temperature water jets are laden with dissolved metals and minerals.
The marine sponge reef biome comprises marine reefs primarily built by marine sponges. The primary frame-building sponges are all members of the order Hexactinosa. They are found only in glacier-scoured troughs of low-angle continental shelf. The seafloor is stable and consists of rock, coarse gravel, and large boulders.
The supralittoral zone is the area above the spring high tide line that is regularly splashed, but not submerged by ocean water. Seawater penetrates these elevated areas only during storms with high tides.
The marine littoral zone is a littoral zone which extends, approximately, from the spray region above the high tide mark to the edge of the coninental shelf.
The marine sublittoral zone is part of the marine littoral zone which is permanently covered by seawater. In physical oceanography, the sublittoral zone refers to coastal regions with significant tidal flows and energy dissipation, including non-linear flows, internal waves, river outflows and oceanic fronts. In practice, this typically extends to the edge of the continental shelf, with depths around 200 meters. In marine biology, the sublittoral refers to the areas where sunlight reaches the ocean floor, that is, where the water is never so deep as to take it out of the photic zone.
A marine benthic biome which is determined by a cold seep.
The marine cold seep biome comprises regions of the marine benthic biome where seepage of methane, hydrogen sulphide, hydrocarbon rich fluids and other fluids occurs.
The dilution basin mediterranean sea biome comprises expressions of the mediterranean sea biome with lower salinity than the surrounding ocean due to freshwater gains such as rainfall and rivers. Water exchange consists of outflow of the fresher mediterranean water in the upper layer and inflow of the saltier oceanic water in the lower layer of the channel. Renewal of deep water may not be sufficient to supply oxygen to the bottom.
A column of solid material which has been progressively deposited around a hydrothermal vent.
A marine hydrothermal vent plume, part of a marine hydrothermal vent, is a high temperature water jet laden with dissolved metals and minerals that is driven by heat generated due to tectonic activity below the vent.
Sediment characterised by a temperature of 15-45 degrees Celsius and high-to-low oxygenation. Often impacted by hydrothermal fluid flows.
Sediment characterised by a temperature of 45-75 degrees Celsius and low to no oxygen content. Often impacted by hydrothermal fluid flows.
Sediment characterised by a temperature of 80-125 degrees Celsius and no oxygen content. Often impacted by hydrothermal fluid flows.
High temperature water ejected from hydrothermal vents and laden with dissolved metals and minerals as a result of percolation through crustal rocks.
Sediment hosting and characterised by active nitrate reducing microbial communities.
A piece of rock which fell vertically through the water column into finer-grained water-deposited sedimentary rocks.
dropstone
Drop stones range in size from small pebbles to boulders.
An accumulation of organic matter that has fallen to the bottom of a body of water.
A accumulation of plant matter that has fallen to the bottom of a body of water.
The carcass of an animal that has fallen to the bottom of a body of water.
Whale fall is the term used for a whale carcass that has fallen to the ocean floor. When a whale dies in shallow water, its carcass is typically devoured by scavengers over a relatively short period of time: within several months. However, in deeper water (depths of 2,000 m/6,600 ft or greater), fewer scavenger species exist, and the carcass can provide sustenance for a complex localized ecosystem over periods of decades.
Seal fall is the term used for a seal carcass that has fallen to the ocean floor.
A wood fall describes an accumulation of woody plant material that has fallen to the ocean floor.
A reef which is located in a marine water body.
A rocky reef which is located in the subtidal zone of a marine water body.
Sediment hosting and characterised by active manganese reducing microbial communities.
Sediment hosting and characterised by active iron reducing microbial communities.
Sediment hosting and characterised by active sulphate reducing microbial communities.
Sediment hosting and characterised by active carbon dioxide reducing microbial communities.
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
Material derived from a biofilm, an aggregate of microorganisms in which cells adhere to each other and/or to a surface. These adherent cells are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS). Biofilm EPS, which is also referred to as slime, is a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides in various configurations.
Material derived from a microbial mat, a multi-layered sheet of micro-organisms, mainly bacteria and archaea. Microbial mats create a wide range of internal chemical environments.
Marine snow is a continuous shower of mostly organic detritus falling from the upper layers of the water column. Its origin lies in activities within the productive photic zone.
Pockmarks are craters in the seabed resulting from the release of gas or liquid. Generally, they are formed in soft, fine-grained seabed sediments by the escape of fluids (gas or water, but mainly methane) into the water column.
A marine sponge reef is marine reefs primarily built by marine sponges. The primary frame-building sponges are all members of the order Hexactinosa. They are found only in glacier-scoured troughs of low-angle continental shelf. The seafloor is stable and consists of rock, coarse gravel, and large boulders.
A collection of tissues joined in structural unit to serve a common function.
A photophore is a light-emitting organ which appears as luminous spots on various marine animals, including fish and cephalopods. The organ can be simple, or as complex as the human eye; equipped with lenses, shutters, color filters and reflectors. The light can be produced from compounds during the digestion of prey, from specialized mitochondrial cells in the organism, called photocytes ("light producing" cells) , or, similarly, associated with symbiotic bacteria in the organism.
Root nodules occur on the roots of plants that associate with symbiotic nitrogen-fixing bacteria.
A specialised organ found in deep-sea tube worms populating hydrothermal vent environments that is colonised by chemosynthetic bacteria which supply the host worm with organic compounds. The term may be applied to similar organs in other worms.
A specialized organ that is linked to the gut in beetles and host to a symbiotic yeast. The yeast cells assist in the digestion of less nutritious foods, supply needed B-vitamins and sterols, and provide resistance to certain toxins.
Determinate nodules are root nodules found on tropical (sub)legumes, such as those of the genera Glycine (soybean), Phaseolus (common bean), Lotus, and Vigna. Determinate nodules lose meristematic activity shortly after initiation, thus growth is due to cell expansion resulting in mature nodules which are spherical in shape.
Indeterminate nodules are found on temperate legumes like Pisum (pea), Medicago (alfalfa), Trifolium (clover), and Vicia (vetch). They earned the moniker "indeterminate" because they maintain an active apical meristem that produces new cells for growth over the life of the nodule. Because they are actively growing, indeterminate nodules manifest zones which demarcate different stages of development/symbiosis.
A part of an indeterminate root nodule where new nodule tissue is formed which will later differentiate into the other zones of the nodule.
indeterminate root nodule active meristem
A part of an indeterminate root nodule permeated with infection threads full of bacteria. The plant cells are larger than in the previous zone and cell division is halted.
indeterminate root nodule infection zone
A part of an indeterminate root nodule where each cell contains a large, central vacuole and the cytoplasm is filled with fully differentiated bacteroids which are actively fixing nitrogen. Typically, the plant provides these cells with leghemoglobin, resulting in a distinct pink color.
indeterminate root nodule nitrogen fixation zone
A part of an indeterminate root nodule where plant cells and their bacteroid contents are being degraded. The breakdown of the heme component of leghemoglobin results in a visible greening at the base of the nodule.
indeterminate root nodule senescent zone
A forest ecosystem which is undergoing climactic ecological succession.
A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor.
A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs.
A grassland ecosystem in which dominant ecological communities have reached their climax successional state.
A woodland biome which has seasonal water availability and includes trees spaced sufficiently far apart to allow an unbroken layer of grass, sedge (Cyperaceae) or rush (Juncaceae) communities to live.
A desert ecosystem which is undergoing climactic ecological succession.
A tundra ecosystem which is undergoing climactic ecological succession.
A mangrove biome is a terrestrial biome which includes, across its spatial extent, mangrove plants (Rhizophoraceae). Mangrove plants are able to withstand high levels of salinity as well as regions of anoxia and frequent tidal inundation. Mangrove biomes often occur near tropical and sub-tropical estuaries and depositional marine coastal environments where fine sediments (often with high organic content) collect in areas protected from high energy wave action.
Preliminary definition. Depending on whether mangrove trees or shrubs are present, this class could be a child of shrubland biome or woodland biome. Consider creating the appropriate classes.
A temperate desert biome is a desert biome which has communities adapted to intermediate insolation, low rainfall, and large temperature variations between winter and summer. Winter temperatures may fall below 0 degrees Celsius. Some precipitation in this biome may fall as snow.
Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established.
A tropical desert biome is a desert biome which has communities adapted to temperatures above a monthly average of 18 degrees Celsius, high daily temperature ranges of approximately 20 degrees Celsius, very high insolation due to inhibited cloud formation, and very low precipitation. Tropical desert biomes located near coasts with cold upwellings may have cooler temperatures and reduced insolution due to fog.
A subtropical desert biome is a desert biome which has communities adapted to temperatures above a monthly average of 18 degrees Celsius, high daily temperature ranges of approximately 20 degrees Celsius, high insolation (but lower than that of a tropical desert biome), inhibited cloud formation, and very low precipitation. Subtropical desert biomes located near coasts with cold upwellings may have cooler temperatures and reduced insolution due to fog.
A montane desert biome is a desert biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
A polar desert biome is a desert biome which is subject to low levels of insolation, annual precipitation less than 250 millimeters, and a mean temperature less than 10 degrees Celsius during its warmest month. Temperature changes in polar deserts frequently cross the freezing point of water.
A savanna biome which is subject to subtropical climate patterns.
A savanna biome which is subject to tropical climate patterns.
A savanna biome which is subject to temperate climate patterns.
A flooded savanna biome is a savanna biome which has very wet to saturated soil moisture content.
A subtropical grassland in which dominant ecological communities have reached their climax successional state.
A montane grassland biome is a grassland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
A coniferous forest biome is a forest biome which contains densely packed populations or communities of coniferous trees, strongly limiting light penetration to the forest floor.
A broadleaf forest ecosystem which is undergoing climactic ecological succession.
A mixed forest in which dominant ecological communities have reached their climax successional state.
A mediterranean forest in which dominant ecological communities have reached their climax successional state.
A tropical broadleaf forest in which dominant ecological communities have reached their climax successional state.
A subtropical broadleaf forest in which dominant ecological communities have reached their climax successional state.
A broadleaf forest which is subject to temperate climate patterns.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius.
A subtropical condition is an environmental condition in which an envrionmental system receives more solar irradiance than those with temperate conditions, but less than those with tropical conditions. At low elevations, this typically results in eight months of the year having average temperatures greater than or equal to 10 degrees Celsius with the coldest monthly temperature averaging between 2 and 13 degrees Celsius.
As with most other climatic zones and conditions, multiple classification schemes have somehat different definitions and criteria. To quote from https://en.wikipedia.org/wiki/ "Several methods have been used to define the subtropical climate. In the Trewartha climate classification, a subtropical region should have at least eight months with a mean temperature of 10 °C (50.0 °F) or above. German climatologists Carl Troll and Karlheinz Paffen defined Warm temperate zones as plain and hilly lands having an average temperature of the coldest month between 2 °C (35.6 °F) and 13 °C (55.4 °F) in the Northern Hemisphere and between 6 °C (42.8 °F) and 13 °C (55.4 °F) in the Southern Hemisphere, excluding oceanic and continental climates. According to the Troll-Paffen climate classification, there generally exists one large subtropical zone named the warm-temperate subtropical zone,[4] which is subdivided into seven smaller areas.[5] According to the E. Neef climate classification, the subtropical zone is divided into two parts: Rainy winters of the west sides and Eastern subtropical climate.[6] According to the Wilhelm Lauer & Peter Frankenberg climate classification, the subtropical zone is divided into three parts: high-continental, continental, and maritime.[7] According to the Siegmund/Frankenberg climate classification, subtropical is one of six climate zones in the world.[8]"
A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions.
This class' definition is less satisfactory than the other latitudinal conditoins.
A mediterranean condition is a subtropical condition in which hot dry summers and winters with moderate to high rainfall.
These regions are under the constant influence of the subtropical ridge.
A subtropical woodland biome which includes communities adapted to hot to warm, dry summers, mild to cold, rainy winters, and the influence of large, usually marine, bodies of water.
A coniferous forest biome which is subject to subtropical climate patterns.
A coniferous forest biome which is subject to tropical climate patterns.
A coniferous forest biome which is subject to temperate climate patterns.
A temperate mixed forest in which dominant ecological communities have reached their climax successional state.
A shrubland biome which is subject to subtropical climate patterns.
A shrubland biome which is subject to tropical climate patterns.
A shrubland biome which is subject to temperate climate patterns.
A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
A mediterranean shrubland biome is a subtropical shrubland biome which includes communities adapted to hot to warm, dry summers, mild to cold, rainy winters, and the influence of large, usually marine, bodies of water.
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
A woodland biome which is subject to tropical climate patterns.
A woodland biome which is subject to temperate climate patterns.
A woodland biome which is subject to subtropical climate patterns.
A montane savanna biome is a savanna biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
A subtropical grassland biome which includes communities adapted to hot to warm, dry summers, mild to cold, rainy winters, and the influence of large, usually marine, bodies of water.
A subtropical dry broadleaf forest in which dominant ecological communities have reached their climax successional state.
A subtropical moist broadleaf forest in which dominant ecological communities have reached their climax successional state.
subtropical moist broadleaf forest biome
A tropical dry broadleaf forest in which dominant ecological communities have reached their climax successional state.
A tropical moist broadleaf forest in which dominant ecological communities have reached their climax successional state.
A savanna biome which is subject to mediterranean climate patterns.
An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration.
Lava is a mixture of molten or semi-molten rock, volatiles, and solids which has extruded beyond a planetary crust.
Some use 'lava' to refer to rock that is formed when lava cools. This is not the intended meaning of this class. See 'igneous rock' or similar.
Felsic lava is lava which is high in silica (> 69 percent by weight), aluminium, potassium, sodium, and calcium, forming a polymerized liquid rich in feldspar and quartz. Felsic lava has a higher viscosity than other magma types. Felsic magmas can erupt at temperatures as low as 650 to 750 °C. Unusually hot (>950 °C) rhyolite lavas, however, may flow for distances of many tens of kilometres
Intermediate lava is lava which, relative to felsic lava, is lower in aluminium and silica (between 52 and 63 percent by weight), and usually somewhat richer in magnesium and iron. The temperature of intermediate lava ranges from 750 to 950 degrees Celsius, destroying polymerized bonds and promoting more fluid behaviour relative to felsic lavas and also a greater tendency to form phenocrysts. Higher iron and magnesium tends to manifest as a darker groundmass, and also occasionally amphibole or pyroxene phenocrysts.
Mafic lava is lava which, relative to other lava types other than ultramafic lava, has a high ferromagnesian content and low aluminium and silica content, with silca making up between 45 and 52 percent of its weight.
Mafic lava generally erupts at temperatures in excess of 950 degrees Celsius. The high temperature and low polymerisation in mafic lava favors low viscosity and chemical diffusion, promoting the formation of large, well-formed phenocrysts.
Lava which, relative to other lava types, has very high magnesium oxide content and less than 45 percent silica by weight.
Ultramafic lava generally erupts at temperatures of 1600 degrees Celsius. Due to its high temperature and composition, the viscosity of ultramafic lava is very low.
Basalt is a volcanic rock which is formed by the rapid cooling of basaltic lava.
A coastal scrubland is a scrubland which is part of a coast.
A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions.
On Earth, polar conditions are such that every month has average temperature lower than 10 degrees Celsius. Note that this class refers to a climatic rather than a positional condition.
An oak woodland is a woodland which has a tree community primarily composed of oak trees.
A conifer woodland is a woodland which has a tree community primarily composed of coniferous trees, from the Division Pinophyta, also known as Coniferophyta or Coniferae.
A juniper woodland is a woodland which has a tree community primarily composed of trees of the genus Juniperus.
A scrubland which is located in a desert.
A piece of rock with a grain size above 300 millimetres in diameter.
A pinyon juniper woodland is a conifer woodland which has a tree community primarily composed of trees of the subsection Cembroides of the genus Pinus and the genus Juniperus.
A cropland ecosystem which is undergoing climactic ecological succession.
A village biome is an anthropogenic terrestrial biome which contains settlements such as villages, towns, and/or small cities and which is primarily used for agricultural activity.
Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined.
A rangeland biome is an anthropogenic terrestrial biome which is primarily used for the rearing and grazing of livestock.
A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use.
An urban biome is a dense settlement biome which has been urbanised.
A coniferous forest biome which includes communities adapted to subpolar conditions.
A subpolar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area and is surrounded by large land masses. This results in very cold winters with temperatures potentially falling to around -40 degrees Celsius and summers which last no more than 3 months of the year with a 24-hour average temperature of at least 10 degrees Celsius.
Note that this class refers to a climatic rather than a positional condition.
A biome which is determined by a freshwater lake.
A freshwater biome which is determined by a freshwater river.
A system which has the disposition to environ one or more material entities.
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
A mineral deposit is a physiographic feature which has unusually high concentrations of one or more minerals.
Note that the definition of the term mineral is debatable; however, a mineral generally must be naturally occuring, stable at room temperature, representable by a chemical formula (unlike rocks, which may include a wide variety of components), are usually formed by geophysical processes (i.e. are abiogenic), and have an ordered atomic arrangement.
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
A hydrothermal vent found on the ocean floor which emits lighter-hued minerals, such as those containing barium, calcium and silicon. These alkaline hydrothermal vents also continuously generate acetyl thioesters, providing both the starting point for more complex organic molecules and the energy needed to produce them.
A fluid front which is 1) thin in comparison to the fluid mass it is a part of and 2) across which a property of that fluid mass varies greatly over short vertical distance, relative to variation across the entire fluid mass.
A similar term exists in linguistics and mathematics. An ecocline, or biological cline, is a related concept; however, may be better placed as a child of a class like "ecotone". Further, some definitions of "layer" require a layer's constiuent materials to have consistent properties, thus "cline" would not qualify as a subclass. The term "gradient" has been proposed as a more suitable superclass. Discussion in Issue #286)
A cline across which the density of a fluid changes rapidly.
A nutricline which is part of a water body.
nutrient gradient
A seep is a spring in which water has filtered through permeable earth to the surface.
MERGED DEFINITION: TARGET DEFINITION: A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor. -------------------- SOURCE DEFINITION: An area of the ocean floor where hydrogen sulfide, methane and other hydrocarbon-rich fluid seepage occurs. Cold seeps are distinct from hydrothermal vents: the former's emissions are of the same temperature as the surrounding seawater, whereas the latter's emissions are super-heated.
A hydrothermal seep is a seep in which diffuse flow of geothermally heated fluids with high methane concentrations. This seep has been proposed as an intermediate between cold seeps and hydrothermal vents.
Water vapour is a vapour which is the gas phase of water.
Perhaps a better relation between water vapour and water can be found in or added to RO?
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
Atmospheric water vapour is water vapour that is part of an atmosphere.
A sedimentary rock which is composed mainly of silt. This rock has a grainsize in the silt range, finer than sandstone and coarser than claystones.
A clastic sedimentary rock which is composed primarily of clay sized particles.
Clastic sedimentary rocks are sedimentary rocks that are composed of silicate minerals and rock fragments that were transported by moving fluids. Clastic rocks are composed largely of quartz, feldspar, rock (lithic) fragments, clay minerals, and mica; numerous other minerals may be present as accessories and may be important locally.
A mudstone is a clastic sedimentary rock which contains a mixture of at least one third of silt- and one third of clay-sized particles.
There is debate on the usage of mudstone and mudrock, and some ambiguity is to be expected. https://en.wikipedia.org/wiki/ The terminology of "mudstone" is not to be confused with the Dunham classification scheme for limestones. In Dunham's classification, a mudstone is any limestone containing less than ten percent carbonate grains. Note, a siliciclastic mudstone does not deal with carbonate grains. Friedman, Sanders, and Kopaska-Merkel (1992) suggest the use of "lime mudstone" to avoid confusion with siliciclastic rocks.
Lime mudstone is a limestone which is primarily composed of either clay-size or both silt-size and clay-size detrital (transported) carbonate grains.
https://en.wikipedia.org/wiki/ The terminology of "mudstone" is not to be confused with the Dunham classification scheme for limestones. In Dunham's classification, a mudstone is any limestone containing less than ten percent carbonate grains. Note, a siliciclastic mudstone does not deal with carbonate grains. Friedman, Sanders, and Kopaska-Merkel (1992) suggest the use of "lime mudstone" to avoid confusion with siliciclastic rocks.
Slate is a metamorphic rock which is fine-grained, foliated, homogeneous, Slates are derived from clastic sedimentary rocks.
A structural basin is a geological depression formed by tectonic warping of previously flat lying rock strata.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO.
Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance. When speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc. This form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.) It has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei. In permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black. In nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze.
A depression caused by the collapse of a pingo.
An ice mass which is formed when moisture, diffused within soil or rock, accumulates and freezes in a localized zone, wedging soil or rock apart.
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories.
A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material.
A solid layer which is composed primarily of sedimentary rock or soil.
Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline.
A lake which is permanently covered by ice, does not mix, and exhibit inverse cold water stratification whereby water temperature increases with depth below the ice surface.
A holomictic lake is a lake which mixes at least once per year. Mixing is caused by a uniform temperature distribution from the upper to lower layers of the lake.
A dimitic lake is a holomictic lake which mixes from top to bottom during two mixing periods each year. Mixing typically occurs during the spring and autumn, when the lake is "isothermal" (i.e., at the same temperature from the top to the bottom). At this time the water throughout the lake is about 4°C, and, in the absence of any temperature or density differences, the lake readily mixes from top to bottom. These lakes are common in regions with temperate climates.
A polymictic lake is a holomictic lake which is too shallow to allow thermal stratification and which can mix from top to bottom through the ice-free period of the year.
A monomictic lake is a holomictic lake which mixes from top to bottom during one mixing period each year.
A monomictic lake which is covered by ice throughout much of the year and only mixes when its surface ice melts and the lake lacks thermal stratification.
A monomictic lake which does not freeze and is thermally stratified throughout most of the year, only mixing in winter when cooler temperatures ease stratification.
A cold polymictic lake is a polymictic lake which is covered by ice in winter.
A warm polymictic lake is a polymictic lake which is not covered by ice at any point during the year.
Class should be populated by inference and asserted subclasses redistributed.
A layer that is part of a marine water body.
A lake bed which is dry. That is, the bed of a dry lake.
Deliberately disjoint with "lake bed", which must be covered with water.
A slope which is part of the seafloor, descends from the continental crust to the oceanic crust, and comprises the continental shelf, continental slope, and continental rise.
On Earth, continental margins constitute about 28% of the oceanic area.
A Taylor column is a column of deflected fluid flow which is formed in a perturbed, rotating fluid, is parallel to the axis of rotation, and extends above the obstacle perturbing the fluid in a rigid manner.
This is an interesting class. It's not really a column in the sense of a water column, nor is it a current, exactly. It may also occur in any fluid, gaseous or liquid.
An atmospheric Taylor column is a Taylor column that is formed in the atmosphere. Atmospheric Taylor columns often form above islands resulting in vortex streets in the atmosphere.
Brackish water which is part of an estuary.
A portion of environmental material which protrudes through a surface layer.
This is kept as a general class. One can specify subclasses by identifying the protruding material (e.g. rock outcroup, mineral outcrop, etc ) and the material(s) the protrusion emerges from. Possible logical definition: A portion of ENVO:environmental material which has_quality PATO:"protruding out of" a ENVO:surface layer of an ENVO:environmental material.
An endolithic environment is an environment that exists within solid rock.
A high pressure environment is an environment in which all material entities are exposed to a high ratio of force per unit area.
A high temperature environment is an environment in which material entities are exposed to increased levels of heat radiation or which have molecules or atoms moving randomly with increased levels of average kinietic energy.
An aquatic environment which is determined by freshwater.
An environmental system which has its properties and dynamics determined by saline water.
An environmental system which is located beyond the Earth's exosphere and away from the Earth's core.
This would need an instance of planet (i.e. Earth) to be fully expressed. Note that this is not necessarily outer space, as it can include planetary environments that are not of Earth.
An environment which has a lower temperature than some local or global average.
The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'.
A haline environment is an environment in which entities are exposed to high concentrations of salt, typically above 2 molar.
A cultivated environment is an environment that has been modified by humans by the preparation of the land, usually for the purposes of growing crops.
A culturing environment is an environment which is maintained by humans for the purposes of preparing cell, organ, tissue and plant tissue cultures.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes.
An acidic environment is an environment in which material entities are exposed to a low pH.
An alkaline environment is an environment in which entities are exposed to high pH, typically greater than a pH of 9.
An environment whose dynamics are strongly influenced by water.
An extreme high temperature environment is a high temperature environment in which entities are exposed to temperatures above 80 degrees Celsius.
The lower threshold, 80 degrees Celsius, is derived from the definition of the obsolete class "extreme high temperature habitat" which this class replaces.
A rocky slope is a slope which has a surface primarily composed of rock.
A marine environment and enviroment which is determined by a marine water body.
An environmental system determined by seawater.
An environment determined by the presence of brackish water.
This may refer to environments submerged in brackish water or those that are determined by its presence, such as a brackish water pond environment.
The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence).
A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
A layer in a water mass, itself composed primarily of water.
This class will eventually be populated by inference, and its asserted subclasses removed.
A subsurface layer in a water body, typically an ocean or lake, in which chlorophyll concentrations reach their maximum.
Logical def is incomplete. Need to express the idea of maximum chlorophyll. This could follow a pattern like: X has_maximum_levels_of Y relative_to Z, i.e. DCM has_maximum_levels_of chlorophyll relative_to subsurface_aquatic_layer May also be useful to include has_decreased_levels_of light intensity relative_to surface aquatic layer Further discussion in Issue #126.
The DCM may or may not indicate greater abundance of photosynthetic, chlorophyll-bearing cells, as shade-adapted cells may have a greater chlorophyll to biomass ration than surface variants. Further, some DCMs may be formed by the sinking of cells from surface zones or the subduction of surface waters, rather than through biotic, community-level processess.
A strand swamp is a swamp that forms linear drainage channels on flatlands.
A dome swamp is a swamp which occurs in a depression where deeper waters at the centre of the swamp allow trees to grow taller relative to those in shallower regions of the depression. This creates a dome-like shape.
The logical def should be improved with the idea of a vegetation unit growing in a depression expressed.
A cypress dome swamp is a dome swamp which has a plant community dominated by Cupressaceae, often swamp cypresses. Swamp cypresses typically belong to the genus Taxodium or the species Glyptostrobus pensilis and Actinostrobus pyramidalis.
Requires import of some taxonomy for differentia
A cypress strand swamp is a strand swamp which has a plant community dominated by Cupressaceae, often swamp cypresses. Swamp cypresses typically belong to the genus Taxodium or the species Glyptostrobus pensilis and Actinostrobus pyramidalis.
A cypress swamp is a swamp which has a plant community dominated by Cupressaceae, often swamp cypresses. Swamp cypresses typically belong to the genus Taxodium or the species Glyptostrobus pensilis and Actinostrobus pyramidalis.
A gravelly slope is a slope which has a surface primarily composed of gravel.
A hillside is a slope that is part of a hill.
A talus slope is a slope which has a surface layer composed of scree.
An understory is a layer of plant life which grows below the canopy without penetrating it.
A shrub layer is a layer of vegetation in a woodland or forest consisting of low, woody vegetation of frutescent form.
A herb and fern layer is a layer of a forest or woodland which is composed of all vascular plant life that are one metre or less in height.
This definition is inclusive of non-herbaceous plants that may be transiently present in the "herb layer". See Gilliam FS (2007) The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems. BioScience. 57(10):845-858. (http://dx.doi.org/10.1641/B571007) for rationale and a review of definitional and terminological variation.
Refers to the ground layer of a forest or woodland where leaf litter or other plant matter accumulates
A biome which is subject to polar climatic conditions.
This class is primarily for inference and, in general, should not be used directly by annotators. If you're an annotator, please consider using a more informative term such as 'tundra biome'.
An altitudinal condition which inheres in a bearer by virtue of the bearer having a monthly mean temperature is less than 10 degrees Celsius and being located at altitudes above the tree line and below the snowline.
Requested term with preliminary def. See Issue 29 on the envo tracker.
An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude immediately below the tree line of an elevation.
Requested in Issue 33 of our tracker. The lower boundry of this condition's range, that is, the lower altitudinal limit of an elevation that is considuered subalpine, is not clear in this definition.
An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line.
The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate.
An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude.
Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change.
An altitudinal condition which inheres in a bearer by virtue of the bearer having extremely limited vegetation cover, silica-enriched soils, and ground cover dominated by snow and ice at altitudes above the snowline.
An upper montane condition is a montane condition in which an altitude range falls immediately below the tree line.
This definition is somewhat odd in that it doesn't clearly define a lower boundary.
A lower montane condition is a montane condition in which an altitude range falls immediately above mid-altitude forests.
This definition does not define an upper boundary.
A montane conifer woodland is a conifer woodland which is located within an altitude range that falls between mid-altitude forests and the tree line.
A field used for the cultivation of corn or related crop plants.
Requested in Issue 112 as part of the curation of metagenome submissions in the European Nucleotide Archive.
An organic material primarily composed of a portion of plant root.
Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.
Autoclaved sand is sand that has been sterlised by exposure to high pressure saturated steam at at least 121 degrees Celsius.
Requested in Issue 116 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.
This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass.
A mesoscale eddy field is an expanse of marine water which includes coherent vortices, as well as a rich cascade of other structures such as filaments, squirts and spirals and is characterized by temperature and salinity anomalies with associated flow anomalies that are nearly in geostrophic balance. Although only the surface expression of mesoscale eddies is visible in satellite images of sea surface height or temperature, they are in fact three dimensional structures that reach down into the pycnocline.
An ice cap climatic condition is a polar condition in which the montly average temperature does not exceed 0 degrees Celsius.
A layer which is determined by a form of vegetation.
A portion of granite is a portion of igneous rock which is intrusive, felsic, granular, and phaneritic.
Requested in issue 45. Some relations to PATO and SWEET classes suggested.
A portion of alkaline water is a portion of water with a pH greater than 7.
Here, we commit to a threshold of pH as this is almost universally accepted.
A portion of acidic water is a portion of water with a pH less than 7.
A cave formed in limestone, usually by dissolution of limestone by acidic groundwater.
Can be linked to a solutional environmental process and acidic groundwater.
A cave formed by the dissolution of soluble rock or other solid material such as limestone, chalk, dolomite, gypsum, salt or marble.
A cave formed at the same time as the surrounding rock.
A cave that is formed by the action of pressurised lava pushing against surrounding rock and then draining away.
A cave formed by erosion caused by flowing streams carrying rocks or sediments.
A glacier cave is a cave formed within or under a glacier.
An ice cave is a bedrock cave which contains year-round ice formations.
A talus cave is a cave formed by the openings between large boulders which have fallen into a random heap.
An anchialine cave is a cave which contains an anchialine pool.
An anchialine pool is a landlocked water body with a subterranean connection to the ocean and which has fresh water towards its surface with saline water in its deeper layers.
An tundra climatic condition is a polar condition in which at least one month's average temperature exceeds 0 degrees Celsius.
Agricultural waste is waste produced as a result of various agricultural operations. It includes manure and other wastes from farms, poultry houses and slaughterhouses; harvest waste; fertilizer run- off from fields; pesticides that enter into water, air or soils; and salt and silt drained from fields.
As with other wastes, this is more a role than a material in itself. This should be revised.
Household waste refers to waste material usually generated in the residential environment. Waste with similar characteristics may be generated in other economic activities and can thus be treated and disposed of together with household waste.
This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with domestic entities.
Biological waste is waste containing mostly natural organic materials (remains of plants, animal excrement, biological sludge from waste-water treatment plants and so forth).
This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being composed primarily of some organic or biological matter.
A dry woodland is a woodland which occurs in areas of rain shadow in a tropical marine climate, receives very little rainfall, typically has rapidly draining soils and trees which have adaptations to dry climates such as thick bark, small leaves, and the disposition to shed their leaves.
A tropical marine condition is a tropical condition in which the ocean strongly influences the climate and a wet and dry season occur.
A semi-evergreen forest is a forest which undergoes a long dry season and, as a consequence, has a two-storey layer structure, a dry canopy, a leaf litter layer that only decays during moist periods trees with very small leaves or which shed their leaves to conserve water and which flower during the dry season and grow during the wet season.
A humid subtropical condition is a subtropical condition in which an environmental system has hot, humid summers, warm to cool dry winters, and average annual precipitation either evenly distributed throughout the year or marked by a dry season or drying trend during winter
In cases where rainfall is evenly distributed throughout the year, this condition falls into the Cfa category of the Köppen climate classification. In cases marked by a dry season or drying trend during winter, this condition falls into the Cwa category of the Köppen climate classification. Environmental systems with this condition usually occur on the eastern side of continents.
An arid subtropical condition is a subtropical condition in which an environmental system has an annual average temperature near 18.2 degrees Celsius with their coldest month averaging between 2 and 13 degrees Celsius, the absence of regular rainfall, and high humidity.
Mild variants are generally located in areas adjacent to powerful cold ocean currents.
A highland subtropical condition is a subtropical condition in which increased elevation results in mild summers, cooler winters, and, in some instances, snowfall associated with montly temperature averages below 22 but above -3 degrees Celsius.
This is an interesting overlap of a latitudinal and altitudinal condition. Some link between this condition and the altitudinal conditions should be considered. This condition corresponds to the Cfb and Cwb categories of Köppen climate classification.
An oceanic temperate condition is a temperate condition which is strongly influenced by oceans and oceanic winds. Summers are cool and winters are cool, but not cold, and there is little frozen precipitation at lower elevations.
This condition is typically present on the western coasts of large continental landmasses.
A continental temperate condition is a temperate condition which is influenced by large land masses. Summers are warm to hot and winters are often long, cold, and snowy.
A cold desert is a desert which has hot summers and cold, dry winters with temperatures below 0 degrees Celsius
This variant of the desert climate is somewhat rare outside of Asia. A cold desert climate is typically found in temperate zones, almost always in the rain shadow of high mountains which restrict precipitation from the westerly winds, or in the case of Central Asia, from the monsoon. The Gobi desert in Mongolia is a classic example of a region with a cold desert climate. Though hot in summer, it shares the very cold winters of the rest of Central Asia. The Kyzyl Kum and Taklamakan deserts of Central Asia and the drier portions of the Great Basin Desert of the western United States are other major examples of BWk climates. The Ladakh region, lying in the Great Himalayas in India also has a cold desert climate.
An evergreen needleleaf forest which is subject to temperate climate patterns.
This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000).
A broadleaf forest which is subject to tropical climate patterns with high rainfall, is located in a lowland area, and is dominated by plants which retain their leaves throughout the year.
tropical lowland evergreen broadleaf rain forest
A deciduous broadleaf forest which is subject to temperate climate patterns.
A deciduous needleleaf forest which is subject to temperate climate patterns.
A deciduous broadleaf forest which is subject to tropical climate patterns.
This class corresponds to the "Tropical Deciduous / semi-deciduous broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical semi-deciduous broadleaf forest" class can be made.
A semi-deciduous broadleaf forest which is subject to tropical climate patterns.
This class corresponds to the "Tropical Deciduous / semi-deciduous broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical deciduous broadleaf forest" class can be made.
tropical semi-deciduous broadleaf forest
A temperate mixed forest which has communities of trees composed primarily of species with broad leaves.
This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed needleleaf forest" class can be made.
A temperate mixed forest which has communities of trees composed primarily of species with needle-like leaves (e.g. conifers).
This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed broadleaf forest" class can be made.
tropical semi-evergreen moist broadleaf forest
A montane forest which is located in a region subject to tropical climate patterns modulated by sufficient elevation to encounter upper montane climate patterns.
A montane forest which is located in a region subject to tropical climate patterns modulated by sufficient elevation to encounter lower montane climatic patterns.
A freshwater swamp forest which is subject to tropical climate patterns.
A sclerophyllous forest which is subject to temperate climate patterns.
A sclerophyllous forest which is subject to tropical climate patterns.
A broadleaf evergreen forest which is subject to temperate climate patterns.
A freshwater swamp forest which is subject to temperate climate patterns.
This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). It is currently unclear how to relate forests and swamps.
A needleleaf forest which is subject to tropical climate patterns.
A mixed needleleaf forest which has communities of trees composed primarily of species with needle-like leaves (e.g. conifers).
This class corresponds to the "Tropical Mixed needleleaf / broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical mixed broadleaf forest" class can be made.
A tropical mixed broadleaf forest which has communities of trees composed primarily of species with broad leaves.
This class corresponds to the "Tropical Mixed needleleaf / broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical mixed needleleaf forest" class can be made.
This class corresponds to the "Tropical Mixed needleleaf / broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical mixed needleleaf forest" class can be made. The relationship between this "forest" class and the mangrove swamp must be clarified.
A portion of respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 10 micrometers or less.
respirable suspended particulate matter
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
An aquatic environment which is the part of a sea, lake, or river that is close to the shore.
The adjacency of water has many consequences including the generation of microclimates and impacts on the biology. This class is intended to capture littoral zones that are associated with marine, freshwater, and any other aquatic environments. Note that there is no single definition of the extent of the "littoral zone", associated with any water body. Here, we use definitions that will be more familiar to marine biologists rather than military organisations, although the latter can be added on request. This class will likely be superceded by a CMECs compliant class.
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A freshwater littoral zone is a littoral zone which extends offshore from the shore of a freshwater body of water to the limit of occupancy of rooted plants.
The littoral zone may form a narrow or broad fringing wetland, with extensive areas of aquatic plants sorted by their tolerance to different water depths. Typically, four zones are recognized, from higher to lower on the shore: wooded wetland, wet meadow, marsh and aquatic vegetation. Keddy, P.A. 2010. Wetland Ecology: Principles and Conservation (2nd edition). Cambridge University Press, Cambridge, UK. Chapter 2.
The eulittoral zone extends from the spring high tide line, which is rarely inundated, to the spring low tide line, which is rarely not inundated. The wave action and turbulence of recurring tides shapes and reforms cliffs, gaps, and caves, offering a huge range of habitats for sedentary organisms.
A zone which is part of the sublittoral zone and is dominated by algae. This zone usually extends up to five metres below the low water mark.
A zone which is part of the sublittoral zone and is dominated by sessile animals such as oysters. This zone usually begins at a depth greater than the infralittoral zone.
A whole plant which is relatively young.
A portion of fine respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 2.5 micrometers or less.
fine respirable suspended particulate matter
A portion of fine respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 100 nanometers or less.
Regulations do not exist for this size class of ambient air pollution particles, which are far smaller than the regulated PM10 and PM2.5 particle classes and are believed to have several more aggressive health implications than those classes of larger particulates.
ultrafine respirable suspended particulate matter
A house is a building that provides a dwelling-place for a living entity.
The provisioning of a dwelling-place can perhaps be modelled as a role.
A human house is a house which provides a dwelling-place for humans.
A garden that is associated with a human house. This association is generally one of spatial proximity or parthood.
A building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
An indoor kitchen is a room or part of a room primarily used for cooking or food preparation, but which may have other funcitons such as dining, food storage, dishwashing, or laundry.
Not a sublcass of room as this may just be part of some room.
A bathroom is a room which contains a washbasin or other fixture, such as a shower or bath, used for bathing by humans.
A living room is a room in a human house which is used for social and domestic leisure activities.
The logical definitions must state which social and leisure activities are included here. Jet-skiing and mass rallies are probably not the range.
A patio is a paved outdoor area, adjacent to a human house, and used for dining or recreation.
An indoor toilet is a room which contains a sanitation fixture used primarily for the disposal of human urine and faeces.
restroom
A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls.
A portion of carbon nanotube enriched soil is a portion of soil with elevated levels of carbon nanotubes.
Logical definition will be created pending import of "carbon nanotube" from CHEBI
A rocky shore is an intertidal area of a seacoast where solid rock is the predominant substrate.
This label is usually used to refer to 'rocky intertidal shores', i.e. a marine environment. Other types of rocky shore should be requested explicitly. Additionally, "rocky" could be a quality, this would link this with rocky deserts etc.
A burrow is a hole or tunnel excavated into the ground by an animal to create a space suitable for habitation, temporary refuge, or as a byproduct of locomotion
Should be better defined logically aggregating 'hole' or 'tunnel' with some sort of relation to 'habitation' etc.
A forest biome which contains densely packed populations or communities of broadleaf trees, strongly limiting light penetration to the forest floor.
A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending.
A forest ecosystem which contains densely packed populations or communities of broadleaf and coniferous trees, strongly limiting light penetration to the forest floor.
A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. The subclasses of this class need to be checked: are they properly placed under other classes or is this corrected and the dominant form of mixed vegetation noted in the label?
Particulate environmental material in which small portions of solid material are surrounded by water.
This class should be populated by inference, relying on 'composed primarily of', many 'pieces of solid material' and 'surrounded by' some 'water'.
waterborne particulate matter
A lava field is an expanse of flat-lying lava flows. Such features are generally composed of highly fluid basalt lava, and can extend for tens or even hundreds of miles across the underlying terrain.
A lava flow is a moving outpouring of lava, which is created during a non-explosive effusive eruption.
A volcano which has been formed as a result of the eruption of andesitic lava.
A volcano which has been formed as a result of the eruption of dacitic lava.
Andesite is an extrusive igneous, volcanic rock, of intermediate composition, with aphanitic to porphyritic texture.
In a general sense, it is the intermediate type between basalt and dacite, and ranges from 57 to 63 percent silicon dioxide as illustrated in TAS diagrams. The mineral assemblage is typically dominated by plagioclase plus pyroxene and/or hornblende. Magnetite, zircon, apatite, ilmenite, biotite, and garnet are common accessory minerals. Alkali feldspar may be present in minor amounts.
Dacite is an igneous, volcanic rock. It has an aphanitic to porphyritic texture and is intermediate in composition between andesite and rhyolite. Dacite consists mostly of plagioclase feldspar with biotite, hornblende, and pyroxene (augite and/or enstatite). It has quartz as rounded, corroded phenocrysts, or as an element of the ground-mass. The plagioclase ranges from oligoclase to andesine and labradorite. Sanidine occurs, although in small proportions, in some dacites, and when abundant gives rise to rocks that form transitions to the rhyolites.
An accumulation of a salt, typically sodium chloride.
salt mass
Lava which is high in silica and low in alkali metal oxides.
Rapid solidification of this lava forms dacite.
An ecosystem which has been subject to a perturbation, that is, the ecosystem has undergone a pronounced change in response to a change in environmental conditions or other perturbation.
This is often used by plant collectors when early successional species are observed in an area.
A ravine is a small, narrow, steep-sided valley that is larger than a gully and smaller than a canyon and that is usually worn by running water.
An environmental zone of varying area which is adjacent to a road.
A grassland which contains a mixture of tall and short grasses.
A wet meadow is a type of wetland with soils that are saturated with water for part or all of the growing season.
Debate exists whether a wet meadow is a type of marsh or a completely separate type of wetland. Wet prairies and wet savannas are hydrologically similar. Wet meadows may occur because of restricted drainage or the receipt of large amounts of water from rain or melted snow. They may also occur in riparian zones and around the shores of large lakes. Unlike a marsh or swamp, a wet meadow does not have standing water present except for brief to moderate periods during the growing season. Instead, the ground in a wet meadow fluctuates between brief periods of inundation and longer periods of saturation. Wet meadows often have large numbers of wetland plant species, which frequently survive as buried seeds during dry periods, and then regenerate after flooding. Wet meadows therefore do not usually support aquatic life such as fish. They typically have a high diversity of plant species, and may attract large numbers of birds, small mammals and insects including butterflies.
A mass of salt which has erupted onto a planetary surface, usually through sedimentary rock.
salt glacier
Adapted from URL:http://earthobservatory.nasa.gov/IOTD/view.php?id=86861
Atmospheric carbon dioxide is an environmental material composed of carbon dioxide in its gaseous form present in an atmosphere.
This could also be considered a part of an environmental material like air.
A disposition which is realised by an environmental system or system parts thereof.
This class and its subclasses are experimental and are being developed with NCEAS use cases in mind.
The disposition of an environmental system to sequester and store carbon.
The disposition of an environment to sequester carbon dioxide, subsequently storing the carbon component thereof.
The disposition of an environmental system to sequester and store some material entity.
A concrete masonry unit is a large, rectangular masonry unit primarily composed of concrete.
A masonry unit is a solid piece of material, usually with a regular shape, used as a component in the construction of buildings. Masonry units are usually composed of brick, stone, marble, granite, travertine, limestone, cast stone, concrete block, glass block, stucco, tile, or cob.
Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time.
Missing the class for "aggregate" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid.
Asphaltic concrete is a concrete which uses refined asphalt as a cement.
Asphalt also known as bitumen is a sticky, black, and highly viscous liquid or semi-solid form of petroleum.
This class refers to naturally-occuring asphalt or bitumen.
Refined asphalt is a sticky, black, and highly viscous liquid or semi-solid with a boiling point above 500 degrees Celsius, obtained from the fractional distillation of crude oil.
Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together.
"Cement" refers more to a disposition than a specific material.
Hydraulic cement is a masonry cement which contains activated aluminium silicates or pozzolans, such as fly ash, allowing it to set in wet conditions or underwater.
Non-hydraulic cement is a cement which sets by reacting with carbon dioxide in the air and will not set in wet conditions or underwater. It is susceptible to attack by aggresive chemicals after setting.
Building walls are bulding parts which serve to support roofs, floors and ceilings; enclose a space as part of the building envelope; give buildings form; and to provide shelter and security.
This is a building part and not the same as a standalone wall, which is a building in its own right.
A boundary wall is a constructed barrier which is usually opaque, constructed from masonry, and of greater structural strength than a fence.
This is not the same as a wall that is part of a building. use ENVO:01000420 for the latter.
A constructed barrier is a freestanding wall, berm, or fence built to limit movement of entities across a boundary.
A fence is a constructed barrier which is generally of lighter construction than a wall and used to provide visual sectioning of spaces.
An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment.
A building envelope is a building part composed of those building parts which physically separate the interior of a building from its surrounding environment. The building envelope provides resistance to air, water, heat, light, and noise transfer. The three basic elements of a building envelope are a weather barrier, air barrier, and thermal barrier.
A ceiling is an overhead interior surface that covers the upper limit of a room. It is not generally considered a structural element, but a finished surface concealing the underside of the floor or roof structure above.
A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering
This class is meant to represent roofs which are parts of buildings, rather than a roofs of cave and other natural formations.
Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather.
Some sort of logical definition towards: composed_primarily_of some ((straw or 'water reed' or rushes or sedge or heather) and has_quality dry) should be considered, where "rushes", "sedge", etc are represented as materials rather than some sort of taxon.
A portion of brick material is a material derived from a brick which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete that has been fire-hardened or air-dried.
A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried.
Generally used to refer to the masonry unit rather than a material.
Plaster is a building material which has the disposition to harden when it reacts with water, liberating heat through crystallization. Plaster is manufactured as a dry powder and is mixed with water to form a paste when used.
Gypsum plaster is a plaster which is formed by partially dehydrating gypsum by heating it to approximately 150 degrees Celsius and grinding the product into a powder. Gypsum anhydride - formed by heating gypsum above 200 degrees Celsius - may also be used as plaster.
Lime plaster is a plaster which is primarily composed of calcium hydroxide and an inert filler (such as sand). Coversion of the calcium hydroxide to calcium carbonate through a reaction with carbon dioxide in the air causes the plaster to set.
Glass is an amorphous (non-crystalline) solid which is often transparent.
This class refers to all forms of glass. For the familiar form present in window panes and drinking glasses, consider silica-based glass.
Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand.
Silica-based glasses are the most common manufactured variety of glass.
Soda-lime glass is a silica-based glass which is composed of approximately 75% silicon dioxide, with sodium oxide and calcium oxide consituting most of its remaining composition.
This type of glass constitutes 90% of manufactured glass.
Flat glass is a soda-lime glass which is composed of approximately 73% silicon dioxide (silica), 14% sodium oxide, 9% calcium oxide, 4% magnesium oxide, 0.15% aluminium oxide, 0.03% potassium oxide, 0.02% titanum dioxide, and 0.01% iron III oxide.
Most flat glass is soda-lime glass produced by the float glass process. It is more water soluble than container glass.
Container glass is a soda-lime glass which is composed of approximately 74% silicon dioxide (silica), 13% sodium oxide, 10.5% calcium oxide, 1.3% aluminium oxide, 0.3% potassium oxide, 0.2% sulphur trioxide, 0.2% magnesium oxide, 0.04% iron III oxide, and 0.01% titanum dioxide.
Container glass is less water soluble than flat glass.
Quartz glass is a glass which is composed of silica in amorphous (non-crystalline) form.
This is "pure" silica glass. As an ENVO:"environmental material" this class assumes that there remains some possibility that 'contaminants' being present.
A building floor is a surface layer which is part of a building and used for walking.
To be more precise, a subfloor and a floor covering may be specified. Please request these classes and propose definitions if they are needed.
A brick building floor is a building floor that is composed primarily of brick material or is built from bricks.
A wooden building floor is a building floor that is composed primarily of wood.
A concrete building floor is a building floor that is composed primarily of concrete
At times, this is called a cement floor, although that is probably not accurate.
A sandy building floor is a building floor that is composed primarily of sand.
A glass building floor is a building floor which is composed primarily of glass.
A dung building floor is a building floor which is composed primarily of dried animal feces.
A stone building floor is a building floor that is composed primarily of rock.
A thatched exterior wall is an exterior wall that is composed primarily of thatch.
A stone exterior wall is an exterior wall that is composed primarily of rock.
A straw exterior wall is an exterior wall that is composed primarily of straw.
A mud exterior wall is an exterior wall that is composed primarily of mud.
A solid, cylindrical object or column with its length greater than its diameter.
This was created in response to a user request, but it is an odd class in that it specifies a shape rather than a particular material entity. It may, therefore, be deprecated when more meaningful or sensible alternatives become apparent.
A pole-reinforced mud exterior wall is a mud exterior wall which is supported and reinforced by poles.
A brick exterior wall is an exterior wall that is built from bricks.
A burnt brick is a brick which has been dried at an elvated temperature in a kiln, furnace, or with similar technology .
An unburnt brick is a brick which has been air dried rather than dried at an elvated temperature in a kiln, furnace, or with similar technology .
A burnt brick exterior wall is an exterior wall that is built from burnt bricks.
An unburnt brick exterior wall is an exterior wall that is built from unburnt bricks.
A dome-shaped mass of salt formed when a thick bed of evaporite minerals (mainly salt, or halite) found at depth intrudes vertically into surrounding rock strata, forming a diapir.
salt dome
A concrete exterior wall is an exterior wall that is composed primarily of concrete.
An iron sheet is a mass of iron which has been forged into a roughly planar form of less than 6 millimetres in thickness.
salt material
A sheet-iron exterior wall is an exterior wall that is built from sheets of iron.
A sheet-iron building roof is a building roof that is built from sheets of iron.
A thatched building roof is a building roof that is built by thatching (or out of thatch).
A wooden building roof is a building roof that is built from wood.
An asbestos building roof is a building roof that is built from asbestos.
asbestos exists in CHEBI and will be imported to complete this class' logical def.
A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications.
A tile building roof is a building roof that is built using tiles.
A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces.
"disposal" may not be the most precise way to describe fill-in latrines. Note that no assertion is made on whether these fixtures are in- or outdoors.
A pit latrine is a latrine which is constructed by digging a hole in the ground.
This class refers to human latrines. Note that some pit latrines can use pour-flush mechanisms. "Infectious diarrhea resulted in about 0.7 million deaths in children under five years old in 2011 and 250 million lost school days.[4][5] Pit latrines are the lowest cost method of separating feces from people.[3]" - https://en.wikipedia.org/wiki/Pit_latrine
A diapir is a type of geologic intrusion in which a more mobile and ductily deformable material is forced into brittle overlying rocks due to its higher buoyancy.
Unclear whether this should be a subclass of intrusion, as diapirism can actually cause fracturing.
diapir
A latrine is a toilet which is of simple construction (relative to a flush or chemical toilet) and typically intended for communal use.
A latrine slab is a broad, flat, thick piece of solid material (typically stone or concrete) used as the floor of a latrine and which includes a hole through which excreta are deposited into a latrine pit.
This could be moved to "surface layer" like other floors, although more thought has to be given to "floor": a role of a surface layer? "The hole in the slab should not be larger than 25 centimeters (9.8 inches) to prevent children falling in." https://en.wikipedia.org/wiki/Pit_latrine
A batholith is an area of mostly continuous plutonic (igneous intrusive) rock that covers an area larger than 100 square kilometers, formed in the planetary crust, and exposed by erosion. On Earth, Batholiths are almost always made mostly of felsic or intermediate rock-types, such as granite, quartz monzonite, or diorite.
The form of erosion should be further specified.
batholith
A latrine pit is an artificial hole or cavity in the ground used to collect human excreta.
A latrine pit is typically at least 3 metres (10 feet) deep and 1 metre (3.2 feet) across.
A pit latrine with a slab floor is a pit latrine which has a latrine slab as a floor.
This class refers to human latrines. "Infectious diarrhea resulted in about 0.7 million deaths in children under five years old in 2011 and 250 million lost school days.[4][5] Pit latrines are the lowest cost method of separating feces from people.[3]" - https://en.wikipedia.org/wiki/Pit_latrine
An outhouse is a small structure, separate from a main building, which covers a pit latrine or a dry toilet.
"Outside North America, the term "outhouse" refers not to a toilet but to outbuildings in a general sense."
An intrusion which is primarily composed of rock which has been formed within a pre-existing fracture in a larger mass of rock.
While some intrusions are still located in the fracture where they formed, others may be (partially) exposed by erosional processes.
rock intrusion
A rock intrusion which is composed primarily of sedimentary rock.
Subclasses of this class will be created by inference.
sedimentary intrusion
A toilet fixture which uses water to flush liquid and solid excreta into a sewage containment or processing facility through a drainpipe.
A toilet fixture which uses little to no water; excreta is removed manually or composted in situ.
Subclasses will probably be filled in by inference.
A chemical toilet fixture is a toilet fixture which uses chemicals to deodorise and treat excreta which is stored in the fixture.
"In the past, disinfection was generally carried out by mixing formaldehyde, bleach or similar chemicals with the toilet water when flushed...[F]ormaldehyde is very irritating to the eyes, ears, skin, nose, and throat, it is being replaced by other proprietary blends such as glutaraldehyde and quaternary ammonium compounds, with non-staining dyes and nature-identical perfume oils. Additionally, enzyme hybrids are sometimes used." https://en.wikipedia.org/wiki/Chemical_toilet
A ventilated improved pit latrine is a pit latrine which includes a vent pipe fitted to the pit with a flyscreen covering the pipe's outlet. Air currents moving across the outlet of the vent pipe create a vaccum which draws odors out of the latrine's superstructure.
A covered latrine is a building which comprises a latrine sheltered by an outhouse.
A covered pit latrine is a building which comprises a pit latrine sheltered by an outhouse.
A covered pit latrine with slab is a building which comprises a pit latrine with a slab floor sheltered by an outhouse.
A flush toilet fixture into which water is manually poured to dispose of excreta.
A pit latrine which includes a water seal (U-trap or siphon) used over one or two offset pits instead of a plain hole or seat. Water is manually poured through the trap to flush excreta into the latrine pit.
A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another.
Atmospheric ozone is an environmental material primarily composed of ozone in its gaseous form and present in an atmosphere.
The layer of the atmosphere which is sandwiched between the troposphere and mesosphere. Of the energy that reaches the Earth from the sun, only 3% is absorbed in the stratosphere, but that includes the vitally important process of absorption of ultraviolet radiation by the stratospheric ozone layer. The stratosphere is cloudless and dust free, and almost unaffected by the turbulent conditions of the underlying level of the atmosphere. (Source: WRIGHT)
Definition from GEMET - will be refined.
The mesosphere is part of the earth's atmosphere which is between the stratosphere and the thermosphere in which temperature decreases with altitude to the atmosphere's absolute minimum
The lowest of the concentric layers of the atmosphere, occurring between the Earth's surface and the tropopause. It is the zone where atmospheric turbulence is at its greatest and where the bulk of the Earth's weather is generated. It contains almost all the water vapour and aerosols and three-quarters of the total gaseous mass of the atmosphere. Throughout the troposphere temperature decreases with height at a mean rate of 6.5°C/km and the whole zone is capped by either an inversion of temperature or an isothermal layer at the tropopause. (Source: WHIT)
The thermosphere is a part of the earth's atmosphere that begins at about 50 miles (80 kilometers) above the earth's surface, extends to outer space, and is characterized by steadily increasing temperature with height
The ozone layer is a layer of gases in the stratosphere which contains high concentrations of ozone gas relative to other parts of the atmosphere.
"The ozone layer contains less than 10 parts per million of ozone, while the average ozone concentration in Earth's atmosphere as a whole is only about 0.3 parts per million. The ozone layer is mainly found in the lower portion of the stratosphere, from approximately 20 to 30 kilometres (12 to 19 mi) above Earth, though the thickness varies seasonally and geographically"- https://en.wikipedia.org/wiki/Ozone_layer
ozone layer
This could be made into an inferred class, rather than having asserted subclasses.
atmospheric layer
A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow.
boundary layer
The ionosphere is a layer of the Earth's atmosphere which extends from about 60 to 1,000 kilometers above the planetary surface and is ionised by solar radiation. It includes the thermosphere and parts of the mesosphere and exosphere.
ionosphere
The exosphere is an atmospheric layer where molecules are gravitationally bound to a planetary body, but where their density is too low for them to behave as a gas by colliding with each other. In the case of bodies with substantial atmospheres, such as Earth's atmosphere, the exosphere is the uppermost layer, where the atmosphere thins out and merges with interplanetary space. It is located directly above the thermosphere.
exosphere
A glaze ice layer is a smooth, transparent and homogeneous ice layer which coats some surface and which is formed when freezing rain or drizzle hits that surface.
glaze ice layer
eutrophic lake
mass of biological material
A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils.
composting toilet
A fuel oil which is 1) composed primarily of alkanes having between 5-15 carbon atoms with the general formula CnH2n+2, 2) is generally odorless or has only a slight odor, 3) produces only small amounts of soot relative to other fuel oils, 4) is highly refined.
paraffin oil
Natural gas is a hydrocarbon gas mixture consisting primarily of methane, but commonly includes varying amounts of other higher alkanes and sometimes a usually lesser percentage of carbon dioxide, nitrogen, and/or hydrogen sulfide. Natural gas is a fossil fuel formed when layers of buried plants and gases are exposed to intense heat and pressure over thousands of years.
natural gas
Liquified petroleum gas or liquid petroleum gas (LPG or LP gas), also referred to as simply propane or butane, are flammable mixtures of hydrocarbon gases used as fuel in heating appliances, cooking equipment, and vehicles.
liquefied petroleum gas
A gas that is primarily composed of hydrocarbon molecules.
hydrocarbon gas
Compressed natural gas is a natural gas stored at high pressures, typically 20–25 Megapascals.
compressed natural gas
Biogas is a mixture of different gases produced by the breakdown of organic matter in the absence of oxygen, is primarily composed of methane and carbon dioxide, and may have small amounts of hydrogen sulfide, water, and siloxanes.
This is distinct from natural gas which is a fossil fuel product.
biogas
Liquefied natural gas (LNG) is natural gas (predominantly methane, CH4) that has been converted to liquid form for ease of storage or transport. It takes up about 1/600th the volume of natural gas in the gaseous state. It is odorless, colorless, non-toxic and non-corrosive. LNG achieves a higher reduction in volume than compressed natural gas (CNG) so that the (volumetric) energy density of LNG is 2.4 times greater than that of CNG or 60 percent of that of diesel fuel.
liquefied natural gas
liquefied hydrocarbon gas
Compressed biogas is biogas stored at increased pressures.
This is distinct from compressed natural gas, which refers to the compressed form of a fossil fuel.
compressed biogas
Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen.
charcoal
A paraffin lamp is a type of lighting device which burns paraffin to generate light and heat.
paraffin lamp
A flat-wick lamp is a simple type of paraffin lamp, which burns paraffin drawn up through a wick by capillary action.
flat-wick lamp
A central-draught lamp is a paraffin lamp which burns a parrafin saturated, tubular wick contained between two structural tubes and supplied with oxygen by a central draught of air through the innermost of these tube.
central-draught lamp
A mantle lamp is a central-draught lamp which includes a pear-shaped, fabric mesh containing thorium or other rare-earth salts placed over the burner. On first use the fabric burns away and the rare-earth salts are converted to oxides, leaving a very fragile structure which incandesces (glows brightly) upon exposure to the heat of the burner flame.
mantle lamp
A lantern is a portable device or mounted fixture comprising a light source protected by a translucent case.
lantern
A lamp is an object which generates heat, light, or any other form of radiation.
lamp
A paraffin lantern is a lantern which houses a parrafin lamp in a structure of soldered or crimped-together sheet metal stampings and glass or other translucent material.
paraffin lantern
A tubular paraffin lantern is a paraffin lantern which includes metal tubes in its casing that direct air to the burning wick.
tubular paraffin lantern
A dead-flame paraffin lantern is a paraffin lantern which has a wick housed in a glass globe with airflow channelled upwards by vents below the burning wick and an open chimney above it.
dead flame paraffin lantern
A hot-blast paraffin lantern is a tubular paraffin lantern which collects hot air from the top of the lantern globe and circulates it, through metal tubes, to the burning wick.
hot-blast paraffin lantern
A cold-blast paraffin lantern is a tubular paraffin lantern which collects cool air from around the top of the lantern globe and circulates it, through metal tubes, to the burning wick.
cold-blast paraffin lantern
An electric lamp is a lamp which produces light from electricity.
electric lamp
A battery-powered electric lamp is an electric lamp which draws its power from a device composed of two or more electrochemical cells that convert stored chemical energy into electrical energy.
battery-powered electric lamp
A candle is a lamp composed of a wax within which an ignitable wick is embedded.
candle
A wax is an environmental material which is primarily composed of lipids or other organic compounds that consist of long alkyl chains. Waxes are are malleable near ambient temperatures and melt at approximately 45 degrees Celsius.
wax
An apiary is a place where beehives of honey bees are kept and maintained by beekeepers.
apiary
A device capable of receiving and/or transmitting information encoded in electromagnetic radiation through wave modulation.
radio device
A cassette deck is a device capable of playing and recording audio compact cassettes.
cassette player
A television set is a device that combines a tuner, display, and loudspeakers for the purpose of converting digital or analog information signals into moving images and sound.
television set
A telephone is a telecommunications device which converts sound into electronic signals suitable for transmission via cables or other transmission media, and reconverts such signals into sound waves.
telephone
A mobile phone is a telephone which transmits sound information to a mobile phone network via radio transmissions.
mobile phone
A landline telephone is a telephone which is connected to a telephone network with wires through which electronic signals are carried.
landline telephone
A refrigerator is a device which consists of a thermally insulated compartment and a mechanical, chemical, or electronic heat pump that transfers heat from the inside of the fridge to its external environment such that the inside of the fridge is cooled to a temperature below the ambient temperature of the room
refrigerator
A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation.
table
A desk is a table which is intended for information-manipulation tasks, including writing and use of interactive electronics.
The intentional nature of this definition is problematic, but the restricted range of activities visited upon a desk is of interest.
desk
A chair is a piece of furniture with a raised surface commonly used to seat a single person.
This class, along with benches, stools, and the like, can be grouped under "seating furniture" or similar. However, this is probably better as an inferred class using some sort of BFO:function in the subclass annotation.
chair
A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds).
The assumption is that furniture is manufactured, which is arguable. Further, according to Black's Law Dictionary (http://thelawdictionary.org/furniture/) many classes can be subclasses of 'piece of furntiure': "This term includes that which furnishes, or with which anything is furnished or supplied; whatever must be supplied to a house, a room, or the like, to make it habitable, convenient, or agreeable; goods, vessels, utensils, and other appendages necessary or convenient for housekeeping; whatever is added to the interior of a house or apartment, for use or convenience. Bell v. Holding, 27 Ind. 173.The term “furniture” embraces everything about the house that has been usually enjoyed there, including plate, linen, china, and pictures. 1 Endicott v. Endicott, 41N. J. Eq. 96, 3 Atl. 157.The word “furniture” made use of in the disposition of the law. or in the conventions or acts of persons, comprehends only such furniture as is intended for use and ornament of apartments, but not libraries which happen to be there, nor plate. Civ.Code La. art. 477." However, this would eventually be absurd and limit other groupings. Perhaps some sort of 'furnishing' BFO:function would be a better way to handle this.
piece of furniture
A sofa is a bench which is partially or entirely upholstered, and often fitted with springs and tailored cushions.
sofa
A bench is a piece of furniture, on which several people may sit at the same time.
bench
A mattress is a mass of material which is able to cushion and support a reclining body and is used as or on a bed.
mattress
A bed frame is a piece of furniture which is used to position a mattress and bed base and may include a means of supporting a canopy.
bed frame
A bed base is a piece of furniture which supports a mattress.
bed base
A framed bed is a piece of furniture which is composed of a mattress supported by a bed base and held in place by a bed frame.
framed bed
A cabinet is a roughly cuboidal piece of furniture which is used to store miscellaneous items in compartments accessible through doors or drawers.
cabinet
A cupboard is a cabinet which is used indoors to store household objects such as food, crockery, textiles and liquor, and to protect them from dust and dirt
cupboard
A clock is an instrument which may indicate, keep, and/or co-ordinate time.
clock
A pressure lamp is a portable paraffin or oil lamp in which fuel is forced up into the mantle or burner by air pressure in the reservoir, which can be increased by pumping with a plunger.
This may be a paraffin or an oil lamp. It can potentially be filled by inference if we can express that any lamp with pressurised fuel in the lamp reservoir is a pressure lamp. See Issue #228.
pressure lamp
A spring through which fresh water flows.
freshwater spring
river water
Rainwater is liquid water which has precipitated in the form of droplets through the condensation of atmospheric water vapour.
rainwater
A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails.
motor vehicle
A truck is a motor vehicle which, as its primary funcion, transports cargo rather than human passangers.
truck
A water truck is a truck which transports water.
water truck
A vehicle is a mobile machine which transports people or cargo.
vehicle
A car is a wheeled motor vehicle used primarily for the transportation of human passengers. Most definitions of the term specify that cars are designed to run primarily on roads, to have seating for one to eight people, to typically have four wheels, and to be constructed principally for the transport of people rather than goods.
car
A cart is a vehicle which has two wheels and is designed to transport human passengers or cargo.
NB: "[A cart]...is different from a dray or wagon, which is a heavy transport vehicle with four wheels and typically two or more horses, or a carriage, which is used exclusively for transporting humans...Over time, the term "cart" has come to mean nearly any small conveyance, from shopping carts to golf carts, without regard to number of wheels, load carried, or means of propulsion." https://en.wikipedia.org/wiki/Cart
cart
An animal-drawn cart is a cart which is attached to one or more working or draught animals.
animal-drawn cart
A boat is a watercraft of any size which is able to float or plane on water.
Difficult to distinguish from "ships". Similar to mountains and hills. " In naval terms, a boat is a vessel small enough to be carried aboard another vessel (a ship). Another less restrictive definition is a vessel that can be lifted out of the water. Some definitions do not make a distinction in size, as bulk freighters 1,000 feet (300 m) long on the Great Lakes are called oreboats. For reasons of naval tradition, submarines are usually referred to as 'boats' rather than 'ships', regardless of their size and shape." - https://en.wikipedia.org/wiki/Boat
boat
A motor boat is a boat which is propelled by a motor.
motor boat
A motor is a machine designed to convert one or more forms of energy into mechanical energy.
motor
A bus is a road vehicle designed to carry many passengers.
bus
A taxicab is a car which may be hired, along with its operator, to transport passengers between locations of their choosing.
Depth can be added with specifications of BFO:role for both the car and the human operator.
taxicab
A watercraft is a vehicle which is able to travel on or through water.
Ships, boats, hovercraft and submarines are all considered watercraft. The term would normally imply some propulsive capability (whether by sail, oar or engine) and hence is distinct from a simple device that merely floats, such as a log raft. - Wikipedia
watercraft
A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other.
bicycle
A motorcycle is a two- or three-wheeled motor vehicle.
motorcycle
A scooter or motor scooter is a motorcycle with step-through frame and a platform for the rider's feet.
motorscooter
A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow.
lentic water body
A lotic water body is a water body in which the accumulated water, in its totality, is flowing.
lotic water body
A closed ecological system is a vivarium which does not rely on matter exchange with any part outside the system.
This class refers to strictly sealed enclosures such as Biosphere 2 (https://en.wikipedia.org/wiki/Biosphere_2), rather than vivaria which allow matter exchange with external environmental systems.
closed ecological system
A mesocosm is a vivarium that is embedded within a natural environment and is used to place a relatively small part of that environment under experimental control for the purposes of scientific investigation.
mesocosm
A microcosm is a vivarium within which a simple ecosystem is artificially established and used to simulate and predict the behaviour of natural ecosystems under controlled conditions.
microcosm
Vaporisation of an element or compound is process whereby that element or compound undergoes a phase transition from the liquid to vapor.
Note that a vapor describes an element or compound in the gas phase at a temperature lower than its critical point,
vaporisation
Boiling is a form of vaporisation which occurs when a liquid is heated to a temperature at which the vapor pressure of the liquid is equal to the pressure exerted on the liquid by the surrounding environmental pressure.
boiling
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
"process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog)
hydrological condensation process
A manufactured structure made of interspaced structural elements such as metal or wooden bars or wires held together such that they may be used to confine, contain, or protect something.
manufactured cage
A drylot is an enclosure of limited size usually bare of vegetation and used for fattening livestock.
drylot
A feedlot is a plot of land on which livestock are fattened for market
feedlot
Leaf litter is dead plant material, such as leaves, bark, needles, and twigs, that has fallen to the ground.
plant litter
The long-term fluctuations in temperature, precipitation, wind, and all other aspects of the Earth's climate. External processes, such as solar-irradiance variations, variations of the Earth's orbital parameters (eccentricity, precession, and inclination), lithosphere motions, and volcanic activity, are factors in climatic variation. Internal variations of the climate system, e.g., changes in the abundance of greenhouse gases, also may produce fluctuations of sufficient magnitude and variability to explain observed climate change through the feedback processes interrelating the components of the climate system.
Definition vebatim from GEMET. Will need to be refined. Further, distinction between "climate change" and (one or many) "climate change process" will need to be discussed. Fluctuations are not processes, per se.
climate change
Acidification of an aquatic environment is a process whereby the pH of an aquatic environment, biome, or water body is lowered.
acidification of an aquatic environment
Ocean acidification is a process during which the pH of a sea or ocean is lowered.
On Earth, the major cause of ocean acidification is the update of carbon dioxide from the atmosphere.
ocean acidification
A chonolith is an igneous rock intrusion of irregular shape with a demonstrable base, absent in other types of irregularly-shaped intrusions.
chonolith
A process which consists of all aerobic respiration processes instantiated in an ecosystem.
ecosystem-wide aerobic respiration
A volcanic eruption is a process during which lava, tephra (ash, lapilli, volcanic bombs and blocks), and assorted gases are expelled from a volcanic vent or fissure.
volcanic eruption
planetary landmass
Adpated from https://en.wikipedia.org/wiki/Planetary_surface
A liquid planetary surface is a planetary surface layer where a liquid material of a planet comes into contact with atmosphere or outer space.
liquid planetary surface
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
outer space
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
This class is meant to be applicable accross planets. Earth's crust would be an instance.
planetary crust
A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition.
Label should be improved to match definition.
planetary structural layer
A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density.
This class is meant to be applicable accross planets. Earth's mantle would be an instance.
planetary mantle
A planetary core is the innermost structural layer or layers of a planet. The core may be entirely liquid, entirely solid, or have both liquid and solid parts.
"Not to be confused with planetary core in the core accretion theory, referring to a central accretionary body surrounded by a halo of dust and gas which serves to trap debris and increase the rate of accretion.." WIkipedia:Planetary_core. This class is meant to be applicable accross planets. Earth's core would be an instance. The "layer" aspect of cores may be problematic.
planetary core
Needs a general definition that holds for Earth as well as other planets.
outer planetary core
inner planetary core
A liquid planetary core is a planetary core which is primarily composed of liquid material.
liquid planetary core
A solid planetary core is a planetary core which is primarily composed of solid material.
solid planetary core
A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties.
Earth's lithosphere includes the crust and uppermost mantle.
lithosphere
An asthenosphere is a layer of a terrestrial-type planet or natural satellite which is highly viscous, mechanically weak, and ductilely deforming.
asthenosphere
Magma is a mixture of molten or semi-molten rock, volatiles, and solids that is found beneath the uppermost solid layer of a planetary body. Besides molten rock, magma may also contain suspended crystals, dissolved gas and sometimes gas bubbles.
magma
A trench is a type of excavation or depression in the ground that is generally deeper than it is wide (as opposed to a wider gully or ditch), and narrow compared to its length (as opposed to a simple hole).
trench
A channel of a watercourse which contains a stream.
stream channel
An ocean strait is a strait which connects two oceans.
ocean strait
A stream channel which contains a river.
river channel
A slum is a heavily populated urban informal settlement with substandard housing in which households lack any one of the following: access to improved water, access to improved sanitation, sufficient-living area, durability of housing, or security of tenure.
slum
Definition linked to a UN Habitat report entitled "What are slums and why do they exist?" as well as sources from the MDGs and Communitas.
An undersea trough is a trough which is below a marine water body.
undersea trough
An explosive eruption is a volcanic process in which pressurised magma is violently expelled and froths into volcanic ash. Explosive eruptions can eject a cloud of rocks, dust, gas, and pyroclastic material which may then collapse, creating a pyroclastic flow of hot volcanic matter.
explosive eruption
An effusive eruption is a volcanic eruption during which lava flows onto the ground.
effusive eruption
A process whereby rising magma cools and solidifies without reaching the surface. Instead, the cooled and solidified igneous mass crystallises within the crust to form an igneous intrusion.
igneous intrusion process
A settlement with a high density of buildings and inhabitants.
See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx
The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.
dense settlement
An igneous intrusion is a mass of rock and minerals formed when magma cools, solidifies, and undergoes fractional crystallisation without reaching the surface.
"Intrusion" can refer to the solidified mass or the molten rock.
igneous intrusion
Tephra is fragmental material produced by a volcanic eruption regardless of composition, fragment size or emplacement mechanism.
tephra
Tuff is a type of rock made of volcanic ash ejected from a vent during a volcanic eruption.
tuff
Scoria is a highly vesicular, dark colored volcanic rock that may or may not contain crystals.
Scoria differs from pumice in having larger vesicles, thicker vesicle walls and being dark colored and denser.
scoria
Pumice is a volcanic rock that consists of highly vesicular rough textured volcanic glass, which may or may not contain crystals.
pumice
A cone that is composed of consolidated volcanic ash.
tuff cone
A role that is realized in some process wherein the bearer is discarded or not utilized further.
waste role
An area of a planet's surface which is primarily composed of water in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of open water generally have less than 25% cover of vegetation or soil. A specific threshold is not asserted in this definition.
area of open water
A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces.
geological fracture
A geological fault is a planar fracture or discontinuity in a volume of rock, across which there has been significant displacement as a result of rock mass movement.
The relationship between faults and active plate boundaries must be further developed, as there is some overlap.
geological fault
An active fault is a fault that is likely to become the source of another earthquake sometime in the future. Geologists commonly consider faults to be active if there has been movement observed or evidence of seismic activity during the last 10,000 years.
active geological fault
A vein is a geological fracture which is filled with minerals precipitated out of an aqueous solution.
vein
A sheet of rock that formed in a fracture in a pre-existing rock body.
dike
Adpated from https://en.wikipedia.org/wiki/Dike_(geology)
A joint is a geological fracture which has no measureable shear displacement
geological joint
A geological fracture across which shear displacement has occurred
Sounds like this should be populated by inference.
shear fracture
A microfracture is a small fracture which is found in a portion of solid material along which further fracturing tends to occur. Microfractures are considered imperfections which to pre-exist any fractures formed by the application of stress to a material.
microfracture
A fiat part of an atmosphere which is defined as a vertical, three-dimensional pillar extending from a unit area on a planetary surface and bounded by the top of the atmosphere.
Once defined, an atmospheric column can be used to quantify an atmospheric parameter such as pressure, ozone or precipitable water.
atmospheric column
Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.
contaminated air
An earthquake is a process during which energy is released in an astronomical body's crust, causing the displacement of crustal parts and the generation of seismic waves.
Elastic strain, gravity, chemical reactions, or even the motion of massive bodies can produce earthquakes.
earthquake
Adapted from URL:http://www.britannica.com/science/earthquake-geology
An earthquake caused by the sudden release of energy accumulated in an astronomical body's crust, as the elastic strain placed on constituent rock masses causes them to fracture.
tectonic earthquake
A megathrust earthquake is a tectonic earthquake which occurs at subduction zones at destructive plate boundaries (convergent boundaries). These interplate earthquakes are the planet's most powerful, with moment magnitudes that can exceed 9.0.
megathrust earthquake
A lake which has concentrations of environmental contaminants high enough to harm the ecosystems associated with it.
polluted lake
A mineral material composed primarily of sodium chloride.
This class is for material primarily composed of sodium chloride. For other pure chemical salts, consider a CHEBI class. Request new ENVO terms for environmental samples of other chemical salts.
sodium chloride salt
A glacial abrasion process is an erosional process during which debris in the basal ice scrapes along the bed, polishing and gouging the underlying rocks, similar to sandpaper on wood.
glacial abrasion
Glacial plucking is an erosional process during which pieces of bedrock are cracked off due to the mechanical force of a moving glacier.
glacial plucking
Glacial ice thrusting is an erosional process during which a moving glacier which has frozen to its bed surges forward and moves large sheets of sediment frozen to the glacial mass.
glacial ice thrusting
water mass
marine water mass
A coast is the area where land meets the sea, ocean, or lake.
Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore'
coast
The general region of indefinite width that extends from a lake inland to the first major change in terrain features.
lake coast
A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami.
tsunami
Mass wasting is the geomorphic process by which solid environmental material such as soil, sand, regolith, and/or rock move downslope typically as a mass, largely under the force of gravity, but frequently affected by water and water content as in submarine environments and mudslides.
Of interest for future development: Some causes of mass wasting earthquakes, increased overburden from structures, increased soil moisture, reduction of roots holding the soil to bedrock, undercutting of the slope by excavation or erosion, weathering by frost heave, bioturbation, volcanic edifice over-steepening. Some processes that reduce mass wasting: Afforestation, Reforestation, Terracing steps on slopes (reduce angle of slope). https://en.wikipedia.org/wiki/Mass_wasting.
mass wasting
A mass wasting flow during which snow rapidly flows down a sloping surface.
avalanche
A landslide is a process whereby a large mass of earth and rocks moves down a hill or a mountainside.
landslide process
rockfall
A material transport process during which a geological surface shifts downward relative to a datum such as sea-level.
geological subsidence
mudslide
A mass wasting flow is a form of mass wasting during which the moving materials behave similarly to a flowing fluid. Water, air and ice are often involved in enabling fluidlike motion of the material.
mass wasting flow
A mudflow is a form of mass wasting which involves very rapid to extremely rapid surging flow of debris that has become partially or fully liquified by the addition of significant amounts of water to clay-rich source material.
"Mudflows are often called mudslides, a term applied indiscriminately by the mass media to a variety of mass wasting events. Mudflows often start as slides, becoming flows as water is entrained along the flow path; such events are often called flow slides." https://en.wikipedia.org/wiki/Mudflow
mudflow
A mass wasting flow during which water-laden masses of soil and fragmented rock rush down the slopes of elevations, funnel into stream channels, entrain objects in their paths, and form thick, muddy deposits on valley floors.
debris flow
A lahar is a type of mudflow or debris flow composed of a slurry of pyroclastic material, rocky debris, and water. The material flows down from a volcano, typically along a river valley.
lahar
A sturzstrom is a landslide consisting which has a great amount of kinetic energy resulting in greater horizontal movement when compared to its initial vertical drop — as much as 20 or 30 times the vertical distance. By contrast a normal landslide will typically travel a horizontal distance that is less than twice the distance that the material has fallen.
sturzstrom
Volcanic ash is an environmental material which consists of fragments of pulverized rock, minerals, and volcanic glass, created during volcanic eruptions and measuring less than 2 millimetres in diameter. Volcanic ash is formed during explosive volcanic eruptions, phreatomagmatic eruptions and during transport in pyroclastic density currents.
volcanic ash
An ash fall process is a process in which volcanic ash formed during an explosive volcanic eruption, phreatomagmatic eruption, or during material transport in pyroclastic density currents is pulled towards the planetary surface by gravity.
ash fall process
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
Hydrological evaporation is the evaporation of water, generally as part of a planetary water cycle.
hydrological evaporation
Soil degradation is a process which results in a change in soil health status resulting in a diminished capacity of the ecosystem in which the soil occurs to provide goods and services for its beneficiaries.
soil degradation
Soil erosion is a process in which exogenic processes remove soil from one location on the Earth's crust and transport it to another location where it is deposited.
"Soil Erosion is a common term that is often confused with soil degradation as a whole, but in fact refers only to absolute soil losses in terms of topsoil and nutrients. This is indeed the most visible effect of soil degradation, but does not cover all of its aspects. Soil erosion is a natural process in mountainous areas, but is often made much worse by poor management practices." http://www.fao.org/soils-portal/soil-degradation-restoration/en/
soil erosion
Coastal flooding is a process in which normally dry, low-lying land near a coast is flooded by sea water.
coastal flooding
Riverine flooding is a process in which the flow rate of river water exceeds the capacity of its channel, thus flooding neighbouring land. Bends and meanders in a river channel are particularly disposed to such flooding.
A disposition class such as 'flooding disposition' may be interesting, especially when attached to things like meanders and bends.
riverine flooding
Flash flooding is a process in which low-lying land is inundated with water for a short period of time and are usually the result of precipitation or a breach in the container of a water body.
Flash floods generally last no more than six hours. http://www.srh.noaa.gov/mrx/hydro/flooddef.php
flash flooding
An unusual accumulation of water above the ground caused by high tide, heavy rain, melting snow or rapid runoff from paved areas.
flood
A coastal flood is a flood which is formed as a result of large amounts of water from marine water bodies or large lakes being transported to usually dry land by displacement processes such as high winds or seismic activity.
coastal flood
A riverine flood is a flood which is formed as a result of a river's flow rate exceeding the capacity of its channel.
riverine flood
A flash flood is a flood formed by the rapid flooding of geomorphic low-lying areas. It may be caused by heavy rain associated with a severe thunderstorm, hurricane, tropical storm, or meltwater from ice or snow flowing over ice sheets or snowfields. Flash floods may also occur after the collapse of a natural ice or debris dam, or a human structure such as a man-made dam. Flash floods are distinguished from a regular flood by a timescale of less than six hours.
flash flood
A storm surge is a coastal flood which is caused by low-pressure weather systems such as tropical cyclones and strong extratropical cyclones, the severity of which is affected by the shallowness and orientation of the water body relative to storm path, and the timing of tides.
Needs links to weather when these phenomena are added.
storm surge
A meteotsunami is a tsunami caused by atmospheric processes and differences in air pressure.
Ambiguity as to whether this label refers to the process or the material entities (the waves). The material entities are a type of severe storm surge.
meteotsunami
A storm surge process is a coastal flooding process which is caused by low pressure weather systems such as tropical cyclones and strong extratropical cyclones, the severity of which is affected by the shallowness and orientation of the water body relative to storm path, and the timing of tides.
Should be linked to the relevant weather classes when these are created.
storm surge process
Areal flooding is a flooding process in which flat or low-lying areas become inundated with water due to water input exceeding infiltration, evaporation, or run off.
areal flooding
Urban flooding is a flooding process in which land or property in a built environment, particularly in more densely populated areas, is inundated due to the rate of water input exceeding that of water drainage provided by the environment's drainage systems.
Relevant to built environments and can be linked to urban flows. Also relevant to water and sanitation SDGs.
urban flooding
Snowmelt is a hydrological melting process in which water is produced by the melting of snow and becomes part of the hydrological surface runoff.
The assertion that the output is freshwater seems reasonable; however, this can certianly be changed if a counter example is provided.
snowmelt
A melting process during which water-based ice, snow, or other solid phase water transitions into a liquid phase.
Here, we've nexted melting within thawing as one approach to resolve the semantics of thawing of ice-free materials. Expert group revision is requried.
hydrological melting process
Icemelt is a hydrological melthing process in which water is produced by the melting of ice and becomes part of the hydrological surface runoff.
icemelt
Meltwater is the water released by the melting of snow or ice, including glacial ice, tabular icebergs and ice shelves over oceans.
meltwater
Melting is a material transformation process which results in the phase transition of a substance from a solid to a liquid.
could replace with http://purl.obolibrary.org/obo/REX_0000177
Note that melting need not be due to warming, thus the classes are separated.
melting
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
Chemical precipitation is a process in which a portion of some solid substance segregates from a material in which that substance or its precursors were dissolved in and settles due to a force such as gravity or centrifugal force. Segregation may occur due to the solubility limits of the precipitating substance being exceeded or due to a chemical reaction that forms a solid product from aqueous reagents.
chemical precipitation process
Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid.
desublimation process
Sublimation is a process during which a portion of some solid undergoes a phase transition into a portion of some gas.
sublimation process
A tectonic uplift process is a geomorphologic process in which a geological surface shifts upward relative to a datum such as sea-level due to forces other than isostatic responses to unloading.
tectonic uplift process
A material transport process during which a mass of air moves through an atmosphere towards a planetary surface.
This process usually refers to large-scale air motion, rather than local winds.
atmospheric subsidence
A process in which a volume of lava emitted during an effusive eruption moves along a solid surface.
lava flow process
A mass of igneous rock formed when hot magma flows out (extrudes) onto a planetary surface as lava or explodes violently into the atmosphere to fall back as pyroclastics or tuff.
igneous extrusion
A dike formed when sediment fills a pre-existing fracture in a mass of rock.
clastic dike
A stock is a discordant igneous intrusion having a surface exposure of less than 100 square kilometres. Stocks differ from batholiths only in being smaller.
Some assertion to indicate that stocks are smaller than batholiths should be made.
stock
A sheet intrusion (or concordant pluton) that has been injected between two layers of sedimentary rock. The pressure of the magma is high enough that the overlying strata are forced upward, giving the laccolith a dome or mushroom-like form with a generally planar base.
laccolith
Adapated from https://en.wikipedia.org/wiki/Laccolith
A large igneous intrusion which is lenticular in shape with a depressed central region.
lopolith
Adapated from https://en.wikipedia.org/wiki/Lopolith
A phacolith is an intrusion parallel to the bedding plane or foliation of folded country rock. More specifically, it is a typically lens-shaped intrusion that occupies either the crest of an anticline or the trough of a syncline.
phacolith
Adapated from https://en.wikipedia.org/wiki/Phacolith
A tabular sheet intrusion that has intruded between older layers of sedimentary rock, beds of volcanic lava or tuff, or along the direction of foliation in metamorphic rock.
sill
A process whereby the precursors of rock, such as magma or sedimentary particles, fill a fracture in a mass of rock.
rock-precursor intrusion process
An environmental system which can sustain and allow the growth of an ecological population.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
An area of a planet's surface which is primarily composed of water ice, present throughout multiple years, in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
This class covers part of the NLCD "Perennial Ice/Snow" class.
area of perennial water ice
A process during which materials deemed as waste are separated and converted into a form which can be used as input by the same processes which generated them.
Recycling-Prozess
proceso de reciclaje
processo di riciclo
資源回收
This has been created for SDGIO. Revision is likely, but the general meaning should be stable. The frame of reference for determining what is 'waste' and what is a 'resource' is unclear.
recycling process
A carbon emission process is any environmental process which outputs a carbon-bearing gas.
Requested for SDGIO. Likely to be revised.
carbon-bearing gas emission process
A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems.
An SDGIO request. Likely to be refined and revised. This looks like an aggregate class, subsuming a range of processes which can lead to degradation.
These anthropogenic ecosystems may include urban or other built-up settlements or anthropogenic ecosystems used for activities such as forestry or agriculture.
land consumption process
Adapted from EEA (1997) The concept of environmental space, Copenhagen, URL: http://www.eea.europa.eu/publications/92-9167-078-2/at_download/file
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
human dwelling
https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015
An area of a planet's surface which is primarily composed of snow, present throughout multiple years, in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
area of perennial snow
An area of a planet's surface which is primarily composed of snow or water ice, present throughout multiple years, in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, these areas are characterised by ice and/or snow cover generally greater than 25% of total cover. The definition of perennial needs clarification.
area of perennial ice or snow
A solid layer which is composed primarily of loose, heterogeneous, superficial material covering solid rock.
The various parts of the regolith are highly variable. Perhaps some sort of "unconsolidated" quality should be used here with "environmental material" to cover this scope. Note that organisms, their parts, or their derivatives are also included.
Regolith typically includes dust, soil, broken rock, and similar materials, but can be highly variable.
regolith
A layer of igneous, sedimentary, and metamorphic rocks that forms continents and the areas of shallow seabed close to their shores, known as continental shelves.
This is an Earth-centred class, but can be generalised to include other planetary bodies.
On Earth, all continental crust ultimately derives from the fractional differentiation of oceanic crust over many eons.
continental crust
Oceanic crust is the uppermost layer of the oceanic portion of a tectonic plate.
oceanic crust
The Mohorovicic discontinuity, usually referred to as the Moho, is the boundary between the Earth's crust and the mantle, indicating a change in composition.
This is and Earth-centred definition, but can likely be applied to other differentiated planetary bodies.
Mohorovicic discontinuity
A lithified mass of rock that lies under the loose softer material (regolith) at the surface of the Earth or other terrestrial planet.
bedrock
An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
The range of entities that are considered "barren land" are not exhaustive, making axiomatisation risky at this stage.
According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition.
area of barren land
A hollow tower of ice formed by the freezing of steam escaping a fumarole.
fumarole-derived ice tower
A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes.
This may not need to be in the atmosphere, also note that "meteor" will do much of the same work.
Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas.
aeroform
A cloud is a visible mass of aerosolised liquid droplets or frozen crystals suspended in an atmosphere above the surface of a planetary body.
On Earth clouds are formed by the saturation of air in the homosphere when air cools or gains water vapor. Please use the "water-based cloud" class and its subclasses for Earth's clouds. Note that this class describes clouds as countable objects, rather than 'cloud material'. It also refers only to clouds made up of a water-based material.
cloud
Polar stratospheric clouds are clouds which form in the winter polar stratosphere at altitudes of 15,000–25,000 metres and which support chemical reactions that produce active chlorine and remove gaseous nitric acid, catalysing ozone destruction.
This class should be linked to ozone layer depletion processes.
polar stratospheric cloud
A settlement with a low density of buildings and inhabitants.
The thresholds for what makes a settlment "sparsely populated" can be determined as needed. These are usually "sparse" in relation to urban environments. If there is a specific threshold that should be added to ENVO, please make a new class request.
sparsely populated settlement
A settlement which has lower population density than a town, city, or other urban environment and is primarily used for agricultural or pastoral activity.
A class created fro SDGIO. The definition of rural is highly varied, dealing with areas, settlements, and populations interchangeably. The 'rural' classes in ENVO aim to clarify these differing definitions. See issue #272.
rural settlement
A settlement which has been established and is managed through officially sanctioned processes and is recognised as legal by a competent authority.
This is merely a defined class and should not have too many subclasses.
formal settlement
A settlement which is not associated with or directed by official planning processes and which typically lacks municipal services and infrastructure such as sanitation, water services, and waste management services.
Can a formerly formal settlement become an informal settlement?
Informal settlements need not be illegal.
informal settlement
A settlement on land that the inhabitants have a legal claim to.
legal settlement
A settlement on land that the inhabitants have no legal claim to or occupy illegally.
illegal settlement
Forest which originally covered a region before changes in the environment brought about by people. (Source: PHC)
primary forest
A carbon emission process is any environmental process which releases carbon dioxide gas into the atmosphere.
Requested for SDGIO. This class may be revised in future once the offical definitions become more clear.
carbon dioxide emission process
A volume of carbon dioxide gas emitted by a carbon dioxide emission process.
This is a working definition for #280. Which processes will ultimately be included in the axioms is still open.
carbon dioxide emission
A road which is usable across all seasons.
Created for SDGIO, indicator 9.1.1. See #272.
all season road
An area which is outside of a town, city, or urban area. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.
rural area
A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
This class may be split. "urban village" doesn't sit well and prevents relations to village biomes.
village
oligotrophic lake
A lake with medium nutrient levels, which allow moderate productivity.
What constitutes a "medium" nutrient level is subject to debate. The thresholds should be set either on a data level or through new subclasses.
mesotrophic lake
A mass of solid material which is primarily composed of plastic.
Plastikstück
pedazo de plástico
pezzo di plastica
piece of plastic
A plastic pellet which is produced such that its size allows it to be rapidly melted and used as input for further downstream manufacturing processes.
nurdle
An environmental zone which contains, as determined by an officially mandated selection process, one or more ecosystems which include, as parts, ecological communities of global significance for conservation due to their vulnerability and irreplaceability.
The narrow synonyms will be made into subclasses in their own right.
Ecologically and Biologically Significant Area
IUCN Important Site for Freshwater Biodiversity
Important Site for Freshwater Biodiversity
The selection process which determines the whether an area is an important site must follow the best practice specifications and guidelines developed by the International Union for Conservation of Nature (IUCN), using globally standardised criteria and thresholds. Note that the label 'important site' is chosen to align with SDGIO. The definition is that of "key biodiversity area".
The system of public works in a country, state or region, including roads, utility lines and public buildings.
We label this as 'public infrastructure', as the OECD definition refers specifically to public constructed features. The parts of public infrastructure are not exhaustive and should be extended as needed.
public infrastructure
This class is created for the SDGIO and the 'public infrastructure' class. The publically accessible attribute could be axiomatised.
public road
A building which is publically accessible.
Created for SDGIO, we treat "public" as "publically accessible" where the semantics of access are dealt with in SDGIO.
public building
A cable used to trasmit electricity from its point of production to its point of consumption.
utility line
A utility line which services the public power grid.
public utility line
A populated place where groups of housing units have been constructed on land that the occupants have no legal claim to, or occupy illegally, or where dwellings are not in compliance with current planning and building regulations.
Informal settlements may be urban or rural.
illegal informal settlement
A planned process during which a portion of environmental material is removed from a material entity.
Created for SDGIO and intended to be a more general form of resource extraction process.
material extraction process
A fire is a process whereby rapid and exothermic oxidation of a material through a combustion process releases heat, light, and other products.
Not to be confused with a flame - the visible portion of gas released by a fire . Oxidation processes such as rusting or biological digestion are not subsumed here.
fire
A conflagration which is uncontrolled and combusts material in a vegetated area, be it rural or wild.
The definition of "wildland" or "wild" is ambiguous.
wildfire
A fire which occurs in a large spatial area poses a risk to human life, animal life, health, and/or property.
conflagration
A portion of gas which is emitted by a fire or other exothermic reaction, is of increased temperature, and typically emits light in the visible range.
flame
A flame which is produced by the combustion of hydrocarbon fuel.
hydrocarbon flame
A wildfire which occurs in a forest, primarily consuming vegetation as fuel.
forest fire
A process whereby a large volume of gas moves due to a disequilibrium of physical forces.
This class refers to all forms of "wind": from the familiar movement of air in the Earth's atmosphere to the solar wind. Use a subclass to be more precise.
mass gaseous flow
A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria.
atmospheric wind
A stream of plasma primarily composed of electrons, protons, and alpha particles ejected from the upper atmosphere of a star.
stellar wind
A mass gaseous flow in which planetary atmospheric gases flow into outer space.
planetary wind
A process whereby a large volume of plasma moves due to a disequilibrium of physical forces.
mass plasma flow
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gaseous environmental material
A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields.
An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88
plasma
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
Considerable debate on the definition of planet exists.
planet
An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces.
Add qualities such as spherical. Request NTRs if not available in PATO.
star
An astronomical body which orbits a planet of comparatively greater mass.
At times, a moon is equated to a natural satellite, however, the latter class includes a broader range of entities. Here, we currently separate moons from other satellites. We can create a logical definition of satellite using an orbital process class.
planetary moon
This class is hard to define and is sometimes treated as equivalent to 'minor planet'.
asteroid
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
There is a need to account for open star clusters which are not gravitationally bound. This would need a superclass other than 'astronomical object', as currently defined.
globular star cluster
An interstellar cloud of dust, hydrogen, helium and other ionized gases
nebula
A galaxy is a gravitationally bound system of stars, stellar remnants, interstellar gas, dust, and dark matter.
galaxy
An astronomical body which is in direct orbit of a star and is massive enough for its own gravity to compress it into a shape preserved by hydrostatic equilibrium (usually a spheroid), but which shares its orbit with other bodies, such as asteroids or comets.
Considerable debate on this definition exists.
dwarf planet
A minor planet is an astronomical object in direct orbit around the Sun that is neither a planet nor exclusively classified as a comet. Minor planets can be dwarf planets, asteroids, trojans, centaurs, Kuiper belt objects, and other trans-Neptunian objects.
This definition is in need of revision - it relies on negation and seems to straddle class and instance level. The definitional space here is contested and quite inhomogeneous.
"Before 2006, the IAU had officially used the term minor planet. During its 2006 meeting, the IAU reclassified minor planets and comets into dwarf planets and small Solar System bodies (SSSB). Objects are called dwarf planets if their self-gravity is sufficient to achieve hydrostatic equilibrium and form an ellipsoidal shape. All other minor planets and comets are called small Solar System bodies. The IAU stated that the term minor planet may still be used, but the term small Solar System body will be preferred. However, for purposes of numbering and naming, the traditional distinction between minor planet and comet is still used."
minor planet
planetary atmosphere
A planetary atmosphere which is composted primarily of dinitrogen and dioxygen gas.
An instance of this class would be Earth's atmosphere.
nitrogen-oxygen planetary atmosphere
A desert surface covered with closely packed, interlocking angular or rounded rock fragments of pebble and cobble size.
desert pavement
A material part of an astronomical body.
Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension.
Note that material entities may have immaterial entities (e.g. sites) as parts.
This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed.
Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.
astronomical body part
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
This is a defined class: most of its subclasses will not be asserted, but filled by inference.
liquid environmental material
An area of a planet's surface which is primarily covered by a forest in which the majority of trees shed foliage simultaneously in response to seasonal change. The surfaces of this area (including the surface of the forest canopy) are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of deciduous forest are dominated by trees generally greater than 5 meters tall, and making up more than 20% of total vegetation cover. The NLCD 2011 continues to state that more than 75% of these trees should shed foliage simultaneously in response to seasonal change. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of deciduous forest
An astronomical body part which includes all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
hydrosphere
An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere.
pedosphere
An astronomical body part which is composed of those parts of a star, distal from the star's core, from which light is radiated into space.
photosphere
A planetary part which is exposed, at least periodically, to light.
In some literature, the term photosphere is used; however, this is more correctly reserved for a part of a star.
planetary photic zone
An astronomical body part which includes those parts of a biosphere that are, at least periodically, illuminated and in which photosynthesis may occur.
Somewhat awkward at the moment, see #314.
illuminated biosphere part
A lake from which water constantly flows out of under almost all climatic circumstances, maintaining low concentrations of dissolved solid relative to endorheic lakes.
exorheic lake
A part of a building roof which overhangs the face of a wall and, normally, projects beyond the side of a building.
The primary function of the eaves is to keep rain water off the walls and to prevent the ingress of water at the junction where the roof meets the wall. The secondary function is to control solar penetration; the eaves overhang can be designed to adjust the building's solar heat gain to suit the local climate, the latitude and orientation of the building, refer to passive solar building design. The eaves overhang may also shelter openings to ventilate the roof space.
eaves
Overhanging eaves where the rafters and underside of the roof are visible from below.
open eaves
Eaves in which projecting roof members are not visible, being closed from view by boarding.
closed eaves
Air which has increased levels of water vapour.
humid air
Air which has a partial pressure of water vapour equal or near equal to its equilibrium vapor pressure at a given temperature.
"Near equal" is meant to reflect that there will be fluctuations around the equilibrium point.
water vapour saturated air
A hydrological precipitation process in which atmospheric water vapour condenses to form droplets of liquid water massive enough to fall to a planetary surface due to the planet's gravity.
This is the process which typically happens on Earth. Other planets may have different liquids involved in the process.
water-based rainfall
A droplet is a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid.
No attempt is made to differentiate between drops and droplets. This may be added, if requested.
droplet
A droplet formed by condensation of vapour in an atmosphere and which is sufficiently massive to overcome atmospheric resistance and fall to a planetary surface due to gravity.
raindrop
A defined class which should be filled by inference.
water droplet
This is the class intended for use when describing raindrops on Earth. These typically have a diamter of 0.1 to 9 millimetres.
water raindrop
A droplet which is spherical in shape and suspended in an atmosphere, being of too small a mass to be pulled to a planetary surface by gravity.
cloud droplet
A cloud droplet composed primarily of water.
water-based cloud droplet
A process in which precipitation falls from a cloud but evaporates or sublimes before making contact with a planetary surface.
virga
Smoke is a collection of airborne solid and liquid particulates and gases emitted when a material undergoes combustion or pyrolysis, together with the quantity of gas that is entrained or otherwise mixed into the mass
smoke
Combustion or burning is a high-temperature exothermic redox chemical reaction between a fuel and an oxidant that produces oxidized, often gaseous products, in a mixture termed as smoke.
Unlike the "combustion" class in the Chemical Methods Ontology, this class is not necessarily a planned process. http://purl.obolibrary.org/obo/CHMO_0001473
combustion process
A chemical decomposition (the separation of a single chemical compound into its two or more elemental parts or to simpler compounds) caused by heat.
thermolysis
A thermolysis process in which organic material is decomposed in the absence of oxygen.
pyrolysis
A fog which is intermixed with smoke or other combustion products and their derivatives.
smog
An area of a planet's surface which is primarily covered by a forest in which the majority of trees maintain their foliage despite seasonal change. The surfaces of this area (including the surface of the forest canopy) are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of evergreen forest are dominated by trees generally greater than 5 meters tall, and making up more than 20% of total vegetation cover. The NLCD 2011 continues to state that more than 75% of these trees should maintain their foliage despite seasonal change - the canopy is never without green foliage. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of evergreen forest
A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.
Fog is more opaque than mist, reducing visibility to under one kilometre. This class refers only to fog formed by materials primarily composed of water. "Fog can be considered a type of low-lying cloud and is heavily influenced by nearby bodies of water, topography, and wind conditions. In turn, fog has affected many human activities, such as shipping, travel, and warfare." https://en.wikipedia.org/wiki/Fog
fog
A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.
This class refers to a portion of crystal and not an individual crystal.
crystal
A crystal which is primarily composed of water ice.
Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions.
water ice crystal
A type of water ice that forms on dead wood with the assistance of the fungus Exidiopsis effusa and takes the shape of fine, silky hair.
hair ice
A vegetated area which includes a community of flowering plants that provide food for local pollinators.
This may or may not be an anthropogenic environment, but its boundaries are maintained by human activity.
Flower strips are often the last refuge organsims whose habitats have been replaced by croplands, urban areas, and othe anthropogenic environments. This has considerable consequences for pollination and other ecosystem services.
flower strip
A flower strip which is present at the margins of cultivated fields.
flower-rich field margin strip
A material which is primarily composed of a substance arranged as a lattice which can trap or contain other molecules.
Not sure if this should be a subclass of crystal. If it is removed, remember to assert that it is a solid.
This class is not to be confused with CHEBI's "clathrate". The latter refers to the pure substance, while this class refers to clathrates found in nature. "Traditionally, clathrate compounds are polymeric and completely envelop the guest molecule, but in modern usage clathrates also include host-guest complexes and inclusion compounds." https://en.wikipedia.org/wiki/Clathrate_compound
clathrate material
A clathrate material in which a large amount of methane is trapped within a crystal structure of water, forming a solid similar to ice.
methane clathrate
An environmental process in which coral expels the symbiotic algae living in its tissue as a result of stress, causing the coral to turn white.
Add relations to coral organisms in NCBI taxonomy.
coral bleaching process
Marl is a mass of calcium carbonate derived from mollusk shells and mixed with silt and clay.
A request from the Agronomy Ontology in Issue #345.
marl
A marine coral reef biome which is located in a region with a tropical climate.
tropical marine coral reef biome
An area of a planet's surface which is primarily covered by a forest in which the trees are a mixture between those that lose and retain their foliage despite seasonal change. The surfaces of this area (including the surface of the forest canopy) are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of mixed forest are dominated by trees generally greater than 5 meters tall, and making up more than 20% of total vegetation cover. The NLCD 2011 continues to state that neither deciduous or evergreen trees make up more than 75% of the total tree cover. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of mixed forest
A marginal sea biome which is located in a region with a temperate climate.
A component of the WWF Temperate Shelf and seas ecoregions grouping
temperate marginal sea biome
A mediterranean sea biome which is subject to temperate climate patterns.
temperate mediterranean sea biome
A marine biome which contains communities adapted to living in an environment determined by an upwelling process.
marine upwelling biome
A marine upwelling biome which is subject to tropical climate patterns.
tropical marine upwelling biome
A marine upwelling biome which is located in a region subject to temperate climate patterns.
temperate marine upwelling biome
An area of a planet's surface which is partly covered by shrubs with ground-hugging stems or low growth habit, in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
As noted in Wikipedia: "Because the criteria are matters of degree rather than of kind, the definition of a subshrub is not sharply distinguishable from that of a shrub"
According to the NLCD 2011, areas of dwarf scrub are dominated by shrubs less than 20 centimeters tall with shrub canopy typically greater than 20% of total vegetation. This type is often co-associated with grasses, sedges, herbs, and non-vascular vegetation. The NLCD 2011 notes that this is intended as an Alaska only land cover. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of dwarf scrub
A turbulent surface layer of a water body maintained by strong currents setting over submerged ridges or shoals or by winds opposing a current.
This should likely be a part of the surface layer rather than a subclass.
turbulent aquatic surface layer
A structure which is built into the container of a water body which allows water to flow out of the container when the volume of the water contained exceeds that of its cavity.
overflow structure
A site at the terminus of a liquid conveyance conduit where the liquid carried is discharged into the sea or a river.
mouth of liquid discharge conduit
An electric power system is a network of electrical components used to supply, transfer and use electric power.
electric power system
A photovoltaic system is a power system designed to supply usable solar power by means of photovoltaics. It consists of an arrangement of several components, including solar panels to absorb and convert sunlight into electricity, a solar inverter to change the electric current from DC to AC, as well as mounting, cabling and other electrical accessories to set up a working system.
photovoltaic system
A group of solar panels, typically belonging to the same photovoltaic system, arranged to maximise interception of solar radiation.
solar panel array
A solar panel array that is integrated into the power system of a human dwelling.
domestic solar panel array
An area of a planet's surface which is primarily covered by a shrubs, young trees, or stunted trees.. The surfaces of this area are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of scrub or shrub are dominated by shrubs; less than 5 meters tall with shrub canopy typically greater than 20% of total vegetation. This class includes true shrubs, young trees in an early successional stage or trees stunted from environmental conditions. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of scrub
A process in which a solid planetary surface is deformed.
This is a class to be filled by inference.
ground deformation process
A puddle is a small accumulation of water, on a surface. It can form either by pooling in a depression on the surface, or by surface tension upon a flat surface.
This class refers only to puddles of water, see https://github.com/EnvironmentOntology/envo/issues/337
puddle of water
Ballast water is water contained in the ballast tanks of sea-going vessels.
This definition could be improved, as ballast water is often used in more general ways, beyond the water contained in a ballast tank at any given time. For example, water which has just been released from a ballast tank is often still refered to as ballast water.
ballast water
A ballast tank is a compartment within a boat, ship or other floating structure that holds water, which is used as ballast to provide stability for a vessel.
ballast tank
A hydrological process during which hail stones fall to the surface of an astronomical body.
This is Earth-centric for the moment, other types of hail (methane etc) exist
hailfall
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.
The threshold of what constitutes "strong" perturbation is not defined here due to considerable semantic variation. If a specific threshold is required, please request a new term.
storm
An atmospheric storm is a process in which a portion of an astronomical body's atmosphere is strongly perturbed from its prevaling weather.
atmospheric storm
An atmospheric storm which occurs in cumulonimbus clouds and during which lightning and thunder occur.
Thunderstorms may or may not involve processes which result in strong winds, heavy rain, snow, sleet, hail, or other forms of precipitation.
thunderstorm
An atmospheric storm during which intense rainfall occurs.
rainstorm
An atmospheric storm during which intense hailfall occurs
hailstorm
An atmospheric storm during which intense snowfall occurs.
snowstorm
An atmospheric storm during which freezing rain falls and accumulates as ice on exposed surfaces.
Note it is a hazard, could perhaps later link to https://github.com/Vocamp/Hazard or https://github.com/Vocamp/Hazard/blob/master/concept-map/ModifiedHazardousSituation.png and https://github.com/SDG-InterfaceOntology/sdgio/issues/14
glaze storm
ice storm
silver storm
glaze event
silver thaw
Icestorms are associated with multiple hazards. Significant accumulations of ice pull down trees and utility lines resulting in loss of power and communication. These accumulations of ice make walking and driving extremely dangerous. Significant ice accumulations are usually accumulations of 0.25 inch or 0.60 cm or more. Has synonyms silver storm, glaze storm.
The U.S. National Weather Service defines an ice storm as a storm which results in the accumulation of at least 0.25-inch (6.4 mm) of ice on exposed surfaces.
icestorm
Hauer RJ, Dawson JO, Werner LP (2006) Trees and Ice Storms - The Development of Ice Storm-Resistant Urban Tree Populations (2 ed.). College of Natural Resources, University of Wisconsin–Stevens Point, and the Department of Natural Resources and Environmental Sciences and the Office of Continuing Education, University of Illinois at Urbana-Champaign. http://web.extension.uiuc.edu/forestry/publications/pdf/urban_community_forestry/trees_and_ice_storms_2006.pdf
An area of a planet's surface which is primarily covered by cultivated or anthropically maintained vegetation planted for recreation, erosion control, or aesthetic purposes interspersed by constructed or manufactured objects and materials. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
This class is in need of refinement, particularly in linking to other entities in the ontology. This would be helped by more clear listings of entities included in this classification. However, the class is suitable for use in annotating remotely sensed land types.
According to the NLCD 2011, areas of developed open space are dominated by vegetation such as lawn grasses and include large-lot single-family housing units, parks, golf courses. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover less than 20% of the area. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of developed open space
An area of a planet's surface which is primarily covered by cultivated or anthropically maintained vegetation and by constructed or manufactured objects and materials covering up to approximately half its extent. Such areas are used for low intensity purposes such as accommodating collections of single-family residential units. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of developed space under low intensity usage are dominated by vegetation such as lawn grasses and include collections of single-family housing units. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover between than 20 - 49% of the area. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition.
area of developed space with low usage intensity
An area of a planet's surface which is primarily covered by constructed or manufactured objects and materials covering from half to three-forths of its extent and by cultivated or anthropically maintained vegetation. Such areas are used for medium intensity purposes such as accommodating dense collections of single-family residential units. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of developed space under medium intensity usage are dominated by vegetation such as lawn grasses and include collections of single-family housing units. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover between than 50 - 79% of the area. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition.
area of developed space with medium usage intensity
An area of developed space used for high intensity purposes such as accommodating dense and multi-occupant residential, commercial, and industrial units. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, areas of developed space under high intensity usage are dominated by constructed features where humans reside and work. Examples include apartment complexes, row houses and commercial/industrial facilities. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover between than 80 - 100% of the area. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition.
area of developed space with high usage intensity
An area of a planet's surface which is primarily covered by sedges or forbs, possibly interpersed with grasses or grass-like plants. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
This class is in need of refinement, particularly in linking to other entities in the ontology. However, it is suitable for use in annotating remotely sensed land types.
According to the NLCD 2011, at least 80% of these areas are covered by sedge or forbs. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that land covered by sedge tundra and sedge tussock tundra are subsumed in this category. The original definition notes that this is intended as an "Alaska only" category.
area of sedge- and forb-dominated herbaceous vegetation
An area of a planet's surface which is primarily covered by gramanoid or herbaceous vegetation and which is not subject to intensive management by humans. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 80% of these areas are covered by grasslands or non-woody, herbaceous plants. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that, while no "intensive" management such as tilling is performed in these areas, they may be used for grazing.
area of gramanoid or herbaceous vegetation
An area of a planet's surface which is primarily covered by fruticose or foliose lichens and which is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 80% of these areas are covered by lichens. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The original definition notes that this is intended as an "Alaska only" category.
area of lichen-dominated vegetation
An area of a planet's surface which is primarily covered by mosses and which is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 80% of these areas are covered by mosses. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The original definition notes that this is intended as an "Alaska only" category.
area of moss-dominated vegetation
An area of a planet's surface which is partly covered by planted grasses, legumes, or mixtures of grass and legumes and used for livestock grazing or the production of seed or hay crops. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 20% of these areas are covered by pasturelands or hayfields. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD also notes that the crops are grown on a perennial cycle in these areas.
area of pastureland or hayfields
An area of a planet's surface which is partly covered either by annual crops and perennial woody crops or by actively tilled land. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 20% of these areas are covered by croplands or actively tilled land. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD provides corn, soybeans, vegetables, tobacco, and cotton as examples of annual crops and the trees and vines in orchards and vineyards as examples of perennial woody crops.
area of cropland
An area of a planet's surface which is partly covered by forest or shrubland vegetation and where the underlying soil or substrate is periodically saturated with or covered by water. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 20% of these areas are covered by forest or shrubland vegetation. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition.
area of woody wetland
An area of a planet's surface which is primarily covered by perennial herbaceous vegetation and where the underlying soil or substrate is periodically saturated with or covered by water. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 80% of these areas are covered by herbaceous vegetation. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition.
area of emergent herbaceous wetland
A hydrological process in which irregular aggregates of snow fall to the surface of an astronomical body.
This is currently bound to water-based snow on Earth, may need revisions for interplanetary applications
snowfall
Water-based rainfall which freezes either 1) on impact with a surface to form a coating of clear ice (glaze) or 2) after percolating through surface layers.
This term exists, we're revising the definition with ESIP semantic Harmonization group, delete the old one. Consider adding axioms like PATO:"decreased temperature" to this and other cold forms of precipitation, such that we can create a grouping class to be filled by inference (with hail, sleet, snow, freezing rain). Something like precipitation below the liquid-solid phase transition point of water.
A surface temperature inversion is usually required. In such an inversion, the surface must have a temperature below freezing, while the temperature of the atmosphere where the precipitation forms is above freezing. Alternately, if the temperature of the ground surface and glazed objects is typically near or below freezing (0C or 32F), it is necessary that the water drops be supercooled before striking. Freezing rain can sometimes occur on surfaces exposed to the air (such as tree limbs) with air temperatures slightly above freezing in strong winds. Local evaporational cooling may result in freezing. Freezing rain frequently occurs, therefore, as a transient condition between the occurrence of rain and ice pellets (sleet). When encountered by an aircraft in flight, freezing rain can cause a dangerous accretion of clear icing. In aviation weather observations, this hydrometeor is encoded ZR by NOAA.
freezing rainfall
A process during which a sudden flow of electricity occurs, often accompanied by a visible release of photons, between two electrically charged objects due to contact, an electrical short, or dielectric breakdown.
This should probably be moved to an ontology of physical processes when one is created, and be imported back into ENVO.
electrostatic discharge process
A sudden electrostatic discharge which occurs during an electrical storm as differentially charged atmospheric entities equalise their charge.
atmospheric lightning
A lightning process during which electrostatic discharge occurs between at least two clouds.
intercloud lightning
A lightning process during which electrostatic discharge occurs within a single cloud.
intracloud lightning
A lightning process during which electrostatic discharge occurs between a cloud and an object on a planetary surface, or a planetary surface itself.
lightning strike
A lightning process during which electrostatic discharge occurs within a single cloud or between multiple clouds.
lightning flash
A blizzard is a severe snowstorm during which snowfall is transported by strong winds, sustained for several hours.
boulbie
buran
purga
The U.S. National Weather Service specifies sustained wind or frequent gusts of 16 m per second (30 kt or 35 mi per hour) or greater, accompanied by falling and/or blowing snow, frequently reducing visibility to less than 400 m (0.25 mi or 0.4 km) for 3 hours or longer. Earlier definitions also included a condition of low temperatures, on the order of -7C (20F) or lower, or -12C (10F) or lower (severe blizzard). The name originated in the United States but it is also used in other countries. In the Antarctic the name is given to violent autumnal winds off the ice cap. In southeastern France, the cold north wind with snow is termed blizzard (see also boulbie). Similar storms in Russian Asia are the buran and purga. In popular usage in the United States and in England, the term is often used for any heavy snowstorm accompanied by strong winds.
To qualify a snowstorm as a blizzard, some sources require the windspeed to be at least 56 km/h and the duration of the storm to be at least three hours. We set no such hard boundaries in this definition, as this should be done with reference to local standards.
blizzard
A ground blizzard is a storm during which snow which has settled on a planetary surface is resuspended in and transported through its atmosphere by strong winds, sustained for several hours.
This form of blizzard does not involve snowfall as the snow which is blown by the winds is already present on the ground. To qualify a snowstorm as a blizzard, some sources require the windspeed to be at least 56 km/h and the duration of the storm to be at least three hours. We set no such hard boundaries in this definition, as this should be done with reference to local standards.
ground blizzard
A lentic water body which is used for the artificial culture of shrimp.
There are multiple subclasses possible for this term, including ponds managed by the traditional (extensive), improved traditional (semi-intensive), and intensive methods of cultivation.
"Shrimp" is a common language term that may refer to multiple crustacean species, typically in the groups Caridea or Dendrobranchiatamarine. These may be marine or freshwater organisms.
shrimp pond
A process during which humans rear animals or plants in bodies of water for harvest and consumption.
Expand the sites of occurrence listed as axioms as new terms emerge.
In 1988, the FAO introduced a definition of aquaculture which reduces its confusion with capture fisheries: Aquaculture is the farming of aquatic organisms, including fish, molluscs, crustaceans and aquatic plants. Farming implies some form of intervention in the rearing process to enhance production, such as regular stocking, feeding, protection from predators, etc. Farming also implies individual or corporate ownership of the stock being cultivated. For statistical purposes, aquatic organisms which are harvested by an individual or corporate body which has owned them throughout their rearing period contribute to aquaculture, while aquatic organisms which are exploitable by the public as a common property resources, with or without appropriate licences, are the harvest of fisheries.
aquaculture process
An archeological site which contains holes humans had dug in the ground, or their remnants, for the purpose of storing and distributing food, drink, and both functional or ritualistic implements during communal eating and drinking.
Feasting pits had a wide variety of social functions throughout time, which extended in scope from the single family group to multiple tribes or villages.
feasting pit site
Pappa, M., Halstead, P., Kotsakis, K., & Urem-Kotsou, D. (2004). Evidence for large-scale feasting at Late Neolithic Makriyalos, N Greece. Food, cuisine and society in prehistoric Greece, 5, 16.
Romero, D., & Lauzon, A. (2015). The Art of Feasting: Style and Identity in a Ritual Area at the Harris Site. In. In L. Ludeman (Ed.), Collected Papers from the 18th Biennial Mogollon Archaeology Conference (pp. 43-50). Las Cruces, New Mexico: Privately published by Lonnie Ludeman.
A river which is heated by geothermal processes such as heat exchange with lava or hydrothermal percolation.
A key example is the Boiling River, or Shanay-timpishka, of the Peruvian Amazon. This river is of high cultural significance and is protected by the shaman of the small town Mayantuyacu, a secluded healing center.
geothermally heated river
A surface layer of a solid environmental material which is formed by the presence and activity of photosynthetic microbial assemblages colonising it.
biocrust
A biocrust which is formed by photosynthetic microbial assemblages colonising the surface layer of a portion of arid soil. Through their successional dynamics, these communities reduce the soil surface's albedo, impart it with stability against erosion, modify its hydrology, and promote its fertility.
Couradeau et al. (2016) assert that any albedo reductions associated with biocrust development are due largely to the accumulation of the microbial sunscreen, scytonemin.
soil biocrust
An electronic telecommunications device that enables the customers of a financial institution to perform financial transactions, particularly cash withdrawal, without the need for a human cashier, clerk or bank teller.
automated teller machine
A solid or liquid particle, usually 0.2 micrometers in diameter, on which water vapour condenses, seeding cloud formation.
cloud condensation nucleus
A process during which a solid particle or liquid droplet catalyses the condensation of water vapour in an atmosphere.
nucleation of cloud condensation
An environmental zone which overlaps a glacier or an ice sheet, and in which ice loss exceeds ice gain.
ice ablation zone
A material decumulation process during which the mass of an existing ice mass decreases in size.
Ice loss could likely become a defined class with some equivalence axioms linking it to processes, along the lines of: 'has part' some (icemelt or 'ice calving process' or 'water ice sublimation process').
ice loss process
A mass wasting process during which refuse from human activities, usually accumulated at a dumping site, falls down a slope under the force of gravity.
Of interest to sustainable development goals, linking production and consumption to human health and environmental impacts.
"At least 48 people have been killed in a landslide at a vast rubbish dump on the outskirts of Ethiopia's capital Addis Ababa, officials say...Hundreds of people attempt to make a living by scavenging at the landfill site, sifting through the rubbish for items they can sell, the BBC's Emmanuel Igunza in Addis Ababa reports" BBC Africa reports
rubbish landslide
A process during which a part of an ice mass breaks away from the main mass.
ice calving process
An animal house which is only partially surrounded by a building envelope.
open animal house
An ice loss process which occurs in the low-altitude area of a glacier or ice sheet below the firn layer.
glacial ice ablation process
A sublimation process during which water ice transitions into a gaseous state.
water ice sublimation process
An animal house which has a complete building envelope.
closed animal house
A manufactured cage which may be used to confine, contain, or protect an animal.
animal cage
A petting zoo is a zoological garden which contains domesticated non-human animals and some wild non-human animals that are docile enough for humans to touch and feed.
Petting zoos are often nested within a zoological garden featuring wild non-human animals, not docile enough for humans to touch.
petting zoo
An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed.
plumbing drain
A facility in which non-human animals are slaughtered and processed for human consumption.
slaughter plant
butchery
abattoir
A facility in which non-human animals are slaughtered and processed, but not for human consumption.
Animals killed in knacker's yards are not fit for human consumption or can no longer be used to perform work.
knackery
A building which is used to care for a human child during the working day by a person, outside the child's immediate family, other than that child's legal guardians.
daycare building
This is a kind of day care facility. A facility need not be a building.
day care building
A building in which fish are subject to a series of operations to prepare them for human consumption.
This is a kind of fish processing facility. Facilities need not be buildings, factory ships may be considered fish processing facilities.
fish processing building
An environment determined by the presence of a mushroom.
mushroom environment
An ecosystem which bridges two or more adjoining ecosystems and through which organisms may move or propagate.
Ecological corridors may or may not provide habitats for the organisms which move through them. They serve to mitigate the effects of habitat fragmentation by allowing genetic exchange between populations that would otherwise be separated by, e.g., human activity.
ecological corridor
An ecological corridor through which organisms move during a migration process.
Should be axiomatised with PCO's migration process once it is released.
This term refers to the ecosystem(s) the organisms traverse, rather than the spatial track they cover. The latter is better placed in a geospatial ontology.
migration path
A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living.
old people's home
nursing home
A human house which serves as a long-term shelter for its inhabitants and within which they store personal property.
This is under "human house" due to the broad definition of "house".
This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays.
residential building
A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services.
restaurant
A part of an ecosystem which may be or has been used for one or more overnight stays by humans sheltering in tents, camper vans, caravans, or improvised shelters.
This is a very ambiguous term with wide-ranging usage patterns across cultural groups and regions.
campground
A campground which has been modified by humans to provide and maintain facilities for camping such as fire pits, road access, latrines, and garbage bins.
dedicated campground
A campground which has no pre-existing facilities installed or maintained by humans, usually found outside of anthropised ecosystems.
impromptu campground
A manufactured product which may hold a volume of heated water suitable for one or more humans to bathe in, usually for the purposes of hydrotherapy or pleasure.
hot tub
An open system in non-equilibrium with its environment that exhibits time translation symmetry breaking.
While the usage of the term is still debated, the general idea is that time crystals (which have been made using ytterbium ions and defect-bearing diamonds) break temporal symmetry analogously to how mineral crystal break spatial symmetry. While spatial crystals are inhomogeneous in space (vs a gas, which is distributed evenly) due to the ordering of their atoms, the properties of atoms in a time crystal are inhomogeneous in the time dimension.
time crystal
Water which is partially contained within a fissure or a geological fracture.
The axiomatisation should be more tuned to the site within the fissure.
While containment is often enough to classify this subtype of water, it is expected that the water's composition is altered by contact with the solid material bounding the fissure's site.
fissure water
Regions of a planet which are not exposed to the planet's atmosphere or space, often comprising parts of one or more planetary structural layers.
planetary subsurface zone
A region which overlaps parts of one or more planetary structural layers which are located below a continental landmass.
We may have to soften dependence on planetary structural layers as some planets haven't differentiated by density.
continental subsurface zone
A hill which has a surface that is partially or wholly covered by plant communities.
This class will be axiomatised to coordinate with the 'vegetated area' class.
vegetated hill
A piece of plastic which has a diameter less than five millimetres.
This classification is based on the thresholds detailed in GESAMP report # 99 on recommendation from the SDG 14 indicator team. While the definition is in accordance with the common use of this term (as per GESAMP report # 99), alternative size classifications exist. Alternative classifications are a piece of plastic which is between 1 and 5 millimetres in diameter, a piece of plastic which has a diameter less than 1 millimetre, or a piece of plastic which has a diameter greater than 330 micrometres. The use of the word diameter in this case was understood to mean the generalised form of diameter, i.e. the largest distance between two points belonging to an object.
microplastic particle
A microplastic particle which is the direct output of a manufacturing process.
Primäres Mikroplastik
microplastica primaria
microplástico primario
primary microplastic particle
A microplastic particle which is derived from the breakdown of larger plastic debris.
Sekundäres Mikroplastik
microplastica secondaria
microplástico secundario
The debris that make up the Great Pacific Garbage Patch constantly release microplastics as they break down.
secondary microplastic particle
An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions.
There are many subtypes of ecotone, some with sharp transitions and others with gradual, patchy transitions between communities. From Wikipedia:Ecotone - The word ecotone was coined from a combination of eco(logy) plus -tone, from the Greek tonos or tension – in other words, a place where ecologies are in tension.
ecotone
An ecotone which bridges a subpolar coniferous forest biome and a tundra biome.
This assumes, of course, that the planet's or planetoid's poles receive less stellar radiation and/or thermal energy than equatorial regions.
Major vegetational ecotones such as that between the northern edge of the Boreal Forest in North America (or taiga in Russia) and the arctic tundra, known as the arctic tree-line ecotone, are controlled largely by large-scale airmass contrasts and are sensitive to climatic change, as noted by R. A. Bryson (1966). Harvey Nichols, Ph.D. , April 23, 2017 Emeritus Professor of Biology.
polar tree-line ecotone
A woodland which has an understory partially covered by lichen mats and tundra-like vegetation.
lichen woodland
A material transformation process during which water ice is formed.
water ice formation process
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
A process during which a natural environmental system is altered by human action.
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
An ecotone which overlaps at least one biome which supports the growth and persistence of trees and at least one that does not. Before ceasing altogether, tree growth becomes sparse and trees appear stunted as conditions become less favourable along this ecotone.
tree line ecotone
A tree line ecotone across which trees cease to grow due to the low temperatures or duration of snow cover that occur at increased elevations above mean sea level.
alpine tree line ecotone
A tree line ecotone across which trees cease to grow due to insufficient water availability due to a lack of water-based precipitation.
desert tree line ecotone
A tree line ecotone across which trees cease to grow due to insufficient water availability caused by exposure to increased solar radiation and a lack of rainfall.
The lack of rainfall in these ecotones is often due to their elevation above the condensation line of atmospheric water vapour.
desert-alpine tree line ecotone
A tree line ecotone which contains gaps in tree coverage due to decreased biodiversity in tree-forming plant species: gaps are above the alpine tree line for some species yet below the desert tree line for others, and no species with intermediate tolerances are present.
Mountain ranges isolated by oceans or deserts may have restricted repertoires of tree species and contain double tree lines.
double tree line ecotone
A planet that is composed primarily of silicate rocks or metals.
terrestrial planet
A planetary atmosphere which is formed as a result of the accretion of gaseous matter from the accretion disc of the planet's star.
Planets such as Jupiter and Saturn have primary atmospheres. Primary atmospheres are very thick compared to secondary atmospheres like the one found on Earth. The primary atmosphere was lost on the terrestrial planets due to a combination of surface temperature, mass of the atoms and escape velocity of the planet.
primary atmosphere
A planetary atmosphere which has formed as a result of its planet's volcanic activity, or by accumulation of material from comet impacts.
A secondary atmosphere is found on many terrestrial planets such as Mercury, Venus, and Mars. Secondary atmospheres are relatively thin compared to primary atmospheres like Jupiter's. Earth has a tertiary atmosphere due to biotic processes.
secondary atmosphere
A planetary atmosphere which has formed as a result of biotic processes modifying a secondary atmosphere.
This definition cites biotic processes; however, the source indicated that other processes may cause a secondary atmosphere to transition into a tertiary one. More input is needed.
Further processing of a secondary atmosphere, for example by the processes of biological life, can produce a tertiary atmosphere, such as that of Earth.
tertiary atmosphere
A sedimentary rock which is primarily composed of the fossilized, siliceous remains of diatoms mixed with varying amounts of other clays and minerals.
This material is easily crumbled into a fine white to off-white powder. The powder has a particle size ranging from less than 3 micrometres to more than 1 millimetre, but typically 10 to 200 micrometres. The diatoms in each deposit contain different amounts of silica, depending on the age of the deposit. The species of diatom may differ among deposits. The species of diatom is dependent upon the age and paleo-environment of the deposit. In turn, the shape of a diatom is determined by its species. The typical chemical composition of oven-dried diatomaceous earth is 80 to 90% silica, with 2 to 4% alumina (attributed mostly to clay minerals) and 0.5 to 2% iron oxide.
diatomite
A piece of rock which is primarily composed of diatomite: the fossilized, siliceous remains of diatoms mixed with varying amounts of other clays and minerals.
Diatomite is easily crumbled into a fine white to off-white powder. The powder has a particle size ranging from less than 3 micrometres to more than 1 millimetre, but typically 10 to 200 micrometres. The diatoms in each deposit contain different amounts of silica, depending on the age of the deposit. The species of diatom may differ among deposits. The species of diatom is dependent upon the age and paleo-environment of the deposit. In turn, the shape of a diatom is determined by its species. The typical chemical composition of oven-dried diatomaceous earth is 80 to 90% silica, with 2 to 4% alumina (attributed mostly to clay minerals) and 0.5 to 2% iron oxide.
diatomite particle
Wastewater which is produced by industrial activity and which contains chemical contaminants other than those associated with urine and fecal matter.
industrial wastewater
A construction which is designed to hold water in which humans may swim or perform other leisure activities.
constructed swimming pool
A constructed swimming pool which is owned by a non-governmental legal entity or a collective of such entities.
private swimming pool
A constructed swimming pool which is owned by a governmental or state entity.
public swimming pool
A hydraulic-engineering installation which transports water - in specified amounts, of a specified quality, and in accordance with a water-consumption plan - from a source of supply into a conduit.
Sources of water include rivers, lakes, reservoirs, and other water bodies. Conduits include canals, pipelines, and tunnels. Water intakes typically transport water for purposes of hydroelectric power engineering, water supply, or irrigation.
water intake
A building which provides the site for food services with little or no waiting staff furnishing table service.
canteen
cafeteria
A food shop which sells a selection of food products that are not typical dietary components of the human population it is co-located with.
deli
The food products sold in a delicatessen are often considered unusual by the majority of its customers and may come from foreign food supplies which are not widely imported into its region of operation.
delicatessen
A truck which is equipped to cook and sell food.
Due to the facilities on board, food trucks are often larger than other trucks with comparable mechanics.
food truck
A restaurant which provides prepared meals or other food products that the purchaser must eat off its premises.
take-out restaurant
A booth with an open window on one side.
The relation between booths and buildings needs to be clarified. Booth should be its own class.
This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries.
kiosk
A kiosk from which food products are sold.
food kiosk
A manufactured product which is designed to catch and hold animals.
animal trap
An animal trap which consists of a container set flush with the ground such that animals moving along the ground may fall in and be available for examination or collection.
pitfall trap
Barber H (1931) Traps for cave-inhabiting insects. J Elisha Mitchell Sci Soc. 46:259–266.
Hertz M (1927) Huomioita petokuoriaisten olinpaikoista. Luonnon Ystava. 31:218–222.
Mitchell B (1963) Ecology of two carabid beetles, Bembidion lampros (Herbst) and Trechus quadristriatus (Shrank). J Animal Ecol. 32(3): 377-392.
A pitfall trap in which a glass, plastic, or metal container devoid of accumulations of any liquid is used to contain any animal that falls inside.
dry pitfall trap
A pitfall trap in which the container used to hold trapped animals is filled with a liquid solution formulated to hold, kill, and preserve any animal or animals which falls within it.
Aqueous solutions used in these traps include: formalin (10% formaldehyde), alcohol, methylated spirits, trisodium phosphate and picric acid.
wet pitfall trap
A channel of an intermittent stream which contains a river when water supply exceeds evapotranspiration and bed seepage.
channel of an intermittent river
A channel through which a directional flow of water periodically occurs, ceasing when bed seepage or evapotranspiration exceed the available water supply.
channel of an intermittent stream
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
This class can refer to the flow of any material in a liquid phase.
mass liquid flow
A material transport process during which a volume of liquid water is transported due to a disequilibria in physical forces.
water flow process
A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body.
technosphere
A food shop in which food products are the primary offer for sale or trade.
grocery store
A part of an ecosystem which has been allocated to host a gathering of people for multiple entertainment or commercial activities.
A good candidate to draft land use semantics around
Fairgrounds, or parts thereof, may be constructed (e.g. concreted over) or be natural (e.g. clearings or heaths), thus land use is the key differentia.
fairground
A fairground which is used to exhibit agricultural technology, livestock, and farm-related activity.
agricultural fairground
A part of an ecosystem where people gather for the purchase and sale of provisions, livestock, and other goods.
Hierarchies based on land use should replace the anthropogenic feature class once we have a stable rationale.
public market
As with campgrounds and fairgrounds, land use is the key differentia here. The regularity of marketplace activities may provide a differentia for further growth of this branch.
market
A food shop in which the food products on offer are restricted to those produced in a region and cultural setting other than that of the shop's locality.
ethnic food shop
An exchangeable device which can be connected to a plumbing system to deliver and drain water.
plumbing fixture
A plumbing fixture which is bowl-shaped and used for washing hands, dishwashing, and other purposes.
sink fixture
A plumbing fixture which may serve as a container for water in which humans or other animals may bathe.
Of course, there are other uses for bathtubs.
bathtub fixture
A plumbing fixture within which a human or other animal may bathe under a spray of water.
As some showers have no drain, this may cause issues with the definition of plumbing fixture.
Indoors, there is a drain in the floor. Most showers have temperature, spray pressure and adjustable showerhead nozzle. Showering is common in Western culture due to the efficiency of using it compared with a bathtub. Its use in hygiene is, therefore, common practice. A shower uses less water on average than a bath: 80 litres for a shower compared with 150 litres for a bath.
shower fixture
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
manufacturing process
A manufacturing process which occurs on a planet.
Whether this is within the planet's Hill sphere, the region which extends from its exosphere to its core, or some other planetary region is not clear.
See https://github.com/EnvironmentOntology/envo/issues/513 for discussion.
planetary manufacturing process
A dry stream channel through which a river had flowed, but now contains no appreciable accumulations of water.
See http://purl.obolibrary.org/obo/ENVO_01000979 for the channel of an intermittent river.
dry river
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
The nature of "structures" must be further specified.
human-directed construction process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump).
environmental system determined by a material
An environmental system determined by the presence of a plant rhizosphere.
rhizosphere environment
An environmental system which is determined by a living organism.
environmental system determined by an organism
An environmental system determined by a green plant.
plant-associated environment
An environmental system determined by an animal.
animal-associated environment
This class (term) is defined by the lack of a quality (i.e. the lack of salinity or increased osmolarity), which is not best-practice ontologically. Use for annotation is generally discouraged and users should use classes which positively describe the material or environment sampled (i.e. stating the qualities the entity has, rather than those it does not).
non-saline environment
Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.
The definition of aquifer is quite permissive, referencing any water bearing rock or unconsolidated material.
groundwater
A lunar rainbow is a rainbow produced by the refraction of light, which has been reflected from a moon's surface, by water droplets in an astronomical body's atmosphere.
lunar rainbow
A rainbow is a photometeor which consists of a spectral separation of light, formed as a result of the reflection, refraction, and dispersion of light in water droplets suspended in an astronomical body's atmosphere.
The term 'rainbow' is usually used to refer to solar rainbows, but greater specificity should be used when possible.
rainbow
A solar rainbow is a rainbow produced by the refraction of light. which has been emitted by a star, by water droplets in the atmosphere of an astronomical body.
The astronomical body where the rainbow occurs is understood to orbit the star which produces the light which forms the rainbow.
solar rainbow
A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body.
meteor
A meteor that is primarily composed of light.
Requires radiative phenomena to be added for axiomatisation.
photometeor
A meteor which is primarily composed of water.
hydrometeor
A photometeor which is formed as a result of sudden electrostatic discharge in the atmosphere.
This phenomenon is often treated as interchangeable with the process of electrostatic discharge that causes it.
light emitted by lightning
A meteor which is primarily composed of rock.
lithometeor
A rainbow which forms from sunlight which has been reflected off a body of water prior to its interaction with water droplets in an atmosphere.
Not to be confused with a reflected rainbow, which is not a photometeor.
reflection rainbow
A solar rainbow which is formed by a narrow band of wavelengths, the rest of the spectrum having been scattered away by an atmosphere.
monochrome solar rainbow
A rainbow which forms through the interaction of sunlight with the water droplets which constitute fog or clouds; light is diffracted by these droplets such that the photometeor appears almost white with faint reds on the sky-facing side and faint blues on the planet-facing side of the bow.
Often, fogbows are treated as separate from rainbows; however, as the formation processes are much the same, we currently classify these as a subclass of rainbow pending input from domain experts.
fogbow
A photometeor which is formed by wave interference of light refracted within water droplets which constitute mist or clouds and consists of one or more concentric, successively dimmer rings, each of which has red wavelengths distant to the glory's centre and blue wavelengths towards the centre.
This is not to be confused with a circular rainbow, which is formed through different processes.
glory
A photometeor which is produced by light that is reflected, refracted, and dispersed by ice crystals, capable of acting as prisms and mirrors, suspended in an astronomical body's atmosphere.
halo
Water which has a very high concentration of nutrients.
The thresholds of eutrophy are fluid and often locally defined.
hypereutrophic water
A lake which is composed primarily of water with very high nutrient concentrations.
hypereutrophic lake
A lake which is primarily composed of water with a concentration of dissolved salts greater than that of ocean water.
hypersaline lake
A lake which is composed primarily water with high concentrations of humic substances and organic acids, resulting in brown- or tea-coloured colouration.
In response to historical misuse of the term in literature, these lakes are better referred to as "humic lakes". Although dystrophic lakes are often considered acidic and nutrient-poor (oligotrophic), these lakes actually vary greatly in terms of both pH and productivity. Due to the low pH associated with dystrophic lakes, few bacterial species and other aquatic life are able to survive. They are common in the taiga of North America and Eurasia.
humic lake
A lake which has formed as the result of processes that are not or are only minimally driven by human activity.
This class is to be filled by inference.
natural lake
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions).
radiation
A radiation process during which energy is transmitted or emitted by means of fast-moving subatomic particles.
particle radiation
A particle radiation process during which subatomic particles move in the same direction.
particle beam radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy.
electromagnetic radiation
A radiation process during which mechanical waves generated by oscillations radiate through an environmental material.
The mechanical waves generated by this process are also referred to as pressure waves.
acoustic radiation
Sediment which has its porespace filled by water which has very low levels of sodium chloride and/or other salts.
We do not specify numeric thresholds for saline vs. non-saline here, as this is variable. Consider specifying this on the information and/or data layer for your purposes. If you require an ENVO class with a fixed threshold, please request one using our issue tracker.
sediment permeated by freshwater
An environmental system which has its properties and dynamics determined by feces.
fecal environment
The label of this EMPO class is ambiguous, but pers. comm. with L Thompson (http://orcid.org/0000-0002-3911-1280) reveals that this is essentially limited to fecal samples.
An environmental system which has its properties and dynamics determined by a bodily secretion of a metazoan.
environment determined by a metazoan secretion
An environmental system which has its properties and dynamics determined by a substance produced by a plant.
environment determined by a plant substance
An environmental system which has its properties and dynamics determined by a biofilm on the surface of a plant.
environment determined by a biofilm on a plant surface
An environmental system which has its properties and dynamics determined by a digestive tract.
digestive tract environment
This EMPO class includes examples of microbial environments determined by the "gut intestine, gizzard, crop, lumen, [and] mucosa".
An environmental system which has its properties and dynamics determined by a biofilm on the surface of a animal.
environment determined by a biofilm on an animal surface
An environmental system which has its properties and dynamics determined by a biofilm on the surface of a fungus.
environment determined by a biofilm on a fungal surface
Sediment which has its porespace filled by water with increased levels of sodium chloride and other salts.
sediment permeated by saline water
Water which contains a slightly increased concentration of dissolved salts, relative to their concentration in freshwater.
The United States Geological Survey classifies slightly saline water as having around 1,000 to 3,000 ppm (0.1–0.3%) of dissolved salts.
slightly saline water
Water which contains a moderately increased concentration of dissolved salts, relative to their concentration in freshwater.
The United States Geological Survey classifies moderately saline water as having around 3,000 to 10,000 ppm (0.3–1%) of dissolved salts.
moderately saline water
Water which contains a highly increased concentration of dissolved salts, relative to their concentration in freshwater.
The United States Geological Survey classifies highly saline water as having around 10,000 to 35,000 ppm (1–3.5%) of dissolved salts.
highly saline water
An environment which is determined by materials which bear significant concentrations of salts.
The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request.
saline environment
An environmental system determined by a fungal structure.
fungi-associated environment
An environmental system which has its properties and dynamics determined by sterile water.
This term can be understood as a negative experimental control primarily composed of sterile water. The quantity of sterile water used may be contaminated; to express pure sterile water, please use http://purl.obolibrary.org/obo/ENVO_00005791
sterile water environment
An environmental system which has its properties and dynamics determined by hypersaline water.
hypersaline water environment
Examples inlcude water from hypersaline samples or brines (>50 psu)
An environmental system which has its properties and dynamics determined by soil.
soil environment
A region which overlaps parts of one or more planetary structural layers which are located below an oceanic plate.
oceanic subsurface zone
An environmental system which has its properties and dynamics determined by the subsurface zone of a planet.
planetary subsurface environment
An environmental system which has its properties and dynamics determined by those parts of a planetary subsurface zone which are not saline.
non-saline planetary subsurface environment
An environmental system which has its properties and dynamics determined by sediment.
sediment environment
An environmental system which has its properties and dynamics determined by sediment permeated by non-saline water.
non-saline sediment environment
An environmental system which has its properties and dynamics determined by sediment permeated by saline water.
saline sediment environment
An environmental system which has its properties and dynamics determined by a biofilm on a surface which is exposed to non-saline materials.
environment determined by a biofilm on a non-saline surface
An environmental system which has its properties and dynamics determined by an aerosol.
aerosol environment
An environmental system which has its properties and dynamics determined by a saline aerosol.
saline aerosol environment
seaspray or other aerosolized saline material (>5 psu)
An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes.
non-saline aerosol environment
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with an animal part or small animal
An environmental system which has its properties and dynamics determined by a biofilm on a surface which is exposed to saline materials.
environment determined by a biofilm on a saline surface
An environmental system determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
An environmental system determined by part of a living or dead fungus.
environment associated with a fungal tissue
A cell culture which is composed of a microbial community of known composition.
Mock communities are typically used as positive controls in experiments.
mock community culture
A cell culture which is composed of a single population of bacterial or archaeal cells.
single strain cell culture
A lake which is contained within a caldera.
caldera lake
Note that this class does not commit to what kind of crater contains the lake in question. Please see the subclasses for more specificity.
crater lake
Water which has an appreciable concentration of dissolved oxygen.
The threshold dissolved oxygen concentration past which water is considered oxic is variable. Typically, this is understood as the concentration at and beyond which organisms inhabiting that water can sustain aerobic metabolism and good health. For most systems, this is above 80% oxygen saturation. Input is welcome here https://github.com/EnvironmentOntology/envo/issues/536
oxic water
Water which has low levels of dissolved oxygen.
As with oxic and anoxic water, the thresholds for hypoxia are variable. Typically, a hypoxic state is asserted when dissolved oxygen levels decrease to a level where they have detrimental effects on aerobic aquatic organisms, typically below 30% oxygen saturation.
hypoxic water
A lake which is contained in a crater formed by a meteorite impact.
meteorite lake
An impact event is a collision between astronomical bodies.
impact between astronomical bodies
QCR: 'has participant' min 2 'astronomical body'
An impact event during which a meteoroid collides with another astronomical body.
meterorite impact
An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids.
meteoroid
A material which is composed primarily of one or more pure metals and which shows their properties.
Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
A lake which is contained in a crater formed by an impact event.
impact crater lake
A crater which was formed as a result of the impact of one astronomical body on another.
impact crater
A lake which is primarily composed of anoxic water.
anoxic lake
A lake which has a hypolimnion composed primarily of anoxic water.
lake with an anoxic hypolimnion
A lake which has a hypolimnion composed primarily of hypoxic water.
lake with a hypoxic hypolimnion
A lake which is primarily composed of hypoxic water.
hypoxic lake
A lake which is primarily composed of oxic water.
oxic lake
A lake which has a hypolimnion composed primarily of oxic water.
lake with an oxic hypolimnion
Environmental variability which inheres in an astronomical body part or in outer space.
This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity.
weather
This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere.
atmospheric weather
space weather
A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in.
This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider.
environmental variability
The disposition of an environmental system, particularly those influencing atmospheres, to manifest a cyclic pattern of weather over time.
The current alignment of "climate" under BFO:disposition is drawing from its very useful etymology (Ancient Greek klima, meaning inclination). The climatic conditions currently used to axiomatise biomes (polar, tropical, etc) may be better placed under this class.
Climate is commonly defined as the weather averaged, or otherwise summarised, over a period of time much longer than the duration of any phenomenon that constitutes weather. The standard averaging period is 30 years, but other periods may be used depending on the purpose.
climate
A process during which water vapour condensing in the atmosphere aggregates into clouds.
cloud formation process
A process during which microscopic solid or liquid objects are formed.
particulate matter formation process
An aerosol formation process which occurs in an atmosphere.
atmospheric aerosol formation
A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere.
formation of solid particles in an atmosphere
formation of a solid aerosol in an atmosphere
A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere.
formation of liquid droplets in an atmosphere
formation of liquid particles in an atmosphere
formation of a liquid aerosol in an atmosphere
An aerosol which has non-gaseous parts that are primarily composed of liquid droplets.
aerosolised liquids
An aerosol which has non-gaseous parts that are primarily composed of solid particles.
aerosolised solids
A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere.
atmospheric formation of a solid aerosol
formation of a solid aerosol in the atmosphere
formation of solid particles from gaseous material in an atmosphere
formation of a solid aerosol from gaseous material in an atmosphere
A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere.
atmospheric formation of a liquid aerosol
formation of a liquid aerosol in the atmosphere
formation of liquid droplets from gaseous material in an atmosphere
formation of liquid particles from gaseous material in an atmosphere
formation of a liquid aerosol from gaseous material in an atmosphere
A lake which is contained in a depression formed by the deformation and resulting lateral and vertical movements of a lithosphere.
tectonic lake
A process during which pieces of a planetary crust and uppermost mantle move.
tectonic movement
A process during which pieces of a planetary crust and uppermost mantle move towards one another.
convergent tectonic movement
A process during which pieces of a planetary crust and uppermost mantle move away from one another.
divergent tectonic movement
A process during which pieces of a planetary crust and uppermost mantle move along each other in a predominantly horizontal manner, either in a sinistral (left lateral) or dextral (right lateral) direction.
transform tectonic movement
A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities.
tectonic plate
A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere.
tectonic plate boundary
A geomorphological feature which is formed where two or more tectonic plates are actively moving away from one another, resulting in deformation of the lithosphere that forms rifts or ridges.
divergent plate boundary
A geomorphological feature which is formed where two or more tectonic plates are actively moving towards one another, resulting in deformation of the lithosphere that forces one plate below the other where it melts in the mantle.
convergent plate boundary
A geomorphological feature which is formed where two or more tectonic plates are actively moving along one another in either a sinistral (left lateral) or dextral (right lateral) horizontal direction.
This class overlaps with the semantics of geographic faults and further work needs to be done to disentangle them.
transform plate boundary
A convergent tectonic movement process during which one plate moves under another and is forced or sinks due to gravity into a mantle.
tectonic plate subduction
An organic material which is primarily composed of dead particulate matter.
A compound astronomical body part in which extensional tectonic processes occur and where the lithosphere is being pulled apart.
rift zone
A lake which fills a basin that has been dammed by wind-blown sand, formed between sand dunes oriented by winds; or formed by wind action under previously arid paleoenvironments.
aeolian lake
A lake which fills a depression where drainage is blocked by solid material transported by a landslide.
landslide lake
A lake which fills a depression where drainage is blocked by solid material transported by a rockslide.
rockslide lake
A rockslide is a process whereby a large mass of rock moves down a hill or a mountainside.
rockslide process
A succession of swirling vortices caused by the unsteady separation of flow of a fluid around one or more blunt bodies.
These vortices are responsible for such phenomena as the "singing" of suspended telephone or power lines, and the vibration of a car antenna at certain speeds.
Karman vortex street
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
A channel which was formed as a result of an annelid burrowing through soil, where organic residues lining the burrow have subsequently initiated fossilization.
fossil worm burrow
A process during which organic substances are replaced with mineral substrances, maintaining part of their anatomical organisation.
fossilization of organic material
Material which is primarily conposed of the vegetation present in tended pastures: mainly grasses, with an interspersion of legumes and other forbs.
forage material
A physical space, which may or may not be in a construction, which is used to store animal feed for agricultural purposes.
This should be moved to "zone", and inference should be used to link to agricultural feature.
feed storage space
A physical space, which may or may not be in a construction, which is used to store animal manure for agricultural purposes.
manure storage space
Manure which has been collected directly or indirectly from dairy cattle, as from flushing of manure from concrete feed lanes, free stalls, and milking facilities.
bovine dairy liquid manure
Manure which is composed primarily of the feces of poultry.
poultry manure
Manure which has been subjected to heat treatment for solidification and/or sterilization purposes.
heat-treated animal manure
Manure which has been subjected to a natural process of 'rotting' or decomposition of its organic matter content by microorganisms under controlled conditions.
composted animal manure
A product which is composed primarily of animal manure that has been heat treated and packaged as a product for commercial or consumer use.
animal manure product
Organic material which is primarily composed of plant structures, living or dead.
plant matter
A planet which is primarily composed of hydrogen and helium.
Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants.
gas planet
A gas planet which 1) is considerably smaller than a gas giant and 2) has a rocky core around which a thick envelope primarily composed of hydrogen, helium, and smaller proportions of volatiles.
The physical make-up of gas dwarfs limit their size, which gravitate towards a total radius between 1.7 and 3.9 Earth-radii.
dwarf gas planet
A gas planet which has mass and size comparable to Jupiter and Saturn.
The definition should be revised to avoid relativisation to instances.
giant gas planet
An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.
ice
An astrogeological volatile which is composed primarily of chemical compounds with freezing points above an approximate threshold of 100 Kelvin.
This is a term native to the fields of planetary science and astrophysics. Water, ammonia, and methane are considered "ices" with freezing points of 273 K, 195 K, and 91 K, respectively.
astrogeological ice
A giant planet which is primarily composed of elements heavier than hydrogen and helium, volatile chemical compounds with freezing points above about 100 Kelvin.
Uranus and Neptune are considered ice giants, a separate class relative to the gas giants, Jupiter and Saturn. Ice giants consist of only about 20% hydrogen and helium in mass. A large portion of the mass in an ice giant was incorporated by the capture of ice (as defined in planetary science) or as gas trapped in water ice.
ice giant
A gas planet which has an atmosphere composed of hydrogen and helium - probably with deep layers of ice, rock or liquid oceans (made of water, ammonia, a mixture of both, or heavier volatiles) - and a small core made of low-density volatiles.
These planets have a mass up to 10 Earth masses, notably smaller than Uranus or Neptune, which are about 14.5 and 17 Earth masses, respectively.
mini-Neptune
An astronomical object which is more massive than the planet Jupiter.
Due to their immense size, super-Jupiter class objects straddle the space between planets and other objects such as brown dwarfs. While they may be more massive than Jupiter, super-Jupiters tend to be the same approximate size, with increasing density as their mass increases up to about 80 Jupiter masses.
super-Jupiter
A process during which one or more entities move along geodesics in a region of spacetime that has been sufficiently curved towards an entity with sufficient mass and/or energy.
gravitational motion
A giant gas planet which has a jovian-scale mass (0.36–11.8 Jupiter masses), a short orbital period (1.3–111 Earth days), and which is close to the star it orbits, resulting in extreme and exotic atmospheric properties.
It is assumed that the mass of a hot Jupiter cannot be greater than approximately 13.6 Jupiter masses, beyond which the planet would start burning deuterium and become a brown dwarf.
hot Jupiter
A gas planet which has a mass similar to that of Neptune or Uranus and which closely orbits its star (normally at a distance less than 1 Astronomical Unit).
Whether this should be classified as a gas planet or an ice giant must be explored.
hot Neptune
A terrestrial exoplanet which is at least ten times the mass of Earth.
mega-Earth
A terrestrial planet which has a mass higher than Earth's, but substantially below the masses of Uranus and Neptune (15 and 17 Earth masses, respectively).
The upper bound of a super-Earth's mass is generally agreed on as 10 Earth masses. In general, super-Earths are defined exclusively by their masses, and the term does not imply temperatures, compositions, orbital properties, habitability, or environments.
super-Earth
A terrestrial planet which has a surface dominated by hot deserts.
This class of planet is still mostly theoretical.
desert planet
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class.
While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b.
ocean planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
ice planet
Ice which is primarily composed of carbon dioxide.
carbon dioxide ice
Ice which is primarily composed of methane.
methane ice
Ice which is primarily composed of ammonia.
ammonia ice
Ice which is primarily composed of carbon monoxide.
carbon monoxide ice
A planet which in primarily composed of an iron-rich core with little to no mantle
Mercury is the largest iron planet in the Solar System, the other terrestrial planets being composed of silicate rocks. Some extrasolar planet candidates that may be composed mainly of iron are KOI-1843 b,[5] Kepler-70b and Kepler-10b.
iron planet
A planet which has a surface layer that nearly completely or completely covered by lava, and which has a substantial portion of its mass composed of lava.
This class of planets is still mostly theoretical, however, lava planets are thought plausible shortly after a terrestrial planet is formed, soon after a terrestrial planet has suffered a large collision event, or if a terrestrial planet is orbiting very close to its star, causing intense irradiation and tidal forces. Likely lava exoplanets include COROT-7b, Kepler-10b, Alpha Centauri Bb, and Kepler-78b.
lava planet
A terrestrial planet which has a mass smaller than Earth's, such that 1) it lacks a magnetic field strong enough to shield its atmosphere from erosion by stellar wind and 2) it has comparatively short periods of geological activity unless it is subject to gravitational tidal forces from a much more massive object.
The first sub-Earths were discovered by the Kepler Orbiting Observatory space telescope on 2012-01-10, orbiting the star Kepler-42. As of June 2014, Kepler has 45 confirmed planets that are smaller than Earth, with 17 of them being smaller than 0.8 Earth radii. In addition, there are over 310 planet candidates with an estimated radius of less than 1 Earth radius, with 135 of them being smaller than 0.8 Earth radii.
sub-Earth
A planet which is formed as a result of a gas giant's hydrogen and helium atmosphere, as well as its outer layers, being stripped away by a stellar wind through photoevaporation and hydrodynamic escape.
This class is largely theoretical, however, some likely candidates exist. HD 209458 b and Gliese 436b are examples of a gas giants that are in the process of having their atmospheres stripped away. COROT-7b is the first exoplanet found that might be chthonian.
chthonian planet
A process during which energetic radiation ionises gas and causes it to disperse away from the ionising source.
This process is responsible for the stripping away of gases from the atmosphere of planets and related bodies by acceleration on interaction with high energy photons and other electromagnetic radiation.
photoevaporation
A gas planet which has an atmosphere composed primarily of helium.
The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated.
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
helium planet
An astronomical body which 1) is held together by its own gravity, 2) can attract other, similar bodies through mutual gravitational influence, and 3) has orbital dynamics that are not significantly affected by gas drag.
In the Solar nebula, planetesimals are usually larger than approximately 1 kilometer.
planetesimal
An astronomical object that forms within a protoplanetary disc when planetesimals and other solid debris aggregate and, due to gravitational forces, fuse and initiate internal melting to produce a differentiated interior.
State that this is derived from a collection of planetesimals.
Protoplanets are thought to form out of kilometer-sized planetesimals that gravitationally perturb each other's orbits and collide, gradually coalescing into the dominant planets. The exact sequence of events which lead to planetary formation from protoplanets is not fully understood.
protoplanet
An astronomical object which is composed of dense gas and dust rotating around a young newly formed star, a T Tauri star, or a Herbig Ae/Be star in a disk-shaped configuration.
protoplanetary disk
A protoplanetary disk which is externally illuminated and undergoing photoevaporation.
proplyd
A planet which is smaller than Mercury but larger than Ceres.
mesoplanet
Because of the short orbits of some binary stars, the only way for planets to form is by forming outside the orbit of the two stars.
circumbinary planet
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
Add and axiomatise with moon and lunar crust
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
volatile astrogeological material
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin.
astrogeological gas
A material which is composed primarily of chemical elements and compounds which have equilibrium condensation temperatures above approximately 1300 Kelvin and which are part of the crust or atmosphere of a moon or planet.
The refractory group includes elements and compounds like metals and silicates (commonly termed rocks) which make up the bulk of the mass of the terrestrial planets and asteroids in the inner belt.
refractory astrogeological material
A process during which gases that constitute a planetary atmosphere escape that planet's gravitational field and move away into outer space.
atmospheric escape
An atmospheric escape process during which atoms that are parts of a planetary atmosphere escape into outer space through numerous collisions with lighter atoms in that atmosphere.
hydrodynamic escape
A cloud which is cirriform and is formed by condensation events centred on an aircraft's contrail.
cirrus homogenitus cloud
A cloud which 1) has been shaped into detached fibrous filaments, 2) is almost exclusively composed of ice crystals, 3) is located in the high level of the atmosphere (high étage).
Add more PATO qualities once they have been added to PATO.
(Eis)-Federwolke
Cirruswolke
Zirruswolke
envoCloudAtlas
When present in aggregates, individual cirrus clouds are organised in patches or narrow bands. When organised in sheets of fibres they can give a silky sheen. When well-illuminated by sunlight (excluding during sunrise and sunset) cirrus clouds appear white or mostly white. Absence of any precipitation.
cirrus cloud
An IUCN protected area in which human visitation, use and impacts are strictly controlled and limited to ensure protection and conservation of natural biodiversity and/or geodiversity, natural ecosystem assemblages and processes, and any associated cultural and spiritual values.
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. Previous anthropogenic impacts (e.g. by early human settlement) may be present in these sites; these should be reversible by either natural processes or brief restorative interventions. Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas.
IUCN strict nature reserve
An IUCN protected area which 1) is dominated by natural ecosystems, 2) is sufficiently large to allow those ecosystems to function and develop without local anthropogenic perturbation, 3) is managed to prevent perturbations by proximate or local anthropisation, including those caused by local and/or indigenous human communities or human visitation.
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. These areas exclude permanent built infrastructure, activities by extractive industries, commercial or intensive agriculture, extensive access by motor vehicles, unregulated visitation supported by any infrastructure, as well as other activities that may lead to significant ecosystem perturbations.
IUCN wilderness area
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
An IUCN protected area which includes a primarily natural formation designated to be of high natural heritage value and the environmental systems which it determines (e.g. the spray zone of a waterfall monument).
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. Further, note that the use of "natural" in the IUCN definition may allow for some anthropisation such as the presence of cave dwellings or spiritual sites. These areas tend to be smaller than other IUCN protected areas and are sites of frequent human visitation and high tourism value. They often serve to conserve natural heritage in land- or seascapes which have otherwise been anthropised. Frequently, these areas have high spiritual and cultural value as well as bio- and geodiversity value. It is not clear what would happen to the status of a IUCN Category III protected area if its key natural monument dies or degrades. IUCN acknowledges that larger ecosystem areas may need protection or management to sustain the area given Category III protection.
IUCN natural monument or feature
An IUCN protected area within which the habitats of or ecosystems used by floral and faunal species deemed to be of international, national, or local importance are maintained, conserved, or restored such that their composition and functional integrity are maintained.
Clarify what is encompassed by floral and faunal. Do microbial and fungal species (e.g. of importance to many marine systems) fall within these categories? Further, create subclasses for habitat and species conservation separately.
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. Note that many Category IV sites require frequent interventions to maintain habitats for the species conserved, particularly as many of these areas are ecosystem fragments which are unable to sustain themselves. Additionally, many are used for public outreach, education, and recreation, implying regular human visitation. What qualifies a species as important is variable and often ill-defined.
IUCN habitat/species management area
An ecosystem which has been causally isolated from a larger ecosystem within which it was previously embedded, such that the direct exchange of materials, resources, and energy between these systems is severely or entirely curtailed.
Often, ecosystem fragments are unable to sustain themselves without human intervention and management as they are not large enough to perform self-sustaining functions (e.g. nutrient recycling) or hold sufficient ecological resources such as genetic diversity of populations.
ecosystem fragment
A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted.
ecosystem fragmentation process
A protected area in which management objectives have been declared, by a local governing body or authority, to adhere to the guidelines set forth by the International Union for the Conservation of Nature (IUCN).
Axiomatise with SDGIO classes once available: https://github.com/SDG-InterfaceOntology/sdgio/issues/114
IUCN protected area
The international recognition of an area as an IUCN protected area generally depends on the assigning government or authority reporting its assignments to the United Nations Environment Programme World Conservation Monitoring Centre.
area protected according to IUCN guidelines
A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective.
Umweltmaßnahme
active ecosystem management process
An active management process which has the conservation of an ecosystem, or a part thereof, as its primary objective.
Umweltschutz
conservation-focused active ecosystem management process
An IUCN protected area which 1) includes entities that have been deemed to be of high scenic quality, 2) is composed of a historically stable assemblage of causally interlinked natural and anthropised ecosystems that provides cultural ecosystem services, and 3) hosts traditional and sustainable human activities.
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. The IUCN note that the integrity of balanced natural and anthropogenic ecosystems may be compromised in some Category V areas, as long as "there is reasonable hope of restoring that integrity".
IUCN protected landscape/seascape
A fiat object part which contains entities of high spiritual or cultural significance to one or more human groups.
sacred site
A process during which an ecosystem fragment loses its system integrity, with many of its resident ecological populations 1) losing their habitats, 2) undergoing a loss of functional and phylogenetic diversity, and 3) undergoing a subsequent genetic destabilisation through inbreeding.
This process may be caused by direct anthropisation (i.e. the fragmentation of ecosystems due to the establishment of cropland) or by more natural events such as forest fires or erosion of land bridges.
ecosystem decay
An ecosystem fragmentation process during which discontinuities emerge in the habitats of one or more ecological populations.
habitat fragmentation process
An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system.
environment associated with an aquatic invertebrate
Not currently live, may need to be switched to alternative PURLs.
Land which is regularly manipulated by human activities, such as plowing or tilling, in order to grow crops.
Consider moving axioms to the quality 'arable' directly. The discontinuous quality on tillage can likely be improved or refined. Also, add axioms for ploughing once it is added to AgrO: https://github.com/AgriculturalSemantics/agro/issues/34
arable land
Land which hosts a community of herbaceous plants - such as grasses and forbs - upon which animals may graze.
See this issue for requests regarding surrounding semantics of grazing: https://github.com/AgriculturalSemantics/agro/issues/32
pasturable land
An environmental system determined by a cnidarian or part of a cnidarian.
cnidarian-associated environment
An environment which has its properties and composition determined by a portion of Bondon cheese.
This class was cross-axiomatised with FOODON, but recent changes in FOODON's alignment (e.g. Bondon cheese as a subclass of an information artifact) have caused reasoning errors. We await FOODON to stabilise these semantics before attempting a reimport and will work with them to this end.
Bondon cheese environment
A surface layer which is composed of the external surface of a root, together with closely adhering soil particles and debris
rhizoplane
Pasturable land which is maintained by human activities in order to provide grazing oppoturnities for livestock.
tended pasturable land
Land which either hosts plant communities upon which animals may graze has been manipulated by tilling, ploughing, or other human activity for the purposes of seed sowing or planting crops.
Add semantics to support "land under market and kitchen gardens and land temporarily fallow (less than five years). The abandoned land resulting from shifting cultivation is not included in this category."
This class does not refer to the land that is potenitally cultivable, only referencing land that is being managed for cultivation. This class has been created to support the FAO definition of arable lands in FAOSTAT.
arable or pasturable land
A quality inhereing in a bearer by virtue of the bearer being periodically and mechanically manipulated to loosen and mix any soil which it has as a part.
arable
Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7.
acidic soil
Volcanic ash which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7.
acidic volcanic ash
A digestive tract environment which has its properties and dynamics determined by the digestive tract of an echinoderm from the class Holothuroidea.
holothurian digestive tract
A bodily fluid which is present in the digestive tract of a member of the Holothuroidea.
holothurian digestive tract contents
This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO.
An organic material which is primarily composed of living or dead algae, along with their exudates.
algal material
Sea ice which has a brown colouration, either due to 1) the presence of pigments which are or were contained in the members of ecological assemblages, such as algal communities, living or trapped within the ice or 2) due to the presence of trapped sediments.
brown sea ice
water surface
The surface layer of a mass of sediment.
sediment surface
A liquid planetary surface which is composed primarily of water.
This includes the surface layers of all volumes of water exposed to space or the planet's atmosphere.
water-based planetary surface
A site in which charged particles are influenced by an astronomical body's magnetic field.
The original definition referenced astronomical objects, however, the text suggests that reference to an astronomical body is more accurate.
Magentospheres are generated by the motion of active hot iron and nickle or metallic planetary cores or by the interactions of plasma in stars.. The magnetic field near the surface of many astronomical bodies resembles that of a dipole. The field lines farther away from the surface can be significantly distorted by the flow of electrically conducting plasma emitted from a nearby star. The structure and behaviour of magnetospheres depend on numerous variables, including the type of astronomical body which generates it, the period of the object's spin, the properties of the axis about which the object spins, the axis of the magnetic dipole, and the magnitude and direction of the flow of stellar wind.
magnetosphere
An environmental disposition which inheres in an entity that intercepts, attenuates, or blocks radiation.
radiation shielding disposition
A radiation shielding disposition which inheres in a material or immaterial entity which attenuates or blocks cosmic rays.
cosmic ray shielding disposition
A magnetosphere which either 1) cannot withstand the pressure of the stellar wind interacting with it, thus allowing the stellar wind to interact with the ionosphere, atmosphere, or surface of the planet generating it or 2) is formed by the interaction of the stellar wind with an astronomical body unshielded by its own magnetosphere.
induced magnetosphere
A magnetosphere which shields the body generating it from the stellar wind by withstanding the stellar wind's pressure before it reaches the body.
intrinsic magnetosphere
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities.
anthropised terrestrial environmental zone
An astronomical body part which is part of a marine environment.
This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density.
marine environmental zone
Soil or sediment which has been eroded and influenced by flowing water and redeposited in a non-marine setting.
alluvium
Sediment which has been transported by flowing water and redeposited in a non-marine setting.
alluvial sediment
A rock which is formed as a result of the lithification of alluvium.
alluvial deposit
A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock.
lithification
An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics.
grassland ecosystem
An area of land used for the herding and grazing of livestock.
ranch
An area of wetland which overlaps a swamp ecosystem.
swamp area
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
wetland ecosystem
A planned process during which an environmental system is modified to mitigate or nullify the impacts of flooding.
defence against flooding
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star.
stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star at wavelengths and frequencies which travel exclusively in a line-of-sight fashion and which may produce molecular rotation and torsion on contact with matter.
This definition focuses on the properties of microwaves rather than their wavelength or frequency limits. Considerable ambiguity exists around the wavelength and frequency thresholds of microwaves. The ISO 21348 definition bounds these waves at 1 mm and 15 mm, with frequencies between 100 GHz and 0.225 GHz.
microwave stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star at wavelengths ranging from millimetre to kilometer scales.
As with microwaves, considerable variation exists in the delimitation of frequency and wavelength thresholds for radiowaves. The ISO 21348 standard allows a wavelength range of 0.10 mm to 100 m and a frequency range of 300 GHz to 3 MHz. However, much lower thresholds also exist.
radio wave stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star when molecules change their rotational-vibrational movements, usually at wavelengths between 760 nm and 1 mm.
infrared stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star at wavelengths between 380 nm and 760 nm.
visible spectrum stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star at wavelengths between 10 nm and 400 nm.
ultraviolet stellar radiation
A stellar radiation process during which penetrating electromagnetic radiation is emitted by high-energy electrons as they fall into a lower state of energy.
Ambiguity exists in the definition of x-rays and their differentiation from gamma rays. Photons with sufficient energy to be classified as x-rays may be emitted by other processes than electrons falling to lower energy states. Most x-rays have wavelengths ranging from 0.01 to 10 nanometers, corresponding to frequencies in the range of 30 petahertz to 30 exahertz and energies in the range of 100 eV to 100 keV.
X-ray stellar radiation
A stellar radiation process during which penetrating electromagnetic radiation is emitted from the radioactive decay (gamma decay) of atomic nuclei.
Ambiguity exists in the definition of gamma rays. As a rule of thumb, gamma rays have energies above 100 keV, frequencies above 10 exahertz, and wavelengths less than 10 picometers. However, regardless of the energy released, electromagnetic radiation from radioactive decay of atomic nuclei is referred to as "gamma rays". In astronomy, however, gamma rays are defined by their energy, and no production process needs to be specified.
gamma-ray stellar radiation
A stellar radiation process during which electromagnetic waves or their quanta are emitted from a star with sufficient energy to disrupt molecular bonds or alter the electron number of atoms.
ionizing stellar radiation
A process during which liquid water accumulates in a site, most often in some form of container.
water accumulation process
A commercial building which contains parts used as workplaces primarily for administrative and managerial workers.
"An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets."
office building
A building which is primarily used to facilitate the buying or selling of goods or services.
"Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally."
commercial building
A process during which wood is processed into beams or planks.
lumber production process
A building part within which administrative work is done by an organisations users in order to support and realise the objectives of that organization.
office
An IUCN protected area within which 1) natural ecosystems and their resources are either conserved or used through non-industrial human activities, 2) usage activites contribute to conservation goals, ensuring inter-generational security for local communities' livelihoods, and 3) the majority of benefits derived from the use of ecosystems are received by communities living near or in the area.
protected area with sustainable use of natural resources
Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas. Note, that the IUCN recommends that a proportion of the area is retained in a natural condition (e.g. a no-take management zone). As this is a recommendation rather than a rule, this ENVO class does not include IUCN categories with strict conservation regimes as necessary parts. An emphasis is placed on the integration of cultural approaches, belief systems and world-views possessed by human populations in and around the protected area into the conservation approaches used. Further, these areas host activities which facilitate scientific research, environmental monitoring, recreation, and "appropriate" small-scale tourism.
IUCN protected area with sustainable use of natural resources
A natural environment which is located on a land mass.
terrestrial natural environment
A natural environment which is within a water body.
aquatic natural environment
A site in which the attraction of satellites by gravitation is dominated by an astronomical body, bounded by a zero-velocity surface.
Hill sphere
QCR: 'process has causal agent' max 1 'astronomical body'
A site in which the combined gravitational pull of the two large astronomical bodies is such that a smaller body, affected only by gravity, can maintain a stable position relative to those two large bodies and orbit with them due to centripetal force.
Lagrangian point
A marginal sea biome which is located in a region with a tropical climate.
A class which is complementary to the WWF Temperate Shelf and Seas ecoregions grouping
tropical marginal sea biome
Organic material which is in a solid phase and contained in sedimentary rock.
kerogen
Kerogen which cotains alginite, amorphous organic matter, cyanobacteria, freshwater algae, and land plant resins, thus having a hydrogen to carbon ratio above 1.25, and oxygen to carbon ratio below 0.15, readily produces liquid hydrocarbons, has reduced concentrations of aromatic structures, and primarily derived from proteins and lipids.
sapropelic kerogen
Kerogen from which heavy hydrocarbons (such as oils) are derived following chemical break down.
labile kerogen
Kerogen from which light hydrocarbons (such as hydrocarbon gases) are derived following chemical break down.
recalcitrant kerogen
Kerogen which is enriched in sulfur compounds, has a hydrogen to carbon ratio under 1.25, an oxygen to carbon ratio between 0.03 and 0.18, derives into mixtures of hydrocarbon gas and oil, and derives from marine organic materials (primarily lipids) which are formed in reducing environments.
planktonic kerogen
Planktonic kerogen which has high concentrations of sulfur compounds.
sulfrous kerogen
Kerogen which derives from land plants, resembles wood or coral in structure, has a hydrogen to carbon ratio under 1, an oxygen to carbon ratio between 0.03 to 0.3, and which primarily produces coal or hydrocarbon gas on degradation.
humic kerogen
Kerogen which has a hydrogen to carbon ratio less than 0.5 and primarily composed of polycyclic aromatic hydrocarbons.
residual kerogen
forest canopy
A canopy which is part of a woodland ecosystem.
woodland canopy
A canopy which is composed of the aboveground portion, or crowns, of a community of crop plants.
crop canopy
A vegetation layer which is formed by a collection of individual plant crowns, themselves constituting part of the aboveground portion of a plant community.
canopy
An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover.
The correct usage of FLOPO terms in the axiomatisation needs to be confirmed.
forest ecosystem
An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement.
cropland ecosystem
An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities are spaced sufficiently far apart to allow sunlight to illuminate the understory.
Woodland understories are often populated with communities of shrubs and herbaceous plants including grasses. There are varying distinctions between woodland and forest, with a large degree of ambiguity.
woodland ecosystem
A process during which humans rear animals or plants on land for harvest and consumption.
agricultural process
An agricultural process during which humans rear plants on land for harvest and consumption.
agronomic process
An agricultural process during which humans rear animals on land for harvest and consumption.
animal husbandry
An aquaculture process during which humans rear crustaceans.
crustacean farming process
An aquaculture process during which humans rear finfish.
finfish farming process
An aquaculture process during which humans rear molluscs.
mollusc farming process
An aquaculture process during which humans rear seaweed.
seaweed farming process
An aquaculture process during which humans rear freshwater macrophytes.
freshwater macrophyte farming process
An aquaculture process during which humans rear animals.
animal aquaculture process
An aquaculture process during which humans rear plants.
This is unlikely to be limited to Viridiplantae, better axiomatisation should be sought in revisions.
plant aquaculture process
A shrimp pond which is embedded in a coastal water body.
coastal shrimp pond
Saline water which is derived from sea water and used during the cultivation of crustaceans.
saline shrimp pond water
A fog which is composed of liquid aerosols and gases derived from volcanic gas emissions (primarily sulfur oxides), formed when sulfur-bearing gases react with sunlight, oxygen, and moisture in an atmosphere.
"Vog and smog are different. Vog is formed when sulfur oxides emitted by a volcano react with moisture to form an aerosol. The aerosol scatters light, thus making the vog visible. Smog is formed largely from the incomplete combustion of fuel, reacting with nitrogen oxides and ozone produced from carbon monoxide by reactions with sunlight. The result is also a visible aerosol."
vog
A process during which materials deemed to be waste are removed from a site and transported to another site designated for its storage.
transport of waste to a designated storage site
A process during which materials deemed to be waste are transported away from a site.
Abfallentsorgungsprozess
proceso de eliminación de residuos
processo di smaltimento rifiuti
waste disposal process
A waste disposal process during which the feces of human children is transported to a designated storage site.
transport of child feces to a designated site
A process during which materials used in a household and deemed to be waste are removed from the housing unit and transported to another site designated for its storage.
transport of household waste to a designated storage site
A site which has been designated as a place where humans may defecate.
area designated for human defecation
A site which has been designated for the storage of waste material.
area designated for waste storage
An environmental pollution process during which the temperature of an environmental system, or parts thereof, is raised above its natural levels.
thermal pollution
A thermal pollution process which occurs in a water body or aquatic environment.
thermal pollution of an aquatic system
Water which accumulates on a solid surface during precipitation events and snow/ice melt.
"Stormwater can soak into the soil (infiltrate), be held on the surface and evaporate, or runoff and end up in nearby streams, rivers, or other water bodies (surface water)."
stormwater
Stormwater which accumulates in an urban ecosystem.
urban stormwater
An area of a planet's surface which is primarily covered by constructed or manufactured objects and materials, possibly interspersed with cultivated or anthropically maintained vegetation.
area of developed space
Stormwater which accumulates in a rural ecosystem.
rural stormwater
A surface layer through which liquids or gases cannot pass.
impermeable surface layer
A construction which comprises a durable surface layer overlying a solid surface intended to sustain vehicular or foot traffic.
constructed pavement
A layer which is primarily composed of some liquid material.
liquid layer
A layer throughout which one or more qualities (e.g. pressure, temperature, velocity, density) maintain an approximately constant value.
Isosurfaces are not equivalent to a "surface layer" in the sense of overlapping an external boundary. Further, this class is concerned only with material isosurfaces, not with mathematical abstractions.
material isosurface
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A solid layer which is primarily composed of some water-based ice.
water ice layer
A road which is primarily composed of asphalt.
asphalt road
A road which is primarily composed of concrete.
concrete road
A constructed pavement which is built on the side of a road and intended for foot traffic.
"In some places, the same term may also be used for a paved path, trail or footpath that is not next to a road, for example, a path through a park."
sidewalk
A road which is used for local access to one or more structures, and is privately owned and maintained by an individual or group.
driveway
A constructed pavement which is used for parking vehicles.
paved parking lot
Dust which is composed primarily of slicon dioxide.
silica dust
Dust which is primarily composed of aluminium particles.
aluminium dust
Dust which is primarily composed of barium particles.
barium dust
Dust which is primarily composed of hydrated magnesium silicate (talc) particles.
talc dust
Dust which is primarily composed of slate particles.
slate dust
A fire which occurs in an industrial area or building.
industrial fire
Dust which is primarily composed of kaolinite particles.
kaolin dust
A land fire which consumes low-growing plants such as scrub and brush.
brush fire
A land fire which occurs in a large uncleared or sparsely settled area (as in Australia) usually scrub-covered or forested.
"Bush" is a rather loosely defined regional term, primarily used in Australia.
bush fire
pasture fire
A fire which occurs on land, typically consuming a terrestrial ecosystem as fuel.
land fire
A vegetated area which has not been cleared or is sparsely settled, usually scrub-covered or forested
bush area
An atmospheric storm which is generated by the heating and convection of moist and unstable air masses.
"Convective storms range from localised thunderstorms (with heavy rain and/or hail, lightning, high winds, tornadoes) to meso-scale, multi-day events."
convective storm
A warm-core cyclone which occurs in the middle and high latitudes, primarily drawing energy from horizontal temperature contrasts between atmospheric fronts.
"When associated with cold fronts, extratropical cyclones may be particularly damaging (e.g. European winter/windstorm, Nor’easter)."
extra-tropical cyclone
A an atmospheric storm which originates over tropical or subtropical waters and possesses a warm-core, non-frontal synoptic-scale cyclone with a low pressure centre, spiral rain bands and strong winds.
tropical storm
An atmospheric storm during which a large mass of atmospheric gas rotates around a centre of low atmospheric pressure, generating high winds which spiral towards that centre.
cyclone
A cyclone which rotates around an area low atmospheric pressure with increased temperature.
The threshold of what is "warm" is variable, and thus data-level thresholding should be applied when using this class.
warm core cyclone
An environmental zone which is part of an atmosphere.
atmospheric zone
A gaseous part of an atmosphere in which gases have reduced atmospheric pressure.
Air is not specified directly (although the definition subsumes air masses) to allow for other forms of low pressure areas in planetary atmospheres.
area of low atmospheric pressure
A layer of liquid that is part of an estuary.
aquatic estuarine layer
A layer of estuarine water which extends a few centimeters from the surface of the water column towards the estuary bed and from the shore to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
estuarine coastal surface layer
A role which is may be realised by an environmental system
An oasis is a vegetated area located in a desert, supplied with water from a water source which it surrounds, and surrounded by arid soil, sand, or rock.
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
An environment which is determined by a bone element.
A liquid astronomical body part which is primarily composed of a continuous volume of liquid water and is held in shape or sustained by an environmental process.
Should create links to envrionmental process with new relation like "sustained_by"
A liquid surface layer which is in contact with air.
liquid air-water interface layer
A surface layer which is composed primarily of some liquid.
liquid surface layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A layer of estuarine water which extends from the surface of the water column to the pycnocline or mid-depth and from the shore to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
"Mid-depth", present in many CMECS classes, is ambiguous and needs refinement.
estuarine coastal upper water column
A pycnocline which is part of an estuarine water body, spanning from the shore to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
estuarine coastal pycnocline
A layer of estuarine water which extends from an estuarine pycnocline or mid-depth to the estuarine bed and from the shore to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
estuarine coastal lower water column
A layer of estuarine water which extends a few centimeters from the surface of the water column towards the estuary bed and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters until the end of the estuary most distal from the coast.
estuarine open water surface layer
A layer of estuarine water which extends from the surface of the water column to the pycnocline or mid-depth and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters until the end of the estuary most distal from the coast.
estuarine open water upper water column
A layer of fresh estuarine water which extends a few centimeters from the surface of the water column towards the estuary bed and from the land-water interface to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
What causes this freshwater layer to be "tidal" is not clearly specified in the current CMECS definition.
estuarine tidal riverine coastal surface layer
A layer of fresh estuarine water which extends from the surface of the water column to the pycnocline or mid-depth and from the land-water interface to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
"Mid-depth", present in many CMECS classes, is ambiguous and needs refinement. What causes this freshwater layer to be "tidal" is not clearly specified in the current CMECS definition.
estuarine tidal riverine coastal upper water column
A body of water which is primarily composed of saline water.
This class has its subclasses populated by inference.
saline water body
A body of water which is primarily composed of freshwater, with low solute content.
This class has its subclasses primarily populated by inference. The threshold for what constitutes "fresh" water is variable and should typically be deferred to an applicatoin layer resource.
fresh water body
A body of water which is primarily composed of brackish water.
brackish water body
A layer of estuarine water which extends from an estuarine pycnocline or mid-depth to the estuary bed and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters to end of the estuary most distal from the coast.
estuarine open water lower water column
A pycnocline which is part of an estuarine water body, spanning from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters until the end of the estuary most distal from the coast.
estuarine open water pycnocline
An estuarine coastal pycnocline which is composed primarily of fresh tidal water.
What causes this freshwater layer to be "tidal" is not clearly specified in the current CMECS definition. Further, the original definition and label do not clearly state whether this is a pycnocline in its own right, or just the tidal freshwater part of the pycnocline. In this ENVO class, we follow the semantics suggested by the label and treat this as a type of estuarine coastal pycnocline.
estuarine tidal riverine coastal pycnocline
A layer of fresh estuarine water which extends from an estuarine pycnocline or mid-depth to the estuarine bed and from the land-water interface to a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters.
estuarine tidal riverine coastal lower water column
A layer of fresh, tidal estuarine water which extends a few centimeters from the surface of the water column towards the estuary bed and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters until the end of the estuary most distal from the coast.
estuarine tidal riverine open water surface layer
A layer of fresh, tidal estuarine water which extends from the surface of the water column to the pycnocline or mid-depth and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters until the end of the estuary most distal from the coast.
estuarine tidal riverine open water upper water column
An estuarine open water pycnocline which is composed primarily of fresh tidal water.
What causes this freshwater layer to be "tidal" is not clearly specified in the current CMECS definition. Further, the original definition and label do not clearly state whether this is a pycnocline in its own right, or just the tidal freshwater part of the pycnocline. In this ENVO class, we follow the semantics suggested by the label and treat this as a type of estuarine open water pycnocline.
estuarine tidal riverine open water pycnocline
A layer of fresh estuarine water which extends from an estuarine pycnocline or mid-depth to the estuary bed and from a fiat boundary where the estuary bed below the water column reaches a depth of 4 meters to end of the estuary most distal from the coast.
estuarine tidal riverine open water lower water column
A biogeochemical cycle which has nitrogen-bearing chemical entities as participants.
nitrogen cycling
A biogeochemical cycle which has sulfur-bearing chemical entities as participants.
sulfur cycling
A biogeochemical cycle which has phosphorous-bearing chemical entities as participants.
phosphorous cycling
A tidal flow process which occurs in an ocean or sea and during which tidal movements generate advective flows, often amplified in velocity when moving through an inlet, pass or channel.
marine tidal flow process
A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged.
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
An ice mass which is attached to a bed underneath a body of water.
anchor ice
A marine current which is maintained by a tidal flow process.
This class aligns to an ambiguously defined unit of the Coastal and Marine Ecological Classification Standard (CMECS), "Tidal Flow" (https://cmecscatalog.org/cmecs/classification/unit/643.html). In CMECS, this is treated as a hydroform, but is defined as a process (while some of its subclasses are not). In ENVO, we have aligned the CMECS unit according to its definition as a process (ENVO:01001333); however, we maintain this class to allow reference to the hydroform maintained by that process.
marine tidal flow
Anchor ice which is attached to a riverbed.
riverine anchor ice
A marine zone in which ocean waters undergo a diurnal (once per day) tidal oscillation - with one high and one low tide per day - due to the supression of a second daily oscillation by the geometry of the ocean basin and obstructions presented by land masses.
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. In this case, the definition aligns with ENVO's "environmental zone" semantics. Alternate classes have been created to accommodate the process of diurnal tidal flow. The as the frequency of the process does not influence the semantics of the resulting hydroform, please use ENVO_01001336 to reference the hydroform rather than the zone or the process. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
diurnal marine tidal flow zone
A tidal flow process which occurs once per day in ocean waters where a second daily oscillation is blocked by land masses or ocean basin geometry.
This class broadly aligns to the Coastal and Marine Ecological Classification Standard (CMECS). This class is provided as the processual equivalent of CMECS unit 664 "Diurnal Tidal Flow" (https://cmecscatalog.org/cmecs/classification/unit/664.html); however, based on its definition, CMECS:664 is more accurately mapped to ENVO:01001338 as the definition aligns with ENVO's "environmental zone" semantics. A class has been created to accommodate the semantics of the resulting hydroform (ENVO:01001336). Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
diurnal marine tidal flow process
A marine tidal flow zone in which ocean waters undergo a semi-diurnal (twice per day) tidal oscillation - with two high and two low tides per day of roughly equal amplitude.
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. In this case, the definition aligns with ENVO's "environmental zone" semantics. Alternate classes have been created to accommodate the process of diurnal tidal flow. The as the frequency of the process does not influence the semantics of the resulting hydroform, please use ENVO:01001336 to reference the hydroform rather than the zone or the process. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
semi-diurnal marine tidal flow zone
An environmental zone in which varying gravitational forces from astronomical bodies, combined with the rotation of the astronomical body containing the zone, cause marine waters to undergo periodic depth oscillations (tides).
marine tidal flow zone
A water flow process during which movements of water masses caused by varying gravitational and rotational forces from astronomical bodies, combined with the rotation of the astronomical body containing the water mass, cause waters to undergo periodic depth oscillations (tides).
tidal flow process
A marine tidal flow process which occurs twice per day, resulting in two high and two low tides per day, both of roughly equal amplitude.
This class broadly aligns to the Coastal and Marine Ecological Classification Standard (CMECS). This class is provided as the processual equivalent of CMECS unit 666 "Semi-diurnal Tidal Flow" (https://cmecscatalog.org/cmecs/classification/unit/666.html); however, based on its definition, CMECS:666 is more accurately mapped to ENVO:01001340 as the definition aligns with ENVO's "environmental zone" semantics. A class has been created to accommodate the semantics of the resulting hydroform (ENVO:01001336). Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
semi-diurnal marine tidal flow process
Anchor ice which is attached to a riverbed where a river flows into a marine water body and which is formed by the freezing of freshwater seeping out of the riverbed's sediments.
fresh water seep riverine bottom-fast ice
freshwater seep riverine bottom-fast ice
freshwater seep riverine anchor ice
An ice mass which is suspended in a water body, being sufficiently buoyant for part of the mass to breach the surface of that water body.
floating ice mass
An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited.
erosion
A zone on a glacier which is roughly linear and where the rates of ice ablation and accumulation are approximately equal.
glacial equlibrium line
A zone in which the deposition and accumulation of an environmental material occurs.
material accumulation zone
A zone in which processes resulting in the removal of one or more environmental materials have higher rates than pocesses which result in their deposition and accumulation.
material decumulation zone
A material accumulation zone in which the rates of ice formation processes exceed those of ice decumulation processes, leading to a net icrease in some mass of ice.
ice accumulation zone
A material decumulation zone in which the rates of ice formation processes are below those of ice decumulation processes, leading to a net decrease in some mass of ice.
ice decumulation zone
An ice accumulation zone which overlaps part of a glacier.
This zone usually occurs at higher elevations and generally overlaps the conversion of snow to glacial ice.
glacial ice accumulation zone
An environmental zone in which the rates of two or more processes are roughly equal to one another.
environmental zone of processual equilibrium
QCR: 'contains process' min 2 'environmental system process'
A glacier which is contained in the site bounded by a volcanic crater.
volcanic crater glacier
crater zone
The site which is located in a volcanic crater.
volcanic crater zone
A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall, and which loses more liquid water by evapotranspiration than is supplied by precipitation.
desert
A climate which is realised through hydrological processes.
hydroclimate
An aerosol formation event which occurs in an atmosphere.
rapid formation of liquid or solid particles from gaseous material in an atmosphere
Note that the detection of such events, and thus the thresholds used to define them in the field, are operational and dependent on the technology and observation strategy used. The event must be intense enough, occur in a large enough area, and persist for enough time to allow the formed particle population to be observed. There are no exact or universally agreed upon thresholds for the intensity, area and duration of such events. If elevated new particle formation rate is observed in the atmosphere (away from direct sources of the related gas-phase molecules) for an operationally defined period of time, practitioners often declare that such an event has taken place.
atmospheric aerosolised particle formation event
An alpine tundra ecosystem which exists above the continuous timberline but below the permanent snowline on elevated land in tropical regions.
Paramo ecosystems are known to be evolutionary hotspots and large daily fluctuations in temperature and humidity, often resulting in dialy freez-thaw cycles.
Paramo
A direction which inheres in an atmospheric wind, typically expressed as the inverse of the direction the wind is moving in.
atmospheric wind direction
atmospheric wind speed
The volume of water which has fallen during a precipitation process.
Niederschlagsmenge
While the precipitated material may be water in any of its forms, the volume that this class refers to is that of liquid water.
volume of hydrological precipitation
A system which consists of an atmosphere, hydrosphere, cryosphere, land surface, and biosphere, forced or influenced by external processes.
This class, from the IPCC report, is naturally focused on the Earth's climate. The report cites the Sun as the agent of the most important forcing processes. It also considers the direct effect of human activities on the climate system an external forcing
climate system
A process during which gas-phase molecules form solid or liquid particles that are stable enough to continue growing in size - via the condensation or aggregation of other gas-phase molecules - at a greater rate than their constituents re-enter gas phase.
formation of liquid or solid particles from gaseous material in an atmosphere
formation of an aerosol in an atmosphere
formation of an aerosol in the atmosphere
formation of particles from gaseous material in an atmosphere
atmospheric secondary aerosol formation process
A process during which particles suspended in a gaseous medium are formed.
aerosolised particle formation process
A material transport process during which solid or liquid particles are directly introduced into a volume of gas.
primary aerosol formation process
An aerosol formation process during which solid or liquid particles are either 1) formed in a volume of gas through gas-to-liquid or gas-to-solid conversions or 2) increase in size through aggregation with other particles.
secondary aerosol formation process
A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas.
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F"
tidal mangrove shrubland
An ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover.
Tundra ecosysems are often underlaid by permafrost, with the result that drainage is bad and the soil may be saturated for long periods. It does not have a permanent snow-ice cover. Productivity is low in this biome because of the extremes of climate.
tundra ecosystem
This definition is a synthesis of the following sources: NSIDC Glossary accessed 2016, IPCC WGII AR5 2014, Van Everdingen International Permafrost Association 2005, AMS - glossary of meteorology, PhysicalGeography.net
A tundra ecosystem which exists at high altitudes and where vegetation is stunted due to low temperatures and high winds.
alpine tundra ecosystem
An aerosol formation process during which the rate of particle formation exceeds that which is normally present in the site of its occurrence.
This is similar to the semantics of storms, where increased rates are observed due to external forcings.
aerosolised particle formation event
A secondary aerosol formation process which occurs in an atmosphere at an increased rate relative to background processes of the same kind.
atmospheric new particle formation event
secondary atmospheric aerosol formation event
A physical quality which inheres in a marine water body by virtue of the height, wavelength, period, and directional energy flux of its waves which evolve into swell through nonlinear dynamics.
sea state
A variability quality which inheres in sea ice, particularly in its concentration, area and extent, type, motion, deformation, age, thickness, and volume.
The EOV specification sheet is simply titled as "sea ice", but the description of the EOV is of the variability of sea ice.
sea ice variability
A marine bed which is covered by animals which have benthic habitats, including attached, clinging, sessile, infaunal, burrowing, laying, interstitial, and slow-moving animals, but not animals that have created substrate.
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. An excerpt of the CMECS description: "Faunal Beds are highly dependent on substrate type. Individual species and entire biotic communities have adapted specialized anatomies and behaviors for survival on hard substrates; other species and communities have specialized and developed adaptations for life on soft substrates. Generalist fauna also occur (e.g., certain holothurians, crustaceans, and sponges) that can succeed on both substrate types. However, substrate type is such a defining aspect of the Faunal Bed class that CMECS Faunal Bed subclasses are assigned as physical-biological associations involving both biota and substrate."
marine faunal bed
A elevation quality which inheres in a marine water body by virtue of the position of that water body's surface layer (adjacent to an atmosphere) relative to some reference elevation.
sea surface height
A submerged bed which underlies a marine water body.
sea bottom
marine bed
A marine faunal bed which is dominated by mussels of the Mytilus or Modiolus genera either 1) resting on the sediment surface, 2) partially embedded in the sediment, 3) attached to conspecifics (by using their byssal threads), or 4) attached to a piece of gravel in slightly gravelly fine sediments.
If individual mussels are present in densities sufficient to construct biogenic substrate, please use the mussel reef class.
mussel bed
A marine reef which is located on a shelf (i.e. in the neritic zone) and primarily composed of self-adhered or conglomerated mussel shells.
The CMECs classification references shelf reefs in the definition. Thus this term is focused only on mussel reefs that are neritic.
neritic mussel reef
A marine reef which is present in the depths beyond (offshore relative to) the continental shelf and primarily composed of self-adhered or conglomerated mussel shells.
This class is an extension of the Coastal and Marine Ecological Classification Standard (CMECS). It provides an oceanic analogue to the neritic mussel reef class (CMECS:338). Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
oceanic mussel reef
An area which is dominated by dense accumulations of mussels attached to a substrate other than conspecifics, including the associated faunal communities and predators present on the mussels (e.g., starfish).
This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. From the CMECs definition: "Areas where mussels have constructed substrate are classified as Mussel Reef. Areas where mussels are not attached to a hard substrate are classified as Soft Sediment Fauna, Mussel Bed."
area of attached mussel assemblages
An area which is dominated by dense accumulations of mussels, of the genus Modiolus, attached to a substrate other than conspecifics, including the associated faunal communities and predators present on the mussels (e.g., starfish).
area of attached Modiolus assemblages
An environmental zone within which ecological communities of animals are attached to some substrate.
area of attached faunal communities
An oceanic mussel reef which is primarily settled by mussels of the genus Bathymodiolus and primarily composed of self-adhered or conglomerated mussel shells
Bathymodiolus-dominated oceanic mussel reef substrate
This class is an extension of the Coastal and Marine Ecological Classification Standard (CMECS). It provides an oceanic analogue to the neritic mussel reef class (CMECS:338), with a focus on Bathymodiolus communities. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
Bathymodiolus-dominated oceanic mussel reef
A marine reef which is primarily composed of self-adhered or conglomerated mussel shells.
mussel reef
A mussel bed which is located in benthic regions beyond (offshore to) a continental shelf.
This class extends the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions.
oceanic mussel bed
A mussel bed which is located in benthic regions that are part of a continental shelf.
neritic mussel bed
An oceanic mussel bed which has mussel communities dominated by members of the genus Bathymodiolus.
Bathymodiolus-dominated oceanic mussel bed
An organic environmental material which is primarily composed of gill tissue.
gill tissue material
Gill tissue material which is part of salt-water mussel in the family Mytilidae
mussel gill tissue material
Mussel gill tissue material which is part of a member of the genus Bathymodiolus.
Bathymodiolus gill tissue material
A material accumulation process during which the solid or liquid parts of an aerosol increase in mass due to mechanical aggregation of existing particles or through chemical conversion of gas-phase material.
accumulation of matter on aerosolised particles
Biomass which is composed primarily of dead organisms, their parts, or their organic derivatives.
necromass
abyssal clay
A soil which has high mineral content and which contain no calcareous material, have less than 10% weatherable minerals its surface layer, and have less than 35% base saturation throughout its volume.
The word "ultisol" is derived from "ultimate", because ultisols were seen as the ultimate product of continuous weathering of minerals in a humid, temperate climate without new soil formation via glaciation.
ultisol
A primary aerosol formation process during which dust particles are suspended in a gaseous medium.
aerosolisation of dust
A process during which dust is aerosolised in an atmosphere.
atmospheric aerosolisation of dust
An aeroform which is formed as a result of strong upper winds spreading a cirrus homogenitus cloud in the atmosphere and, in turn, causing internal tranformations which result in the cloud taking on the appearnce of natural cirri-form clouds.
Once these clouds resemble natural cirri-form clouds (Cirrus, Cirrocumulus, Cirrostratus), they are classified as such.
homomutatus cloud
An environmental process during which a haze is formed by the aerosolisation of solid particles, including natural materials and anthropogenic pollutants, in an atmosphere.
haze formation process
An aersolised mass of dust, smoke, or other dry particulates which scatters visible light thus obsscuring visibility through an atmosphere.
haze
A haze formation process which has an increased rate relative to that which is usually present in a given site.
haze formation event
An ecosystem which is of larger scale than an ecoregion and which includes smaller ecosystems determined by the presence of ecological assemblages that have at least some cohesion over evolutionary time frames.
Assemblages within provinces will show endemism, principally at the level of species. While this may be partly explained by historical isolation, abiotic environmental features and coniditions will play a strong role. These may include geomorphological features (isolated island and shelf systems, semi-enclosed seas); hydrographic features (currents, upwellings, ice dynamics); or geochemical influences (broadest-scale elements of nutrient supply and salinity).” Examples include Cold Temperate Northeast Pacific, Tropical Northwestern Atlantic, and Cold Temperate Northeast Pacific.
ecological province
An anthropogenic environment which is bounded by the building envelope of a laboratory and in which a system of manufactured products exert control on one or more of its environmental conditions.
laboratory environment
A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed.
research laboratory
laboratory facility
A cloud which 1) has been shaped into structural elements resembling grains or ripples, 2) is almost exclusively composed of ice crystals, 3) is located in the high level of the atmosphere (high étage).
Cirrocumulus-Wolke
Hohe Schäfchenwolke
Zirrokumulus
When present in aggregates, individual cirrocumulus clouds are merged or separate, and regularly arranged in a thin patch, sheet or layer. Most of the small structural elements have an apparent width of less than one degree. Strongly supercooled water droplets may occur but are usually rapidly replaced by ice crystals. When well-illuminated by sunlight (excluding during sunrise and sunset) cirrocumulus clouds appear white. Absence of any precipitation.
cirrocumulus cloud
A cloud which 1) occurs in the form of a smooth or fibrous veil, 2) is composed of few small ice crystals, 3) is located in the high level of the atmosphere (high étage).
Cirrostratus
Hohe Schleierwolke
Zirrostratus
Cirrostratus clouds totally or partly cover the sky and are always thin enough to show the disc of the local star. When well-illuminated by sunlight (excluding during sunrise and sunset) cirrostratus clouds appear transparent or whitish. Cirrostratus clouds generally produce halo phenomena; sometimes the veil of cirrostratus is so thin that a halo provides the only indication of its presence. Absence of any precipitation.
cirrostratus cloud
A cloud which 1) has been shaped into laminae, rounded masses or rolls, 2) is exclusively composed of water droplets, 3) is located in the middle level of the atmosphere (middle étage).
This definition is very odd, it seems to allow for such a wide range of variation that the boundaries of this class become suspect. Add more PATO qualities once they have been added to PATO.
Altocumulus-Wolke
Grobe Schäfchenwolke
Altocumulus clouds are sometimes fibrous or diffuse and may or may not be merged. When present in aggregates, individual altocumulus clouds are organised in patches, sheets or layers. Most of the regularly arranged small elements in this cloud type often have an apparent width of between one and five degrees. When well-illuminated by sunlight (excluding during sunrise and sunset) altocumulus clouds appear white, grey, or both white and grey, often with shading. The composition of altocumulus clouds leads to low transparency and sharp outlines of the elements. Absence of any precipitation.
altocumulus cloud
A cloud which 1) occurs in the form of a striated, fibrous, or uniform sheet or layer, 2) is composed of water droplets and ice crystals, 3) is located in the middle level of the atmosphere (middle étage).
Altostratus-Wolke
Mittelhohe Schichtwolke
Striation occurs in the form of grooves or channels in cloud formations, arranged parallel to the flow of the air. When well-illuminated by sunlight (excluding during sunrise and sunset) altostratus clouds appear greyish or bluish. Altostratus clouds do not show halo phenomena when scattering visible range stellar radiation. Altostratus clouds have parts thin enough to reveal the local star at least vaguely, as through ground glass or frosted glass. Altostratus may produce rain, snow or ice pellets. Altostratus is usually found in the middle level, but it often extends higher. Altostratus is generally a layer of great horizontal extent (several tens or hundreds of kilometres) and fairly considerable vertical extent (several hundreds or thousands of metres). In the most complete case, three superposed parts can be distinguished: (a) An upper part, composed wholly or mainly of ice crystals, (b) A middle part, composed of a mixture of ice crystals, snow crystals or snowflakes and supercooled water droplets, (c) A lower part, composed wholly or mainly of ordinary or supercooled water droplets or drops. Sometimes the cloud may consist of only two parts, either: 1) An upper part like (a) above and a lower part like (c) or, 2) An upper part like (b) and a lower part like (c). Less frequently, the entire cloud may also be like (a) or like (b) alone.
altostratus cloud
A cloud which 1) occurs in the form of a layer, 2) is composed of water droplets (sometimes supercooled) and raindrops, or snow crystals and snowflakes, or of a mixture of these liquid and solid particles, 3) is located in the middle level of the atmosphere (middle étage).
Nimbostratus-Wolke
Regen-schichtwolke
Low, ragged clouds frequently occur below the nimbostratus layer, with which they may or may not merge. When well-illuminated by sunlight (excluding during sunrise and sunset) nimbostratus clouds appear grey, often dark grey in colour. Nimbostratus clouds usually have no discernible base. Nimbostratus generally covers a wide area and is of great vertical extent. Nimbostratus is diffused by more or less continuously falling rain or snow or ice pellets, which in most cases reaches the ground. Sometimes nimbostratus clouds have the appearance of being illuminated from the inside. Nimbostratus is almost always found in the middle level, but it usually extends into the other two levels. Nimbostratus is thick enough throughout to blot out the local star.
nimbostratus cloud
A cloud which 1) has been shaped into non-fibrous tessellations, rounded masses, or rolls, 2) is primarily composed of water droplets, and may contain raindrops or, more rarely, snow pellets, snow crystals and snowflakes, 3) is located in the low level of the atmosphere (low étage).
Haufenschichtwolke
Stratocumulus-Wolke
When present in aggregates, individual stratocumulus clouds are organised in patches, sheets or layers. Most of the regularly arranged small elements in this cloud type often have an apparent width of more than five degrees. When well-illuminated by sunlight (excluding during sunrise and sunset) stratocumulus clouds appear grey or whitish, or both grey and whitish in colour. The cloud almost always has dark parts. Fibrous structural elements may emerge when virga is formed. Stratocumulus can have weak falls of rain, snow or snow pellets. Stratocumulus may also be shaped into structural elements which are similar to but do not exactly resemble the ones noted in the definition.
stratocumulus cloud
A cloud which 1) occurs in the form of a layer with a fairly uniform base or, less frequently, ragged patches, 2) is composed of small water droplets, 3) is located in the low level of the atmosphere (low étage).
Stratus-Wolke
niedere Schichtwolke
When well-illuminated by sunlight (excluding during sunrise and sunset) stratus appears grey in colour. Stratus clouds only produce halo phenomena at very low temperatures. Stratus can have weak falls of drizzle, snow or snow grains. Stratus may allow a clearly visible outline of the local star to be seen through its mass.
stratus cloud
A cloud which 1) has been shaped into rising mounds, domes, or towers with a bulging upper part resembling a cauliflower and a near horizontal or ragged base, 2) is mainly composed of water droplets, 3) is located in the low level of the atmosphere (low étage).
Add more PATO qualities once they have been added to PATO. Note that the domed quality refers to the cauliflower shape (which is itself a variant of domed). This should be replaced with cauliflower shaped once in ENVO.
Cumuluswolke
Haufenwolke
Kumuluswolke
Quellwolke
When well-illuminated by sunlight (excluding during sunrise and sunset) cumulus has has brilliant white sunlit parts and a dark grey base. Cumulus clouds have sharp outlines. When of great vertical extent, cumulus may release precipitation in the form of showers of rain, snow or snow pellets. Cumulus clouds usually have their bases in the low atmospheric level (low étage), but their vertical extent is often so great that their tops may reach into the middle and high atmospheric levels (middle and high étage).
cumulus cloud
A cloud which is formed by condensation events triggered by some anthropogenic processes or the outputs thereof, such as aircraft contrails or emissions from chimneys.
homogenitus cloud
A mining process during which materials are extracted from benthic environments deep below the ocean surface, where no stellar radiation reaches..
"The most valuable of the marine mineral resources is petroleum. About 15% of the world's oil is produced offshore, and extraction capabilities are advancing. One of the largest environmental impacts of deep sea mining are discharged sediment plumes which disperse with ocean currents and thus may negatively influence the marine ecosystem. Coal deposits known as extensions of land deposits , are mined under the sea floor in Japan and England."
benthic deep-sea mining
A cloud which develop locally over forests as a result of increased humidity due to evaporation and evapotranspiration from the tree canopy.
These special clouds will be given the name of the appropriate genus, followed by any appropriate species, variety and supplementary feature, and followed by the special cloud name “silvagenitus” (for example, Stratus silvagenitus).
silvagenitus cloud
A cirrus cloud which occurs as a detached unit or a thin veil and consists of nearly straight or irregularly curved filaments that do not terminate in hooks or tufts.
The species-level term, 'fibratus', applies mainly to clouds of the Cirrus and Cirrostratus genera
cirrus fibratus cloud
A cloud which 1) has been shaped into dense, mountain-like forms or one or more tower-like forms with a flattened upper portion, which often spreads out in the shape of an anvil or plume, 2) is composed of water droplets and, especially in its upper portion, ice crystals, 3) is located in the low level of the atmosphere (low étage), but can extend into the middle and high level of the atmosphere.
Cumulonibus-Wolke
Gewitterwolke
Cumulonimbus clouds have a very dark base which may be merged with low ragged clouds which frequently form underneath this cloud. The upper portion may be smooth, fibrous, or striated. Cumulonimbus also contains large raindrops and, often, snowflakes, snow pellets or hailstones. The water droplets and raindrops may be substantially supercooled. Cumulonimbus is frequently associated with precipitation, sometimes in the form of virga. Cumulonimbus is often accompanied by lightning, thunder or hail. Cumulonimbus usually have their bases in the low level, but their vertical extent is often so great that their tops may reach into the middle and high levels.
cumulonimbus cloud
A mining process during which materials are extracted from the surface, or below the surface, of the ocean floor.
sea bed mining
A cirrus cloud which does not have grey parts and which is often shaped like a comma, terminating at its highest point in a hook, or in a tuft, the upper part of which is not in the form of a rounded protuberance.
cirrus uncinus cloud
A cirrus cloud which 1) is structurally organised in patches, 2) is sufficiently dense to appear greyish when viewed towards the local star and 3) may veil, the local star, obscure its outline, or even hide it entirely.
Cirrus spissatus often originates from the upper part of a Cumulonimbus.
cirrus spissatus cloud
A cirrostratus cloud which occurs as a detached unit or a thin veil and consists of nearly straight or irregularly curved filaments that do not terminate in hooks or tufts.
cirrostratus fibratus cloud
A stratocumulus cloud which 1) has linearly arranged cumuliform protuberances which resemble crenellated turrets or towers, some of which are taller than they are wide in some portion of their upper parts, 2) possess a lower region or base which connects these protuberances.
The species-level term, 'castellanus', applies to Cirrus, Cirrocumulus, Altocumulus and Stratocumulus genera. The castellanus character is especially evident when the clouds are seen from the side.
stratocumulus castellanus cloud
A cirrus cloud which 1) has linearly arranged cumuliform protuberances which resemble crenellated turrets or towers, some of which are taller than they are wide in some portion of their upper parts, 2) possess a lower region or base which connects these protuberances.
cirrus castellanus cloud
A cirrocumulus cloud which 1) has linearly arranged cumuliform protuberances which resemble crenellated turrets or towers, some of which are taller than they are wide in some portion of their upper parts, 2) possess a lower region or base which connects these protuberances.
cirrocumulus castellanus cloud
An altocumulus cloud which 1) has linearly arranged cumuliform protuberances which resemble crenellated turrets or towers, some of which are taller than they are wide in some portion of their upper parts, 2) possess a lower region or base which connects these protuberances.
altocumulus castellanus cloud
A cloud which is primarily composed of water-based aerosols.
On Earth clouds are formed by the saturation of air in the homosphere when air cools or gains water vapor. Note that this class describes clouds as countable objects, rather than 'cloud material'. It also refers only to clouds made up of a water-based material.
water-based cloud
An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce.
Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia.
land conversion process
A land conversion process during which terrestrial ecosystems are altered to facilitate agricultural activities such as crop cultivation or the rearing of livestock.
This process typically relies on the conversion and development of forests, savannas or grassland. Creation of farmland from wasteland, deserts or previous impervious surfaces is considerably less frequent because of the presence of degraded soil or the lack of fertile soil.
agricultural land conversion process
An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment.
There are multiple systems of land use classification. This hierarchy aims to be generally applicable, but national systems can be added on request.
land use process
A land use process during which humans access and manage forest ecosystems for 1) the provisioning of wood, forages, water, wildlife, and recreation as well as a broad range of other ecosystem services or 2) the maintenance of the forest ecosystem's health.
"Modern forestry generally embraces a broad range of concerns, in what is known as multiple-use management, including the provision of timber, fuel wood, wildlife habitat, natural water quality management, recreation, landscape and community protection, employment, aesthetically appealing landscapes, biodiversity management, watershed management, erosion control, and preserving forests as 'sinks' for atmospheric carbon dioxide. A practitioner of forestry is known as a forester. Other common terms are: a verderer, or a silviculturalist. Silviculture is narrower than forestry, being concerned only with forest plants, but is often used synonymously with forestry."
forestry
A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit.
terrestrial mining
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
Deforestation which is planned and executed by humans.
planned deforestation
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem.
mining
A mining process during which rock or mineral deposits are extracted from the terrestrial surface layers of an astronomical body.
quarrying
A mining process which occurs in a marine ecosystem.
marine mining
A mining process during which coal is extracted from the rocky portion of an astronomical body.
This may be either terrestrial or marine.
coal mining
A mining process during which metal ores and minerals that lie near the terrestrial surface of an astronomical body are extracted by removing the overlying material and breaking and loading the ore.
opencast mining
A land use process during which terrestrial environments are modified such that they can grow crop plants or allow the rearing of animals to provide food, fiber, medicines, or other products used by humans.
"Agriculture includes horticulture, fruit growing, seed growing, dairy farming, the breeding and keeping of livestock (including any creature kept for the production of food, wool, skins or fur), the use of land as grazing land, meadow land, osier land, market gardens and nursery grounds, and the use of woodlands where that use is ancillary to the farming of land for other agricultural purposes."
agriculture
A planned environmental usage process during which humans access an environment in order to promote the refreshment of their physical and psychological health through relaxation and leisure activities.
usage of an environment for recreation
A planned environmental usage process during which an environment facilitates the movement of materials and material objects (persons or goods) from place to place, typically with the assistance of a vehicle.
usage of an environment for transportation
A planned environmental usage process during which an environment supports 1) enterprises concerned with the provision to the public of essentials, such as electricity or water or 2) the basic network or foundation of capital facilities or community investments which are necessary to support economic and community activities.
usage of an environment for infrastructure and utilities
A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans.
This class does not include environments which are primarily used for commerce or industry.
usage of an environment for residential activity
A planned environmental usage process during which an environment supports welfare activities organised by the state or a local authority and carried out by trained personnel.
Services include those provided by health care facilities, places of religious worship, educational facilities, police stations, fire stations, coastguard facilities, public sanitation, non-human animal welfare services, detention services, and other public services.
usage of an environment for community and social services
A planned environmental usage process during which an environment supports the sale of goods to ultimate consumers, usually in small quantities.
This class includes activities carried out in shops, showrooms, cafes, travel agents, hairdressers, facilities providing financial and professional services, restaurants, public houses, and bars.
usage of an environment for retail activity
A planned environmental usage process during which an environment supports activities which aim to protect citizens or any geographical area by preparing for or by using military means to resist the attack of an enemy.
This class includes activities carried out in defence establishments, including camps, airfields, and live firing training areas. It excludes sites where defence personnel reside, such as barracks.
usage of an environment for defence
A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production.
This class includes environments used to support the facilities engaged with a broad variety of manufacturing activities from food and tobacco, to textiles, metals, vehicles, and chemicals.
usage of an environment for industry
A planned environmental usage process during which an environment supports facilities associated with commerce or the earning of a livelihood through means other than manufacturing or the provision of a public service.
This class includes activities carried out in commercial offices, meeting centres, art studios, recording studios, film sets, warehouses, and distribution centres.
usage of an environment for business
A habitat which supports the persistence and growth of a population of Calyptra moths and which overlaps mesic meadows and edges and clearings in vegetated areas.
Calyptra habitat
A mountain which is located on land and which is bounded by an atmosphere or outer space.
terrestrial mountain
A mountain that is part of a polar environment.
polar mountain
A mountain that is part of a temperate environment.
temperate mountain
A mountain that is part of a tropical environment.
tropical mountain
A montane forest ecosystem which 1) is evergreen, 2) present on mountains where there is frequent cloud and mist cover, 3) which has a large proportion of ferns and mosses in its plant communities, growing on all tree trunks and branches present in the ecosystem, and 3) harvests aerosolised water and adds it to the terrestrial water supply.
cloud forest
A visible mass of water droplets or ice crystals suspended in the air at or near a planetary surface, formed when humid air cools rapidly.
This class refers only to mist formed by materials primarily composed of water. Mist is less dense than fog, and visibility is typically greater than one kilometre.
mist
A mountain which has a maximum elevation greater than 2500 metres above sea level.
On Earth, mountains in this category cross the atmospheric oxycline above which oxygen concentrations fall below the physiological tolerance threshold of most humans. Note that the threshold elevations are inconsistent between the various reports which list this classification: while some have overlapping thresholds, others are non-overlapping. The latter model is used in ENVO for coherence and to adhere to the Kapos et al. 2000 reference.
high-elevation mountain
A mountain which has a maximum elevation between 300 and 2499 metres above sea level and slopes greater than or equal to two degrees of inclination.
On Earth, mountains in this category are below the atmospheric oxycline above which oxygen concentrations fall below the physiological tolerance threshold of most humans. Note that the threshold elevations are inconsistent between the various reports which list this classification: while some have overlapping thresholds, others are non-overlapping. The latter model is used in ENVO for coherence and to adhere to the Kapos et al. 2000 reference.
mid-elevation mountain
A high-elevation mountain which has a maximum elevation greater than 4500 metres above sea level.
UNEP-WCMC class 1 mountain
A high-elevation mountain which has a maximum elevation between 3500 and 4500 metres above sea level.
UNEP-WCMC class 2 mountain
A high-elevation mountain which has a maximum elevation between 2500 and 3500 metres above sea level.
UNEP-WCMC class 3 mountain
A mid-elevation mountain which has a maximum elevation between 1500 and 2499 metres above sea level and a slope greater than or equal to two degrees.
UNEP-WCMC class 4 mountain
A mid-elevation mountain which has a maximum elevation between 1000 and 1499 metres above sea level and either 1) a slope greater than or equal to five degrees or 2) a local elevation range, within a 7 kilometre radius, of greater than 300 metres above sea level.
UNEP-WCMC class 5 mountain
A mid-elevation mountain which has a maximum elevation between 300 and 999 metres above sea level and a local elevation range, within a 7 kilometre radius, of greater than 300 metres above sea level.
UNEP-WCMC class 6 mountain
An elevated inner basin or plateau surrounded by mountains, but not - itself - a mountain.
This is an odd class, as it's not a mountain in itself but is used to classify elevated basins and plateaus surrounded by mountains.
UNEP-WCMC class 7 mountain
An ecosystem which overlaps those areas of the foreshore and seabed that are exposed to the air at low tide and submerged at high tide.
These semantics link with those of environmental zones. Use this class to refer to the ecosystem rather than the area that it occupies.
intertidal ecosystem
A system of constructed and manufactured products which are used by humans to produce data, information, or knowledge about material, immaterial, or processual entities.
observing system
An observing system which generates long-term data about one or more entities of interest, typically using standardised methodology.
observatory system
atmospheric observatory system
marine observatory system
terrestrial observatory system
astronomical observatory system
An observatory system which includes components used to generate (meta)genomic, (meta)transcriptomic, (meta)proteomic, metabolomic, and other omic data, information, and knowledge.
omics observatory system
A liquid astronomical body part which is continuous and is delimited by physical discontinuities or non-liquid boundaries.
body of liquid
A part of an astronomical body which is primarily composed of liquid material.
liquid astronomical body part
A part of an astronomical body which is primarily composed of gaseous material.
gaseous astronomical body part
A part of an astronomical body which is primarily composed of fluid.
fluid astronomical body part
A building which is primarily used for the long-term habitation of humans.
domestic building
A prison facility which is owned and operated by a state.
public correctional center
public correctional centre
public correctional facility
public detention center
public detention centre
public gaol
public jail
public lock-up
public penitentiary
public remand center
public remand centre
detention center
gaol
penitentiary
remand center
public prison
A tornado is an aeroform consisting of at least one rapidly rotating column of air that is in contact with both the surface of an astronomical body and pendant from within or beneath a cumulonimbus or cumulus cloud.
twister
whirlwind
This class refers to tornados on Earth, but can be used as the basis for a more generalised class for tornados which a composed of gaseous materials other than air.
tornado
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
land surface
surface of an astronomical body
A fire whirl is a whirlwind induced by the contraction and rotation of intense, rising heat and turbulent, eddying air masses resulting from a large fire and made up of a core of burning matter surrounded by a rotating pocket of air.
fire devil
fire swirl
fire tornado
fire twister
firenado
Note that this not a sublcass of "tornado": this is a different phenomenon formed as a result of convection induced by fire.
fire whirl
A tornado which comprises two or more columns of spinning air rotating about their own axis and at the same time around a common center.
multiple vortex tornado
A tornado which a) is not associated with a mesocyclone and is thus relatively weak and short-lived, b) is centred on a small, smooth condensation funnel which often does not reach the planetary surface, and c) forms a distinctively laminar cloud of dust when it makes contact with the land.
dust-tube tornado
fair weather waterspout on land
land spout
landspout
A tornado which connects a cumulus or cumulonimbus cloud to a body of water, often transporting water from that water body along the spiraling winds constituting its vortex.
water spout
Wikipedia notes that there is disagreement over whether to classify waterspouts as true tornadoes.
waterspout
A vehicle which is able to travel through air in an atmosphere.
aircraft
A slope of land descending laterally from a hill, mountain or main crest of a ridge.
spur
A mass of environmental material which has been formed as the result of its transport into an existing mass of another material.
intrusion
An elevation which is flattened across its highest surface.
flattened elevation
A remote sensing process during which image data about an astronomical body or object is generated by sensors mounted on a satellite.
satellite imaging
A remote sensing process during which image data about a planet is generated by sensors mounted on a satellite.
satellite imaging of a planet
moonmoon
Dioxygen which is the solute in a solution with ocean water as its solvent.
dioxygen dissolved in marine water
This is the label that GOOS uses in its EOV specification sheet, found here: https://www.goosocean.org/components/com_oe/oe.php?task=download&id=35904&version=2.0&lang=1&format=1
A macronutrient role which inheres in nitrate, nitrogen dioxide, ammonium, silicon, or phosphate dissolved in ocean water.
inorganic macronutrient dissolved in ocean water
A system which is composed of carbon-based chemical entities dissolved in or otherwise part of an ocean or sea and the atmosphere adjacent to it, undergoing constant exchange through biogeochemical cycling.
To measure the state and dynamics of the ocean's carbonate system, at least two of the following qualities must be measured: Dissolved Inorganic Carbon (DIC), Total Alkalinity (TA), Partial pressure of carbon dioxide (pCO2), and pH.
carbonate system of ocean water
A process by which landforms are formed from the thawing of ice-rich permafrost or the melting of massive ground ice.
Landforms found in Thermokarst terrain include alases, thermokarst lakes, and thermokarst mounds. Landscape dominated by depressions, pits, and caves that is created by the thawing of ground ice in high latitude locations. Resembles karst landscape but is not created by chemical weathering.
thermokarst formation process
An active ecosystem management process which targets an agricultural ecosystem.
Agrarumweltmaßnahme
agricultural environment management
active agri-ecosystem management process
A pollution process during which artificial light with wavelengths in the visible spectrum is released into the environment.
Lichtverschmutzung
This form of pollution is typically the result of urbanisation or similar land use change.
anthropogenic light pollution
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product.
radiation from a manufactured product
Radiation from a manufactured product during which light between the wavelenghts of 380 nm and 760 nm is emitted.
optical radiation from a manufactured product
visible spectrum radiation from a manufactured product
A solid surface layer which is that part of a glacier in contact with a planetary atmosphere, water body, or solid material partially surrounding that glacier.
glacial surface layer
A velocity quality which inheres in the surface layer of a glacier.
glacial surface layer velocity
A tundra biome which exists at high altitudes and where vegetation - dominated by a few species of dwarf shrubs, a few grasses, sedges, lichens, and mosses - is stunted due to low temperatures and high winds.
The absence of trees in this biome is primarily due to high altitude rather than high latitude. On Earth, it lies roughly between the summer isotherm of 10 degrees Centigrade and the snow line. Primary productivity is low in this biome because of the extremes of climate.
alpine tundra biome
An ice mass which has calved off an larger mass of ice.
This definition is intentionally broad to include the multiple existing and used definitions of ice calfs.
ice calf
An ice calf which is suspended in a water mass, being partially exposed to an atmosphere.
floating ice calf
An ice calf which is frozen to the bed of an ocean or other water body.
anchored ice calf
terrestrial ice calf
A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects.
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
Water ice which is formed by the freezing of fresh water.
freshwater ice
Sea ice which 1) has formed on the submerged surface (i.e. the base) of an existing mass of sea ice and 2) is composed of columnar crystals due to the downward growth of the crystals into the water.
Congelation ice usually forms through the fusion/coalescence of platelets into solid ice.
congelation sea ice
Common in limnology, but frequently used in other contexts (e.g. on roads).
Water ice which has formed in a mass of permafrost.
permafrost congelation ice
Freshwater ice which forms downward from the surface of a freshwater water body and is transparent due to a reduced number of air bubbles trapped in its mass.
congelation ice in a fresh water body
Freshwater ice which forms on a solid substrate through the freezing of freshwater.
freshwater congelation ice
Freshwater congelation ice which has formed on a solid substrate in an ice cave.
ice cave congelation ice
A floating mass of ice which is 1) unattached to land or land-fast ice and 2) moved by the action of winds or currents.
Prior to approximately 2014, drift ice was synonymous with the various grades of pack ice, described as very open (with an ice concentration of 1/10 to 3/10), open (4/10 to 6/10, with many leads and polynyas and the floes generally not in contact with one another), close (7/10 to 8/10, composed of floes mostly in contact), very close (9/10 to less than 10/10), and compact (10/10, with no water visible, called consolidated pack ice if the floes are frozen together). This is deprecated, with pack ice now referring to drift ice with a concentration equal to or above 7/10; however, other usages are still common.
drift ice mass
A drift ice mass which is composed primarily of sea ice.
drifting sea ice mass
Researchers of sea ice typically refer to this class simply as "drift ice".
An area in which masses of drift ice aggregate such that they cover a minimum of 7/10ths-8/10ths of the surface the water body they are floating in.
area of pack ice
An environmental zone that overlaps that part of a water body covered or partially covered by sea ice.
area of sea ice
An area in which masses of drift ice aggregate such that they cover less than 7/10ths of the surface the water body they are floating in.
area of drift ice
A mass of sea ice which 1) is less than 2 meters in thickness and 2) forms along the coast, where it is attached to the shore, to an ice wall, to an ice front, or between shoals or grounded icebergs.
Fast ice is central to the livelihoods of Arctic coastal communities who use it to access fishing and hunting grounds. Vertical fluctuations may be observed during changes of sea level. Fast ice may be formed on site from sea water or by freezing of pack ice of any age to the shore, and it may extend a few yards (meters) or several hundred miles (kilometers) from the coast. Fast ice may be more than one year old and may then be prefixed with appropriate age category (old, second- year, or multiyear). If it is thicker than about 7 ft (2 m) above sea level, it is called an ice shelf.
fast ice
Small, needle-like (spicules), plate-like, or discoid crystals derived from nearly pure fresh water, suspended in a water body.
Needs to have axioms added pertaining to the semantics of colloids and suspensions once they have been resolved see: https://github.com/pato-ontology/pato/issues/91#issuecomment-290711238 Currently the new ice classes are not specific to sea water as they may form in non marine systems, but it would be good to confirm this especially for frazil ice.
Typically 3 to 4 millimeters in diameter. These may form in both marine water and fresh water. They represent the first stages of sea ice growth; they merge under calm conditions to form thin sheets of ice on the surface (frazil ice), and consist of nearly pure fresh water. In fresh water, they form in supercooled water that is too turbulent to permit coagulation into sheet ice. This is most common in swiftly flowing streams. They may accumulate as anchor ice on submerged objects obstructing the water flow.
frazil
Land which is below the freezing point of water.
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
frozen land
Frozen soil which is firmly cemented by water ice, is subject to brittle failure, and exhibits practically no consolidation under load.
hard-frozen soil
Soil which is below the freezing point of water.
frozen soil
Frozen soil which is cemented by water ice but has viscous properties due to its high, unfrozen water content and therefore will compress and deform under load.
plastic-frozen soil
Frozen soil which has very low total water content and is not cemented by ice; its compressibility is the same as that of unfrozen soils having the same composition, total water content and density.
friable-frozen soil
An ice mass which constitutes that part of a glacier which has the lowest elevation.
glacier snout
An ice mass which has been drilled from an accumulation of snow and ice that has built up over many years and that has recrystallized and has trapped air bubbles from previous time periods.
TODO: add axiom to show this is the output of a "sampling process"
The composition of an ice core can be used to reconstruct past climates and climate change; typically removed from an ice sheet (Antarctica and Greenland) or from high mountain glaciers elsewhere.
water ice core
An ice field which is primarily composoed of sea ice floes greater than 10 kilometers across.
The floes in a sea ice field must be greater than 10 km across, at least at one location in the field.
sea ice field
Note that SWEET's IceField only refers to sea ice fields.
An ice field which is constituted by a continuous accumulation of snow and glacier ice that completely fills a mountain basin or covers a low-relief mountain plateau.
The definition in the GCW assessment notes that the depth of snow or ice must be of "a substantial depth". This is in need of specification. When the thickness become great enough, tongues of ice overflow the basins or plateaus as Valley Glaciers.
glacier ice field
An advective transport process during which a mass of ice is transported from one location to another.
mass ice flow
An iceberg which 1) has a flat upper surface, 2) is derived from an ice shelf, ice tongue, or floating tidewater glacier via detachment.
Newly formed tabular icebergs have nearly vertical sides and flat tops. In the Antarctic, they may be tens of kilometers wide, up to 160 km (100 miles) long, and as much as 300 m (1000 ft) thick, with about 30 m (100 ft) exposed above the sea surface. In the Arctic, large icebergs of this type are called ice islands, but they are considerably smaller than the largest of the antarctic variety. Has synonyms tabular berg, table iceberg. Formerly called barrier iceberg.
tabular iceberg
This synonym is no longer in common use.
An ice mass which is composed of a large amount of sea ice in the form of a hummock or a group of such hummocks, frozen together and separated from any surrounding ice by sea water.
Floebergs may float up to 17 ft (5 m) above sea level.
floeberg
An ice mass which is composed primarily of sea ice.
sea ice mass
An elevation which is formed by pressure at the point of contact between ice floes, resulting in a conglomeration of broken ice.
Sea ice hummocks may be fresh or weathered. The weathering of hummocks is similar to young mountain peaks with steep slopes that erode into smooth, rolling hills, in this case during the summer melt season. The submerged volume of broken ice under the hummock, forced downwards by pressure, is termed a bummock.
sea ice hummock
A hummock which is primarily composed of soil that has been pushed up by frost action.
Permafrost hummocks are often found in uniformly spaced large groups. Hummocks can form in areas of permafrost or seasonally frozen ground, and are one of the most common surface features of the Arctic.
frost-formed hummock
A valley glacier which has one or more tributary glaciers as parts.
branched valley glacier
A valley glacier which does not have any tributary glaciers flowing into it.
Definition should be revised in a positivist mode.
simple valley glacier
A glacier which flows into a larger glacier.
Tributary glaciers usually merge into a glacier which is at lower elevation.
tributary glacier
A surface layer which is composed primarily of ice.
ice surface layer
An ice surface layer which is primarily composed of water ice.
water ice surface layer
An two-dimensional continuant fiat boundary which overlaps the surface layer of a mass of ice.
This class was created during a semantic harmonisation exercise with the SWEET resource, currently adminstered by Earth Science Information Partners. Its subclass(es) are mapped to the corresponding SWEET terms, which were determined to align with fiat boundaries rather than physical ones.
two-dimensional fiat ice surface
A two-dimensional fiat ice surface which overlaps the surface layer of a mass of water ice.
This class was created during a semantic harmonisation exercise with the SWEET resource, currently adminstered by Earth Science Information Partners. It is mapped to the corresponding SWEET term, which was determined to align with fiat boundaries rather than physical ones.
two-dimensional fiat water ice surface
An ice mass which has broken away from a larger ice mass on land, such as a glacier or ice shelf, and may be either afloat or aground.
The greater part of an iceberg's mass (4/5 to 8/9) is below sea level, which makes them dangerous to shipping in high and mid-latitude regions of the ocean. The top of an ice berg usually protrudes more than 5 m above water-level and typically extends from tens of meters to many tens of kilometres across. Icebergs may be described as tabular, dome-shaped, sloping, pinnacled, dry-docked, blocky, weathered or glacier bergs in addition to having a size qualifier. Icebergs are not sea ice, when they melt they add fresh water to the ocean. The unmodified term "iceberg" usually refers to the irregular masses of ice formed by the calving of glaciers along an orographically rough coast, whereas tabular icebergs and ice islands are calved from an ice shelf, while bergs formed from sea ice are called floebergs. In decreasing size, they are classified as: ice island (few thousand square meters to 500 km^2 in area); tabular iceberg; iceberg; bergy bit (less than 5 m above sea level, between 1 and 200 m^2 in area); and growler (less than 1 m above sea level, about 20 m^2 in area). Alaskan icebergs rarely exceed 500 feet in maximum dimension. Antarctic icebergs originate from the ice mass of the Antarctic continent that has accumulated over many thousands of years.
iceberg
Land ice is any part of the Earth's seasonal or perennial ice cover that has formed over land as the result, principally, of the freezing of precipitation; opposed to sea ice formed by the freezing of seawater. Thus, an iceberg or tabular iceberg is land ice as well as its parent glacier, ice sheet, or ice shelf. The two major concentrations of land ice are the ice sheets of Greenland and Antarctica. Glaciers and ice caps are the other important forms; however, some members of the glaciology community hold that glaciers (i.e. rock glaciers) need not have any ice.
land ice mass
A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point.
freezing
A freezing process during which liquid water is transformed into water ice.
freezing of water into water ice
An ice lead which occurs in a marine water body and is bounded by sea ice.
sea-ice lead
Alignment uncertain, to be revised pending SWEET clarification.
A surface layer of a water body which has been formed as the result of surface ice fracturing and moving apart.
Generally, leads are wide enough (and deep enough) for navigation by surface vessels. The term is generally applied to linear features. If the open area is very large it may be called a polynya, although the application of these terms is under debate.
ice lead
An ice lead between a mass of fast ice and a mass of pack ice.
flaw lead
An ice lead which occurs between the shore and pack ice.
shore lead
A water surface that is part of a water body.
surface layer of a water body
An ice lead within which new, nilas, and young ice has formed.
frozen lead
A drift ice mass which has an ice concentration above or equal to 7/10: which covers 70% or more of a given area of a water body.
pack ice mass
Prior to approximately 2014, "pack ice" was used for all ranges of drift ice concentrations, thus the terms were in close synonymy.
Ice which has formed as the result of freezing of water which was part of a water body.
In the United States, NOAA considers ice formed from the freezing of the waters of the Great Lakes as being the same as sea ice. This class attempts to provide a distinction for clarity.
water-body-derived ice
An environmental zone which overlaps that part of an ocean or sea within which 1) sea ice is present only part of the year, 2) extends from the permanent ice zone to the boundary where winter sea ice extent is at a maximum, and 3) primarily overlaps first-year ice when seasonal ice is present.
As this part of the environment is defined by a seasonal process, some of its differentia aren't physically there at all times of its existence.Thus, all boundaries of this entity are fiat.
area of seasonal sea ice
A layer which is composed of ground that 1) remains unfrozen due to increased solute concentration and 2) is present within a mass of permafrost.
cryopeg
An environmental material which is primarily composed of a dispersed phase of insoluable particles, approximately between 1 nanometer and 1 micrometer in maximum dimension, distributed throughout a material acting as a medium of suspension.
Wikipedia lists several forms of colloidal suspension such as colloidal aerosols, colloidal emulsions, colloidal foams, colloidal dispersions, or hydrosols.
colloidal suspension
An environmental material which is solid, jelly-like, and exhibits no flow when in steady state material and which contains liquid dispersed in and held in place by cross-linked structures of a solid medium.
gel
A gel which is primarily composed of a network of polymer chains that are hydrophilic, sometimes found as a colloidal gel in which water is the dispersion medium.
hydrogel
Particulate environmental material which 1) is primarily composed of a fine, granular material such as sand, silt, or clay suspended in and saturated by water and 2) readily liquefies when weight is applied, losing strength and permitting objects to sink until their weight and buoyancy offset the weight of the displaced quicksand.
quicksand
An aggregate of raindrops falling to a planetary surface during a precipitation process.
rain
Rain which is composed of water droplets falling to a planetary surface during a rainfall process.
water-based rain
Sound which is lower in frequency than 20 Hertz, or cycles per second.
20 Hertz is the average limit of human hearing.
infrasound
An environmental zone which 1) contains ecosystems, constructed features, or other entities deemed to be of natural, historical, cultural, or other significance and 2) has been afforded legal protections restricting one or more forms of use by a competent authority.
protected area
An elevation which is formed as an ice mass forms under soil, resulting in upwards deformation of the land surface.
frost heave
An ecoregion which is located on a landmass.
terrestrial ecoregion
A surface layer which is part of an ocean or sea.
At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases. Sea surface layer is also used to refer to the surfaces of oceans.
sea surface layer
Land which is present within a forest biome.
forest floor
speed of a water current
The original label in the NERC VS P01 was: "Speed of water current (Eulerian measurement) in the water body". We don't address the methodological dimension here.
A hydroform which is maintained by a continuous, directed movement of water, generated by disequilibria in a water mass.
Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength.
water current
A fuel oil which 1) is derived from petroleum oil, 2) has a strong odor, 3) produces large quantities of soot relative to other fuel oils, 4) is less refined than fuel oils such as paraffin.
For speakers of British English, kerosene is often referred to as paraffin.
kerosene oil
cryospheric layer
A layer of environmental material which is subject to freeze-thaw cycles.
active layer in a cryosphere
A warming process during which the thermal energy in a portion of environmental material is sufficient to melt water-based ice or snow.
Note that ice or snow need not be present in the material in order for it to undergo thawing. The semantics of 'thaw' vs 'melt' are debated in fields such as permafrost geology/physics. This module is thus likely to be dynamic.
thawing process
A process during which the temperature of a portion of environmental material is increased, along with the kinetic energy of its constituent molecules.
Note that melting need not involve warming (e.g. due to extreme gravitational effects). See the melting hierarchy for more terms.
material warming process
A thawing process during which permafrost is warmed beyond the melting point of water-based ice, snow, or other forms of solid water.
permafrost thawing process
Permafrost which contains inclusions of water-based ice.
ice-bearing permafrost
A process during which the temperature of a portion of environmental material is decreased, along with the kinetic energy of its constituent molecules.
Note that ice formation, freezing, etc may have this process as a part, but may also occur without temperature decreases (e.g. through extreme gravitational effects). See the material congelation process hierarchy for more.
material cooling process
Soil which is directly exposed to the atmosphere - with no intervening layer of plant life or other cover - and thus the effects of weathering and erosion.
bare soil
A material accumulation process during which the mass of snow on a surface increases.
This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute. The scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired. Some definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved.
snow accumulation process
A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass.
ice accumulation process
A material accumulation process during which a accumulation of snow and ice forms or increases in mass.
snow and ice accumulation process
A object which is composed primarily of water-based snow and ice.
mass of ice and snow
A positional quality inhering in a bearer by virtue of the bearer being located within a glacier or ice sheet, between their summer surface or bed.
englacial
An environmental system process which occurs within a glacier or ice sheet.
englacial process
A glacial surface layer which is present at the point in time where any given part of a glacier reaches its minimum annual mass.
Note that the glacial summer surface is diachronous. The time that the summer surface is present on a glacier can vary from point to point along the entire glacier. That is, while a high-elevation region of a glacier may have reached its minimum, lower elevation regions may still be ablating. The summer surface is the surface on which the first snow of the new balance year falls. It is easily detectable when it consists of glacier ice, which now includes superimposed ice added during the previous balance year. In the firn area it is recognizable as a well-marked crust, that is, a thin, relatively strong layer with a density near that of ice, and sometimes also (or instead) as a layer of depth hoar at the base of the current year's accumulation. The crust typically originates by recrystallization of the surface snow in late summer to form glaze. It may also be marked by an accumulation of sediment or wind-blown dust. It can be difficult to detect when melting and snowfall alternate during the transition between the ablation season and the accumulation season. In some mass-balance programmes the summer surface is 'labelled' in the vicinity of stakes with a distinctive material, such as sawdust, during a visit late in the ablation season.
glacial summer surface
A glacial surface layer which is adjacent to the bedrock or debris over which a glacier flows.
glacial bed
A tundra ecosystem which is subject to polar climatic conditions.
polar tundra ecosystem
An ecosystem which is determined by the presence of rounded mineral concretions primarily composed of manganese hydroxides on the seafloor.
These are typically found in deep-sea environments - where polymetallic nodules (rounded mineral concretions containing manganese hydroxides and a variety of other minerals) are found at the surface at densities of up to 70 % of the surface area. The nodules provide a substrate for attached hard-bottom fauna to settle in areas where soft-sediments prevail.
polymetallic nodule ecosystem
A water flow process during which fresh or brackish groundwater flows from from a landmass into the sea.
submarine groundwater discharge process
A water flow process during which water flows out of an aquifer.
groundwater discharge process
A water flow process during which water is transported through an aquifer.
groundwater flow
An environmental pollution process during which contaminants derived from agricultural activity are released into an environmental system.
Verschumutzung durch Landwirtschaft
Examples include the release of pesticies and/or antibiotic-laden animal waste into water bodies.
agricultural pollution
An active agri-ecosystem management process during which the variability of land use types or the spatial structure of land under agricultural production is increased.
Agrarlandschaftsdiversifizierung
This includes the introduction or balancing of cover types such as forests, crops, grassland, or land covered by crop cultivars such as wheat, maize, legumes, vegetables.
agricultural landscape diversification process
A conservation process during which the variability of life - from genes to ecosystems - is preserved.
biodiversity conservation process
A biodiversity conservation process during which the variability of insect communities, or parts thereof, is preserved.
Like other forms of conservation, planned management actions (i.e. preservation, maintenance, sustainable use, recovery, enhancement) of natural resources or of a particular ecosystem is typically employed to halt, reverse or slow-down the die off of insects from the impacts of anthropic exploitation or pollution.
insect conservation process
An active agri-ecosystem management process during which an ecosystem is modified for the production of one or a small collection of crops or other agricultural products.
Spezialisierung der Landwirtschaft
Agricultural specialisation is often a means to produce sufficiently large quantities of crops to compete in global markets. Entire landscapes and regions are often dedicated to such production.
agricultural specialisation process
Soil in which segregated ice will form (causing frost heave) under the required conditions of moisture supply and temperature.
The label would apply to all soils in which frost can form, however, the definition of this class suggests that ice segregation is a key property that differentiates this type of soil from others.
frost-susceptible soil
The authoritative definition can be found in the USPA Glossary. Note that the original definition references "earth materials" rather than "soil".
A process during which microscopic solid particulates are formed from liquid materials in an atmosphere.
formation of solid particles from liquid material in an atmosphere
formation of a solid aerosol from liquid material in an atmosphere
A process during which supercooled water droplets in a cloud freeze into ice crystals.
glaciation of water droplets in a cloud
An interval of time within an ice age and during which temperatures fall resulting in planet-wide glacier advances.
Note that there has been long debate over the usage of this term, leading to some of the ambiguity resolved across the various classes featuring 'glaciation' as a label or synonym in ENVO. For example, see https://www.cambridge.org/core/journals/journal-of-glaciology/article/glacierization/354F9D3447C4AE8159D984B235114DE6/core-reader
glaciation
An interval of time within an ice age and during which temperatures rise and result in planet-wide glacier retreat.
interglacial
A temporal interval during which a planet's surface and atmospheric temperatures fall, resulting in the presence or expansion of continental and polar ice sheets or alpine glaciers.
ice age
Carbonate which is formed as the result of some biological process.
material primarily composed of biogenic carbonates
That part of an atmosphere which is composed of gaseous material.
gaseous part of an atmosphere
A solid material which does not have a regularly organised internal structure.
amorphous solid
A colloidal suspension which is dispersed through a part of a hydrosphere.
colloid suspended in a hydrosphere
Colloidal sediment which is suspended in a part of the hydrosphere.
suspended colloidal sediment
An environmental material which is denser than bromoform.
Axiomatising this with relational density qualities pinned to bromoform would be the next step.
heavy fraction material
An environmental material which is less dense than bromoform.
light fraction material
Waterborne particulate matter which is part of a hydrosphere.
particulate matter in a hydrosphere
An aerosol that is suspended in an atmosphere.
atmospheric aerosol
An estuary in which mixing by tidal forcing exceeds the force of riverine output, resulting in thorough homogenisation of the estuary's water column and the disappearance of a vertical salinity gradient and the freshwater-seawater boundary.
well-mixed estuary
A material transformation process during which solid or liquid particles form and are suspended in a mass of air, thus creating an aerosol.
aerosol formation process
An environmental process which involves glaciers or ice sheets.
Note that ice sheets and glaciers are confounded and confused in multiple communities and across multiple sources.
glacial process
A glacial ice loss process during which the snout (toe) of a glacier shrinks following successive years of negative mass balance.
Glacial retreat is usually evident from the recession of the ice margin on land, or calving in the sea, but also from down-wasting.
glacial retreat
An ice calving process during which a mass of ice falls from a larger mass onto land.
calving of ice onto land
An ice calving process during which a mass of ice falls from a larger mass into a body of water.
calving of ice into water
A frost action process which occurs in cold environments which are not part of a glacier.
Past usage of this term referenced climatic and geomorphic conditions in areas periperal to Pleistocene ice sheets and glaciers. Modern usage refers, however, to a wider range of cold climatic conditions regardless of their proximity to a Glacier, either in space or time. Many, but not all, Periglacial Environments possess Permafrost; all are dominated by Frost Action processes.
periglacial process
A material transport process during which alternate freezing and thawing of moisture in soil, rock and other materials results modifications of those materials and in the formation of structures on, or in, the ground.
Frost action in soils describes the processes of Frost Heave that occurs in the ground during the freezing period, and Thaw Weakening that occurs as the seasonally Frozen Ground thaws. Although it normally refers to seasonal freezing and thawing processes and effects, the term Frost action has also been used to describe the long-term heaving that occurs when soils are subjected continuously to a freezing temperature over a long period of time (years). Frost action contributes to the mechanical weathering (disintegration or breakdown) of soil and rock materials, by frost wedging, Cryoturbation activity, and to the development of cryotexture and cryogenic fabric in soils.
frost action process
A frost action process during which objects embedded in the ground are cumulatively displaced upwards.
frost jacking
A frost action process during which the soil particles are differentially displaced according to their size ranges.
frost sorting
A frost action process during which the pressure of water freezing in cracks, crevices, pores, joints or bedding planes results in the mechanical disintegration, splitting or break-up of rock.
frost wedging
A frost action process during which soil is displaced.
The processes that form irregular structures in earth materials characterized by folded, broken and dislocated beds, and lenses of unconsolidated deposits, including organic horizons and even bedrock. These processes include deep frost penetration, frost action, frost heaving, thaw settlement and all differential movements, including expansion and contraction due to temperature changes and the growth and disappearance of ground ice bodies, whether perennial or seasonal. Low temperatures alone are not enough to produce cryoturbation; the water-ice phase change is necessary. Cryoturbation is an important process in the development of patterned ground.
cryoturbation of soil
A mass of soil moved or disturbed by frost action.
soil cryoturbate
A water flow process which comprises a sudden‐onset high‐magnitude discharge of water and sediment from a glacial source
Glacial runs occur in virtually all glaciated regions of the world and are most commonly directly sourced from any part of a glacier where water can accumulate into a lake. A jökulhlaup usually occurs because a glacial lake drains rapidly due to failure of an ice dam or moraine dam.
glacial run
A physical quality inhering in a bearer by virtue of the bearer being derived from, part of, or otherwise dependent on the seas or oceans.
This class takes the broader meaning of this term. Note that some usages refer to smaller bodies of water, as seas and gulfs, as distinguished from large oceanic bodies.
thalassic
Part of an atmosphere which contains a weather front, bounded by frontal surfaces.
frontal zone
atmospheric frontal zone
An aquaculture process during which marine organisms are cultivated in the open ocean, an enclosure in the ocean, or in tanks, ponds or raceways which are filled with seawater.
mariculture process
A mariculture process during which organisms are cultivated in cages which allow the passage of materials such as wastes, pathogens, antibiotics, and - should a containment breach occur - cultivated organisms themselves to and from the surrounding marine environment.
open cage mariculture process
A construction which contains the equipment needed to perform mariculture in open cages - permitting the exchange of material with the surrounding marine water.
open cage mariculture facility
A gaseous surface layer which is composed of the warmer air mass(es) along the horizontal density and temperature discontinuity in a weather front.
frontal surface
As stated in the AMS Glossary, this is one interpretation of the term "front", namely "frontal surfaces across which the horizontal density gradient is discontinuous (frontal surface usually refers specifically to the warmer side of the frontal zone);"
frontal surface of a weather front
A surface layer which is composed primarily of some liquid or gas.
fluid surface layer
A cline across which one or more solid environmental materials dissolve into their surrounding fluid.
lysocline
A cline across which nutrient content of a fluid changes rapidly.
nutricline
A cline which is part of a marine water body.
marine cline
A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface.
fluid interface layer
A layer which is composed primarily of some fluid.
fluid layer
A fluid interface which separates two fluid masses with differing properties.
fluid front
A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses.
gaseous front
A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena.
This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms."
weather front
An object which is composed of a continuous mass of air.
air mass
A fluid surface layer which is composed primarily of some gaseous material.
gaseous surface layer
A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface.
interface layer
A mass of gas which is separated from its surroundings by either 1) a thin liquid layer or 2) a physical or compositional discontinuity.
The thin liquid layer case applies to, e.g., soap bubbles in air. The physical or compositional discontinuity case applies to, e.g., bubbles of CO2 in air or bubbles of air in water.
bubble
An object which is composed primarily of an environmental material
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of environmental material
An mass of environmental material which is composed primarily of a solid environmental material
mass of solid material
An object which is composed primarily of a fluid.
fluid mass
mass of fluid
An object which is composed primarily of a gas.
gaseous mass
mass of gas
An object which is composed primarily of a liquid.
liquid mass
mass of liquid
An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity.
mass of compounded environmental materials
A bubble which is composed primarily of methane.
methane gas bubble
A material isosurface within which pressure is approximately constant.
isobaric surface
A material isosurface within which salinity is approximately constant.
isohaline surface
A material isosurface within which density is approximately constant.
isopycnal surface
A material isosurface within which temperature is approximately constant.
isothermal surface
An isobaric surface that is part of an atmosphere.
envoAtmo
atmospheric isobaric surface
A weather front which separates air masses of tropical and polar origin.
envoPolar
polar front
An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year.
tropical environment
An environment which has a climate with warm temperatures and with meagre precipitation.
subtropical environment
An environment which is located in a part of an astronomical body subject to polar climatic conditions.
polar environment
An environment which is located in a part of an astronomical body subject to subpolar climatic conditions.
subpolar environment
An environment which is located in a part of an astronomical body subject to temperate climatic conditions.
temperate environment
A weather front which is nonoccluded and which moves in the direction of the warmer air mass it is adjacent to, such that colder air will occupy the site where warmer air was previously present.
The direction of motion determines whether fronts are "cold", "warm", etc. A front is said to be cold if it's moving in the direction of the warmer air mass it is adjacent to. From the perspective of an observer on the ground, this appears as though the colder air "replaces" the warmer air mass.
cold front
A weather front which is nonoccluded and which moves in the direction of the colder air mass it is adjacent to, such that warmer air will occupy the site where colder air was previously present.
warm front
A weather front at which warm air is ascending to high altitudes along the frontal surface.
anafront
A weather front at which warm air is descending to lower altitudes along the frontal surface.
katafront
A weather front which exists in an equatorial trough separating the air of the Northern and Southern Hemispheres of an astronomical body.
tropical front
Note there is controversy if such fronts exist or at least are compatible with frontal theory.
intertropical front
An air mass which is part of the free atmosphere, including the troposphere and stratosphere.
upper air
An atmospheric layer which 1) is located above the planetary boundary layer, 2) in which the effect of friction between moving air masses and the planetary surface is negligible, and 3) in which the air is usually treated (dynamically) as an ideal fluid.
"The base of the free atmosphere is usually taken as the geostrophic wind level."
free atmosphere
A weather front which is part of a mass of upper air.
upper front
A weather front which separates air behind a cold front from air ahead of a warm front.
occluded front
An occluded front which is adjacent to a cold front 1) that is moving away from the coldest air in the vicinity, 2) where the neighbouring cold front undercuts the neighbouring warm front in the occulsion zone, and 3) where the coldest air in the vicinity replaces less cold air towards the surface of the astronomical body.
cold occluded front
An occluded front which is adjacent to a warm front 1) that is moving in the direction of the coldest air in the vicinity, 2) where the original cold front is forced aloft at the warm front surface, and 3) where the coldest air is replaced by less cold air at the surface of the astronomical body.
warm occluded front
An occluded front which is 1) adjacent to a cold and a warm front with no appreciable difference between the temperatures of their bordering air masses and 2) which creates a pressure trough, a wind-shift line, a band of cloudiness, and precipitation at the surface of the astronomical body.
neutral occluded front
A cold front which forms behind a frontal cyclone and within a cold air mass with an appreciable horizontal temperature gradient.
secondary cold front
An atmospheric wind during which cold atmospheric gas flows downwards towards the surface of an astronomical body.
"From its etymology, the term means simply "going down" or "descending," and thus could refer to any descending flow; some authors have further generalized it to include downslope flows such as the foehn or chinook even though they do not represent a flow of cold air. This concept has given rise to the expression katafront, which indicates flow down a sloped cold-frontal surface."
katabatic wind
A katabatic wind during which atmospheric gas flows down the slope of an elevation, typically during periods of light larger-scale winds.
"The many synonyms for downslope flow are sometimes used interchangeably, and this gives rise to ambiguity and confusion. Downslope can be used generically to denote any wind flow blowing down a slope, or it is used specifically for katabatic flows on any scale, such as the nocturnal slope-wind component of mountain–valley wind systems or mountain–plains wind systems." Note also that slope winds are typically classed separately from fall winds, which occur at larger scales.
downslope katabatic wind
A katabatic wind which is driven by the cooling and subsequent sinking of atmospheric gas masses.
cooling-driven katabatic wind
A downslope katabatic wind during which warm, dry atmospheric gas descends along the lee side of a mountain range as a result of synoptic-scale, cross-barrier flow over that range.
foehn wind
An environmental process during which a system does not thermally interact with its surroundings by virtue of a temperature difference between them.
"In an adiabatic process any change in internal energy (for a system of fixed mass) is solely a consequence of working. For an ideal gas and for most atmospheric systems, compression results in warming, expansion results in cooling."
adiabatic process
An adiabatic process during which no condensation of water vapor occurs and no liquid water is present.
dry-adiabatic process
An adiabatic process which involves air saturated with water vapour and the presence of liquid water.
moist-adiabatic process
A katabatic wind during which the low temperature and increased density of a cold mass of atmospheric gas accelerates its descent.
"A fall wind is a larger-scale phenomenon than the individual-slope scale and is produced by accumulated cold air spilling down a slope or over a mountain range. The cold air often either accumulates on a plateau or other elevated terrain, or is part of an extensive cold air mass approaching a mountain range as a cold front."
fall wind
A fall wind which has a source so cold that, when the atmospheric gas reaches the lowlands or coast, the dynamic warming is insufficient to raise its temperature to the normal level for the region; hence it appears as a cold wind.
bora
An atmospheric wind which rapidly forms, lasts for a duration in the order of minutes, and then rapidly decreases in speed.
squall wind
A storm which is nautical, localised, and of high severity local storm considered as a whole: that is, winds and cloud mass and (if any) precipitation, thunder and lightning.
nautical squall
A wind which is driven by the acceleration of flow through a gap, constriction, or channel resulting from large-scale pressure gradient, or by Venturi acceleration through a constricting passage.
jet-effect wind
A jet-effect which passes through a gap, constriction, or channel between mountains in a mountain range or between ranges themselves.
mountain-gap wind
An atmospheric wind which moves up or down a slope and is driven by heating or cooling of that slope.
slope flow
An upslope wind driven by heating at the slope surface under fair-weather conditions.
Unlike the term "katabatic wind", anabatic wind has a focused meaning and suffers from less ambiguity, thus the more precise treatement of this term and its place deeper in the hierarchy.
anabatic wind
A process during which direct stellar radiation interacts with a planetary surface.
insolation process
The broader term can also refer to the amount of radiation received, rather than the process.
A material cooling process during which a portion of gaseous environmental material loses thermal energy to its surroundings.
cooling of a gas
A material cooling process during which a portion of liquid environmental material loses thermal energy to its surroundings.
cooling of a liquid
A material cooling process during which a portion of solid environmental material loses thermal energy to its surroundings.
cooling of a solid
A material cooling process during which a portion of fluid environmental material loses thermal energy to its surroundings.
cooling of a fluid
A material warming process during which the thermal energy in a volume of fluid increases.
warming of a fluid
A process of warming a fluid during which the thermal energy in a volume of gas increases.
warming of a gas
A process of warming a fluid which includes a volume of liquid as a participant.
warming of a liquid
A material warming process during which the thermal energy in a mass of solid material increases.
warming of a solid
A fluid astronomical body part which is plume shaped.
plume
A downslope katabatic wind which is generated by the cooling of atmospheric gas in contact with terrain surfaces.
Note that slope winds are typically classed separately from fall winds, which occur at larger scales.
drainage wind
A front which shows very little mobility.
"Conventionally, a front that is moving at a speed less than about five knots is generally considered to be quasi-stationary. In synoptic chart analysis, a quasi-stationary front is one that has not moved appreciably from its position on the last previous synoptic chart (three or six hours before)."
quasi-stationary front
A drainage wind which flows along the icy surface of a glacier.
glacier wind
An advective transport process during which a fluid moves.
mass fluid flow
A mass fluid flow which moves in the same direction as a planet's rotation, rotating due to a Coriolis effect.
cyclonic circulation
An atmospheric storm during which winds flow with increased rates.
wind storm
A wind storm during which strong gusts of wind occur, transporting atmospheric gas in a linear fashion.
straight-line wind
A downdraft which is of high intensity and which spreads radially, with high speed, across the planetary surface upon reaching it.
downburst
A macroburst during which no or very little rain is generated.
dry macroburst
A macroburst during which large amounts of rain are generated.
wet macroburst
A downburst during which high winds occur over an area less than four kilometres in diameter.
microburst
A downburst during which high winds occur over an area larger than four kilometres in diameter.
macroburst
A microburst during which large amounts of rain are generated.
wet microburst
A microburst during which no or very little rain is generated.
dry microburst
A katabatic wind which is sudden and strong.
downdraft
A material transport process during which parts of an elastic material oscillate around their positions of equilibrium.
vibration process
A vibration process which occurs in the solid parts of an astronomical body as low-frequency acoustic waves pass through them.
seismic vibration process
A seismic vibration process which is caused by a volcanic eruption.
volcanic seismic vibration
A seismic vibration process which is caused by the impact of a solid object on the surface of an astronomical body.
impact-driven seismic vibration
An impact event is a collision between material entities, resulting in changes in one or both of those entities.
This class is valid for impacts of celestial bodies as well as impacts of missiles, etc. See https://github.com/EnvironmentOntology/envo/issues/860
impact event
A seismic vibration process which is caused by an explosion.
explosion-driven seismic vibration
A seismic vibration process which is caused by mass wasting.
mass-wasting-driven seismic vibration
A seismic vibration process which is caused by the collapose of a material entity, sending kinetic energy into astronomical body.
collapse-driven seismic vibration
A process during which the ability of a material entity to maintain its internal organisation fails, resulting in deformation and a breakdown of that organisation.
This is a very general concept, and should likely be elevated to OBO Core rather than held in ENVO.
structural collapse process
A structural collapse process during which the walls of cave are unable to support the load placed upon them.
cave collapse
A seismic vibration process which is caused by an earthquake.
earthquake-driven seismic vibration
A tectonic earthquake which precedes the strongest tectonic earthquake in a series, linked to the same release of energy in the crust.
foreshock
A tectonic earthquake which 1) is embedded in a series of tectonic earthquakes, linked to the same release of energy in the crust and 2) has the largest magnitude of the series.
mainshock
A tectonic earthquake which 1) is embedded in a series of tectonic earthquakes, linked to the same release of energy in the crust and 2) occurs after the mainshock.
aftershock
A fault across which older rocks are pushed above (away from the core of an astronomical body) younger rocks.
thrust fault
A tectonic earthquake which occurs along a thrust fault which does not breach the surface of an astronomical body.
blind thrust earthquake
A thrust fault which does not breach the surface of an astronomical body.
blind thrust fault
An environmental zone which includes those regions of an astronomical body which are not exposed to its atmosphere or space.
subsurface zone of an astronomical body
A tectonic earthquake which has two or more mainshocks of similar magnitude, and which originate from the same fracture zone and stress field.
The mainshocks may be separated by seconds or years. Mainshocks must be within 1.2 units of magnitude of one another and have nearly identical seismic waveforms.
multiplet tectonic earthquake
A tectonic earthquake which occurs at the boundary between two tectonic plates.
interplate earthquake
QCR: 'has participant' min 2 'tectonic plate'
A tectonic earthquake which occurs within the interior parts of a tectonic plate.
intraplate earthquake
QCR: 'has participant' max 1 'tectonic plate'
An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert.
desert ecosystem
A solid astronomical body part which is part of the landmass of that body.
part of a landmass
A large continuous area of land, either surrounded by sea or contiguous with another landmass.
landmass
A surface of an astronomical body which is part of a water body present on that body.
liquid surface of an astronomical body
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
compound astronomical body part
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
land
A sea which shalowly covers central areas of continents during periods of high sea level that result in marine transgressions.
inland sea
aquatic ecosystem
marine ecosystem
freshwater ecosystem
An ecosystem which primarily occurs on land.
terrestrial ecosystem
A forest ecosystem which includes communities adapted to 1) hot to warm, dry summers, 2) mild to cold, rainy winters, and 3) the influence of large, usually marine, bodies of water.
mediterranean forest
A broadleaf forest which is subject to tropical climate conditions.
tropical broadleaf forest
A broadleaf forest which is subject to subtropical climate conditions.
subtropical broadleaf forest
A broadleaf forest which is subject to temperate climate conditions.
temperate broadleaf forest
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
ecosystem process
A mixed forest which is subject to temperate climatic conditions.
temperate mixed forest
A mixed forest which is subject to tropical climatic conditions.
tropical mixed forest
A tropical mixed forest in which dominant ecological communities have reached their climax successional state.
tropical mixed forest biome
A tropical broadleaf forest which 1) s subject to a year-round warm climate 2) may receive several hundred centimeters or rain per year and 3) are subject to long dry seasons which last several months.
tropical dry broadleaf forest
A tropical broadleaf forest which 1) has low variability in annual temperature, 2) high levels of rainfall (>200 centimeter annually), and 3) has tree communities dominated by semi-evergreen and evergreen species.
tropical moist broadleaf forest
A subtropical broadleaf forest which 1) s subject to a year-round warm climate 2) may receive several hundred centimeters or rain per year and 3) are subject to long dry seasons which last several months.
subtropical dry broadleaf forest
A subtropical broadleaf forest which 1) has low variability in annual temperature, 2) high levels of rainfall (>200 centimeter annually), and 3) has tree communities dominated by semi-evergreen and evergreen species.
subtropical moist broadleaf forest
A forest ecosystem which is subject to tropical climate conditions.
This class is primarily to be populated by inference.
tropical forest
A forest ecosystem which is subject to subtropical climate conditions.
subtropical forest
A forest ecosystem which is subject to temperate climate conditions.
temperate forest
A grassland ecosystem which is subject to tropical climatic conditions.
tropical grassland
flooded grassland
montane grassland
A grassland which is subject to subtropical climatic conditions.
subtropical grassland
A grassland which is subject to mediterranean climatic conditions.
mediterranean grassland
temperate grassland
subpolar grassland
A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
construction
An object which is formed as a result of one or more biological processes and is composed primarily of organic material.
organic object
Cell culturing is the aseptic maintainance and growth of collections of cells outside of an organisms or natural environment in a suitable culture medium.
cell culturing
A manufactured product which has been designed to contain a mass of biomaterial.
biomaterial containment unit
A biomaterial containment unit which is designed to allow the growth and propagation of the biomaterial it contains.
biomaterial culturing unit
A biomaterial culturing unit which is designed to promote the growth of selected cell populations (often at the expense of others) within a community by altering the conditions of the environment within its confines.
enrichment culturing unit
A biomaterial culturing unit which is designed to promote the growth and propagation of cells in an artificial medium.
cell culturing unit
cultured organic material
Sediment through which hydrothermally modified fluids flow, altering its properties through interaction with their own.
hydrothermally-influenced sediment
An enrichment culturing unit which contains environmental material bearing ecological assemblages undergoing selection through experimentally imposed conditions.
active enrichment culturing unit
A plume which is composed primarily of bubbles.
bubble plume
An ecosystem process during which the species composition of an ecosystem gradually changes as species which are more adapted to the prevailing conditions in the ecosystem replace those which are less adapted.
ecological succession
An active enrichment culturing unit which contains environmental material maintained under conditions with no free oxygen.
active anaerobic enrichment culturing unit
An active enrichment culturing unit which contains environmental material maintained under conditions that favour the reduction of sulphate.
active sulphate-reducing enrichment culturing unit
An ecological succession process during which 1) organisms in ecological communities possess high adaptation to the conditions in the ecosystem, 2) participant communities largely fill available niches, 3) individual organisms are typically replaced by others of the same species, 4) a near equilibrium is maintained between gross primary production and total respiration and across biogeochemical cycles.
climactic ecological succession
An ecosystem which is formed as a result of human activity or impact.
anthropised ecosystem
An anthropised ecosystem which is determined by the presence of humans and their constructions.
human settlement
A biome which is subject to tropical climatic conditions.
tropical biome
A biome which is subject to temperate climatic conditions.
temperate biome
A biome which is subject to subtropical climatic conditions.
subtropical biome
A biome which is subject to mediterranean climatic conditions.
mediterranean biome
A biome which is subject to subpolar climatic conditions.
subpolar biome
A biome which is subject to alpine altitudinal conditions.
alpine biome
A biome which is subject to montane altitudinal conditions.
montane biome
A biome which is subject to subapline altitudinal conditions.
subalpine biome
A biome which is subject to arid environmental conditions.
arid biome
An environment in which living organisms have a low likelihood of being harmed or killed
safe environment for living organisms
An environment in which material entities have a low likelihood of being damaged or destroyed.
This branch will be axiomatised in subsequent revisions, most likely using classes from NBO and OAE. See https://github.com/EnvironmentOntology/envo/pull/899 for a link trail.
safe environment
An andosol which derives its silica content from glass and tephra ejected during a volcanic eruption.
volcanic soil
An environmental process during which momentum is transferred from one material entity to another.
Momentum is a bit tricky, it's the product of mass and velocity thus can be understood as rest energy and kinetic energy. But this is variable.
momentum transfer process
QCR: 'has participant' min 2 'material entity'
A momentum transfer process which unfolds as winds generate drag at the bottom of the atmosphere,coupled to dynamical forcing at the surface of the ocean.
atmosphere-ocean momentum transfer process
A rate which inheres in an atmosphere-ocean momentum transfer process.
ocean surface stress
Frost which is composed of interlocking ice crystals formed by vapour transfer (sublimation followed by deposition) of water vapour on some surface.
hoar
Hoar which is usually cup-shaped and facetted and which forms within dry, low-density snow beneath the snow surface.
Depth hoar is associated with very fast crystal growth under large temperature gradients. Sometimes a layer of depth hoar forms just above, and may assist in identifying the summer surface. The low density and low strength of depth hoar can make it difficult to retrieve unbroken core sections during coring, and can complicate estimates of accumulation by microwave remote sensing. Layers of depth hoar also increase the likelihood of avalanching. This is one way in which firn formation may begin. Depth hoar is similar in physical origin to crevasse hoar.
depth hoar
hoarfrost
Water ice which 1) has a white or milky and opaque appearance, 2) has a granular texture, and 3) is formed as a result of the deposition and rapid freezing of supercooled water drops as they make contact with an exposed object.
The previously use definition was: Frost which is 1) composed primarily of granular ice tufts, 2) formed on the windward sides of exposed objects through contact with supercooled fog or cloud, and 3) built out directly against the wind.
Rime is denser and harder than hoarfrost, but lighter, softer, and less transparent than glaze. Rime is composed essentially of discrete ice granules and has densities as low as 0.2-0.3 g cm-3. Glaze is generally continuous but with some air pockets and has much higher densities. Factors that favor rime formation are small drop size, slow accretion, a high degree of supercooling, and rapid dissipation of latent heat of fusion. The opposite effects favor glaze formation. Both rime and glaze occur when supercooled water drops strike an object at a temperature below freezing. Such formation on terrestrial objects constitutes an ice storm; on aircraft, it is called aircraft icing (where rime is known as rime ice). Either rime or glaze may form on snow crystals, droxtals, or other ice particles in the atmosphere. When such a deposit is wholly or chiefly of rime, snow pellets result; when most or all of the deposit is glaze, ordinary hail or ice pellets result. The alternating clear and opaque layers of some hailstones represent glaze and rime, deposited under varying conditions around the growing hailstone.
rime
glaze
An environmental material which is primarily composed of minute ice crystals forming a fuzzy layer over a cold surface by direct deposition of water vapor.
In British usage, a day on which the minimum temperature at the level of the ground or on the tops of low, close-growing vegetation falls to -0.9C (30.4F) or below (also called a "day with ground frost"). In more general usage, "frost" can refer to the condition that exists when the temperature of the Earth's surface and Earthbound objects fall below the melting point of water (0 degrees Celsius or 32 degrees Fahrenheit). Depending upon the actual values of ambient-air temperature, dewpoint, and the temperature attained by surface objects, frost may occur in a variety of forms. These include a general freeze, hoarfrost (or white frost), and dry freeze (or black frost). If a frost period is sufficiently severe to end the growing season (or delay its beginning), it is commonly referred to as a killing frost.
frost
A field in which geothermal processes occur.
This will usually be a part of a rocky planet's crust, with that planet being of sufficient size and age to allow geothermal activity. Such activity may also arise from gravitational effects of large bodies near a rocky astronomical body.
In many geothermally active fields, wells can be drilled to obtain elements contained in solution in hot brines or to tap heat energy.
geothermally active field
A process during which one entity loses energy to another entity.
energy transfer process
A positional quality inhering in a bearer by virtue of the bearer being located in the vicinity of - but not adjacent to or within - a glacier or ice sheet.
periglacial
A geothermally active field within which geothermally heated aqueous fluids are discharged from the the surface of a rocky planet.
Hydrothermal activity in such fields often forming hot springs, geysers or other features at which anomalously hot water is released.
hydrothermal field
A material accumulation process during which the volume of liquid entity increases.
liquid accumulation process
An infrared radiation process which 1) transmits radiant energy has wavelengths between 3.0 and 100 μm, 2) is emitted from a planet and its atmosphere out to space in the form of thermal radiation.
In the Earth's climate system, long-wave radiation involves processes of absorption, scattering, and emissions from atmospheric gases, aerosols, clouds and the surface.
outgoing longwave radiation
An area density which inheres in a clouds by virtue of some influence exerted their mass exerts on a given area.
Positioning under area density may need discussion.
cloud cover
A temperature of air at which air become saturated with water vapour and below which airborne water vapour will condense to form liquid water (dew).
dew point
An atmospheric wind which 1) has an increased rate relative to other winds in the same region and 2) is followed by a lull.
According to U.S. weather observing practice, gusts are reported when the peak wind speed reaches at least 16 knots and the variation in wind speed between the peaks and lulls is at least 9 knots. The duration of a gust is usually less than 20 seconds.
wind gust
An electromagnetic radiation process during which radiant energy with wavelengths in the visible, near-ultraviolet, or near-infrared spectra is realised.
There is no standard cut-off for the near-infrared range; therefore, the shortwave radiation range is also variously defined. It may be broadly defined to include all radiation with a wavelength of 0.1 micrometers and 5.0 micrometers or narrowly defined so as to include only radiation between 0.2 micrometers and 3.0 micrometers.
shortwave radiation
Electromagnetic radidation which involves radiant energy in a spectral range (wave band) between 400 to 700 nanometers, that photosynthetic organisms are able to use in the process of photosynthesis.
Many definitions specify that this is Solar radiation, but consistency is lacking.
photosynthetically active radiation
The concentration of carbon dioxide when measured in air that is part of an atmosphere.
concentration of carbon dioxide in an atmosphere
A planned process during which an oil or gas well is modified.
Interventions may change state of the well or well geometry, provide well diagnostics, or manage the production of the well.
well intervention
A well intervention during which the production of an oil or gas well is increased by improving the flow of hydrocarbons from the reservoir into the well bore.
well stimulation
A well stimulation technique during which bedrock formations are fractured through the injection of pressurized proppant-bearing liquid into a well-bore.
When the hydraulic pressure is removed from the well, small grains of hydraulic fracturing proppants (either sand or aluminium oxide) hold the fractures open.
hydraulic fracturing
A liquid environmental material which is composed primarily of water ammended with thickening agents and proppants.
fracking liquid
A well which has been drilled in order to extract natrual gas from subterranean reservoirs and bring it to the surface.
gas well
A depression in the ground resembling a hole or cavity, either natural or anthropogenic.
pit
A pit which is used for the collection and storage of manure.
manure pit
A construction in which eggs are hatched under artificial conditions.
hatchery
A hatchery in which the eggs of poultry are hatched under artificial conditions.
poultry hatchery
A debris flow which is causally preceded by rainfall.
debris flow following rainfall
Snow which is composed of heavily rimed particles typically 2 to 5 millimeters in diameter (0.1 to 0.2 inch).
Subclass by shape into conical, hexagonal, and lump (irregular) graupel. Mark Parsons notes that the formational processes may be a source of useful differentia to distinguish graupel from other snow types.
snow pellets
Often indistinguishable from very small soft hail except for the size convention that hail must have a diameter greater than 5 mm. Sometimes distinguished by shape into conical, hexagonal, and lump (irregular) graupel.
graupel
transient tracer
A transient tracer role which inheres in chemical entities in seawater.
The axiomatisation includes the tracers mentioned in the corresponding GOOS EOV specification sheet, viewable here: https://www.goosocean.org/index.php?option=com_oe&task=viewDocumentRecord&docID=17476
marine transient tracer
Compounds which realise this role can be used in the ocean to quantify ventilation, transit time distribution and transport time-scales. These compounds are all conservative in seawater, or have well-defined decay functions, and a well-established source function over time at the ocean surface.
oceanic transient tracer
A positional quality which inheres in a bearer by virtue of the bearer in being in physical contact with, or close to, a glacial margin.
The meaning of "close to" is hard to represent accurately. Community agreement on this is not visible.
proglacial
In SWEET this is modelled as a process, however the GCW definitions to not support this understanding.
A positional quality which inheres in a bearer by virtue of the bearer in being in physical contact with or below a glacial bed.
The lower bound of "below" is ambiguous.
subglacial
A positional quality which inheres in a bearer by virtue of the bearer in being in physical contact with the upper surface of a glacier or objects on top of the glacier.
supraglacial
Hoar which a) forms on surfaces, b) occurs when the temperature of the surface is colder than the air above and colder than the frost point of that air.
When buried by snowfall, surface hoar may be considered depth hoar. The crystals formed by surface hoar are usually leaf-, fern- or plate-shaped and facetted. Two types of surface hoar are the fernlike ice crystals deposited directly on a snow surface and the hoarfrost that has grown primarily in two dimensions, as on a window or other smooth surface.
surface hoar
A water ice crystal which is a part of a deposit of hoarfrost and which only grows by desublimation.
hoar crystal
A landform which occurs on the surface of an astronomical body.
geographic feature
The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.
surface landform
A landform which is submerged underneath a body of liquid.
submerged landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.
landform
A paper product which has been manufactured to facilitate the writing of letters.
letter paper
A mineral spring through which water with elevated concentrations of calcium hydroxide flows.
calcic spring
A mineral spring through which water with elevated concentrations of lithium salts flows.
lithia spring
A spring through which water with elevated concentrations of iron salts flows.
chalybeate spring
A spring through which water with elevated concentrations of hydrated double sulfate aluminium salts flows.
alum spring
A mineral spring through which water with elevated concentrations of sodium, calcium, or magnesium salts flows.
saline spring
salt spring
A mineral spring through which water with a high pH flows.
alkaline spring
A mineral spring through which water with elevated levels of dissolved carbon dioxide gas flows.
soda spring
A mineral spring through which water with elevated levels of radioactive material flows.
radioactive spring
A spring through which water with a neutral pH flows.
neutral spring
A spring through which water with a low pH flows.
acid spring
acidic spring
reef
A vehicle designed to fly in outer space.
spacecraft
A disposition of a material entity which is realised when it is saturated with liquid water.
water-holding capacity
A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate.
particle
A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay.
clay particle
particle of clay
A one-dimensional temporal region which spans the duration an astronomical body completes one rotation on its axis.
day
A day during which water-based rainfall occurs.
The threshold of precipitation at which humans consider a day 'rainy' is aribitrary.
rainy day
Percolation during which water moves through the interstices of soil.
water percolation through soil
percolation of water through soil
A material transport process during which a fluid is filtered through porous soild or semi-solid materials.
This is not necessarily advective, and the properties of and processes participated in by the fluid may change.
percolation
A material transport process during which a liquid which is not absorbed or otherwise held in place by a material is transported away from its location.
Drainage may occur due to natural (e.g. gravitational) or artificial processes (e.g. pumping)
drainage process
A material transport process which arises spontaneously due to physical heterogeneities in a portion of a material and forces which act throughout its volume.
Most commonly, convective flows are generated by heterogeneities in density or the effects of gravity. When the cause of the convection is unspecified, convection due to the effects of thermal expansion and buoyancy can be assumed. Convection frequently occurs in fluids, but may also take place in soft solids or mixtures where particles can flow.
convective transport process
A physical quality of a process which is characteristic of processes that transport material within a volume due to the combined effects of material property heterogeneity and body forces across that volume.
convective
A physical quality of a process which is characteristic of process that transport material without, themselves, changing the qualities of those materials or the processes that are unfolding within them.
advective
A material transport process during which material moves from a region of higher concentration to a region of lower concentration.
diffusion
Diffusion is also applied to the movement of energy, thus the more specific label. This class will be repositioned (but with the core of its definition intact) if we include other forms of diffusion in ENVO.
material diffusion process
An energy transfer process during which a material entity receives energy through radiation.
The term irradiation usually - but not always - excludes the exposure to non-ionizing radiation, such as infrared, visible light, microwaves from cellular phones or electromagnetic waves emitted by radio and TV receivers and power supplies. Please use the subclasses of this term for precision.
irradiation
Irradiation during which a material entity receives energy through ionizing radiation.
irradiation by ionising radiation
Usage of this term typically excludes low or background levels of exposure, and is often linked with a purpose such as sterilisation. This class does not differentiate on such a basis, and subclasses - e.g. "irradiation by ionizing radiation for sterilization" can be created for specific applications if required.
irradiation by ionizing radiation
Irradiation during which a material entity receives energy through non-ionizing radiation.
irradiation by non-ionising radiation
Note that some forms of ultraviolet radiation can be ionising, thus it is not included in the logical axioms of this class.
irradiation by non-ionizing radiation
Irradiation during which a material entity receives energy through photosynthetically active radiation.
irradiation by photosynthetically active radiation
Wave energy which inheres in perpendicular electric and magnetic fields and which is realised when they oscillate and propagate.
electromagnetic radiant energy
electromagnetic wave energy
Energy which inheres in a wave and is realised during its propagation.
wave energy
A part of an environmental system whose boundaries are determined by fiat.
Subclasses of this class have fiat (and only fiat) boundaries - that is, boundaries which are determined by human consensus or opinion rather than (and sometimes in contrast to) well-defined physical discontinuities. We distinguish these from entities that have fuzzy or hard to define boundaries that do overlap some form of physical discontinuity.
fiat part of an astronomical object
A gaseous part of an atmosphere in which gases have increased atmospheric pressure.
area of high atmospheric pressure
A hypodermic needle is a medical instrument made from a hollow needle. It is commonly used with a syringe to inject substances into the body of an organism.
A textile is a manufactured product comprised of a network of natural or artificial fibers (often referred to as thread or yarn).
Bedclothing is a textile covering used on a bed as a sheet, blanket, or pillowcase.
A pockmark field is an undersea feature formed by shallow seabed depressions, typically several tens of metres across and a few metres deep. Generally, they are formed in soft, fine-grained seabed sediments by the escape of fluids (gas or water, but mainly methane) into the water column.
Nesting material is an animal habitation consisting of matierals used to cushion, insulate and protect the young of the organism. The adult will use the material to form a protective structure to house and raise their young. Nests are built primarily by birds, but also by mammals, fish, insects and reptiles.
Tissue culture is the culture of cells, tissues or organs in a nutrient medium under sterile conditions.
This branch should be moved to OBI or a more appropriate ontology.
A cell culture is a growth of cells in vitro in an artificial medium for experimental research.
Plant tissue culture is the growth or maintenance of plant cells, tissues, organs or whole plants in vitro.
Organ culture is the aseptic culture of complete living organs of animals and plants outside the body in a suitable culture medium. Animal organs must be small enough to allow the nutrients in the culture medium to penetrate all the cells.
An organic material which is primarily composed of some natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids.
A bodily fluid material which is composed primarily of blood, a bodily fluid composed of blood plasma and blood cells suspended within the plasma that circulates around the organism's body. Blood performs may important functions including the supplying of oxygen and nutrients, removal of waste, circulation of white blood cells, detection of antibodes, coagulation, transportation of antibodies and the regulation of pH and body temperature.
A bodily fluid material which is composed primarily of amniotic fluid, a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided.
A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body.
A bodily fluid material which is composed primarily of bile, a bodily fluid consisting of a bitter, yellow or green alkaline fluid secreted by hepatocytes from the liver of most vertebrates. In many species, bile is stored in the gallbladder between meals and upon eating is discharged into the duodenum where the bile aids the process of digestion of lipids.
A bodily fluid material which is composed primarily of aqueous humour, a bodily fluid consisting of a thick watery substance that fills the space between the lens and the cornea.
An excreta material which is composed primarily of sweat, an excreta consisting primarily of water as well as a smaller amount of sodium chloride that is excreted by the sweat glands in the skin of mammals.
A bodily fluid material which is composed primarily of chyme, a bodily fluid consisting of a liquid substance found in the stomach before passing through the pyloric valve and entering the duodenum. It results from the mechanical and chemical breakdown of a bolus and consists of partially digested food, water, hydrochloric acid, and various digestive enzymes.
A bodily fluid material which is composed primarily of blood plasma, a bodily fluid that comprises the liquid component of blood, in which the blood cells are suspended. It makes up about 55% of total blood volume.
A bodily fluid material which is composed primarily of ear wax, a bodily fluid consisting of a yellowish, waxy substance secreted in the ear canal of humans and many other mammals. It plays an important role in the human ear canal, assisting in cleaning and lubrication, and also provides some protection from bacteria, fungi, and insects.
A bodily fluid material which is composed primarily of cerebrospinal fluid, a clear bodily fluid that occupies the subarachnoid space and the ventricular system around and inside the brain. CSF is a clear bodily fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.
A bodily fluid material which is composed primarily of chyle, a bodily fluid consisting of a milky fluid consisting of lymph and emulsified fats; formed in the small intestine during digestion of ingested fats.
A bodily fluid material which is composed primarily of breast milk, is a bodily fluid produced that is secreted from two milk-secreting glandular organs on a female's chest.
A bodily fluid material which is composed primarily of vitreous humor, a bodily fluid consisting of a clear gel that fills the space between the lens and the retina of the eyeball of humans and other vertebrates.
A bodily fluid material which is composed primarily of a pleural effusion, a bodily fluid that is produced in excess and accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Excessive amounts of such fluid can impair breathing by limiting the expansion of the lungs during inhalation.
A bodily fluid material which is composed primarily of a volume of tears, a bodily fluid consisting of a drop of the clear salty liquid secreted by glands (lacrimal glands) in the eyes. Tears wet the membrane covering the eye and help rid the eye of irritating substances.
A bodily fluid material which is composed primarily of an oronasal secretion, a bodily fluid secreted from the body via the mouth or nose.
A bodily fluid material which is composed primarily of saliva, a slightly alkaline secretion of water, mucin, protein, salts, and often a starch-splitting enzyme (as ptyalin) that is secreted into the mouth by salivary glands, lubricates ingested food, and often begins the breakdown of starches.
A bodily fluid material which is composed primarily of sebum, an oily bodily fluid secreted from the sebaceous glads that is made of fat (lipids) and the debris of dead fat-producing cells. In the glands, sebum is produced within specialized cells and is released as these cells burst. Sebum acts to protect and waterproof hair and skin, and keep them from becoming dry, brittle and cracked. It can also inhibit the growth of microorganisms on skin.
A bodily fluid material which is composed primarily of pus, a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.
A bodily fluid material which is composed primarily of synovial fluid, a bodily fluid secreted by the synovial membrane into the joint cavity to form a thin layer at the surface of cartilage.
A bodily fluid material which is composed primarily of mucus, a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
A bodily fluid material which is composed primarily of lymph, a bodily fluid consisting of a usually clear coagulable fluid that passes from intercellular spaces of body tissue into the lymphatic vessels, is discharged into the blood by way of the thoracic duct and right lymphatic duct, and resembles blood plasma in containing white blood cells and especially lymphocytes but normally few red blood cells and no platelets.
A bodily fluid material which is composed primarily of interstitial fluid, a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
A biological product is an environmental substrate comprised of any virus, therapeutic serum, toxin, antitoxin, or analogous product available to prevent, treat or cure diseases or injuries in man.
This definition should be revised, it is currently too ambiguous.
Siliceous ooze is a marine sediment composed of the debris of plankton with silica shells, such as diatoms and radiolaria. This ooze is limited to areas with high biological productivity, such as the polar oceans, and upwelling zones near the equator. The least common type of sediment, it covers only 15% of the ocean floor. It accumulates at a slower rate than calcareous ooze: 0.2-1 cm / 1000 yr.
Red clay, also known as pelagic clay, accumulates in the deepest and most remote areas of the ocean. Containing less than 30% biogenic material, its composition is a varied mix of very fine quartz and clay minerals, authigenic deposits precipitated directly from seawater, and micrometeorites. Though called "red" because it sometimes takes the color of oxidized iron minerals, it is usually brownish in color. Its ultimate origin is uncertain, but red clay seems to be mostly derived from distant rivers, and windblown dust. Covering 38% of the ocean floor, it accumulates more slowly than any other sediment type, at only 0.1-0.5 cm / 1000 yr.
Calcareous ooze is a marine sediment composed primarily of the shells--also known as tests--of foraminifera, coccolithophores, and pteropods. This is the most common pelagic sediment by area, covering 48% of the world ocean's floor. This type of ooze is limited to depths above the Carbonate Compensation Depth at time of burial. It accumulates more rapidly than any other pelagic sediment type, with a rate that varies from 0.3 - 5 cm / 1000 yr.
Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs.
Most animal feed is from plants but some is of animal origin. Fodder refers particularly to food given to the animals (including plants cut and carried to them), rather than that which they forage for themselves. It includes hay, straw, silage, compressed and pelleted feeds, oils and mixed rations, and also sprouted grains and legumes.
Contaminated animal feed is an animal feed that has become contaminated with or come contact with microorganisms or toxic chemicals.
Coastal water is a marine water body bordering a coast.
A canopy designed to protect against precipitation or sunlight.
A skin obtained from animals for human use typically from deer or cattle sources used to produce leather, shoes, fashion accessories, musical instruments.
A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.
Food material which can be used to meet nutritional requirements of plants.
A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments.
A soil consisting of the upper layer of soil on the surface consisting of loose material capable of supporting life composed of a mixture of mineral and organic matter.
A written message from one person to another addressed to a person or organization.
This is a legacy term, formerly in the manufactured product hierarchy under "paper product". A "letter paper" term is now present where this term once was. ENVO is not the right ontology for the generically dependent continuant class, but will host it for now.
An environmental material that is the non-aqueous, non-gaseous residues that remain after something is burned.
ash
A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams.
a type of rock that contains sufficient minerals with important elements including metals that can be economically extracted from the rock.
The primary uranium ore mineral is uraninite
Dust which is derived from mineral material.
Dust which is composed of fibrous material.
Dust which is composed primarily of some metallic material.
Dust which is derived from clay material.
Dust that comes from grain and all the other substances associated with its cultivation & harvesting.
A surface mine that utilizes a technique of extracting rock or minerals from the earth by their removal from an open pit or borrow.
A gas, smoke, or vapor that smells strongly or is dangerous to inhale.
A wax that is naturally synthesized by a plant or animal.
A white or colourless soft solid derivable from petroleum, coal or oil shale, that consists of a mixture of hydrocarbon molecules containing between twenty and forty carbon atoms.
An organic-rich fine-grained sedimentary rock containing kerogen from which liquid hydrocarbons called shale oil can be produced.
A drainage process during which water is transported away from peat.
Any liquid, liquefiable, or mastic composition that, after application to a substrate in a thin layer, converts to a solid film. It is most commonly used to protect, color, or provide texture to objects.
A planned process that is the movement of people, animals and goods from one location to another.
the residue powder that is derived from the combustion of wood.
wood ash
Ash that is produced from the burning of coal.
coal ash
A very fine, powdery material composed mostly of silica made from the burning of finely ground coal in a boiler.
fly ash
a coarse, angular ash particle that is too large to be carried up into the smoke stacks so it forms in the bottom of the coal furnace.
bottom ash
molten bottom ash from slag tap and cyclone type furnaces that turns into pellets that have a smooth glassy appearance after it is cooled with water.
boiler slag
a material leftover from the process of reducing sulfur dioxide emissions from a coal-fired boiler that can be a wet sludge consisting of calcium sulfite or calcium sulfate or a dry powered material that is a mixture of sulfites and sulfates.
flue gas desulfurization material
A human construction which serves as a memorial.
Monuments can commemorate people, animals, populations, events, or any other entity.
constructed monument
A human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions.
nuclear reactor
A nuclear reactor which uses a neutron moderator to slow neutrons until they approach the average kinetic energy of the surrounding particles.
The term fast neutron may later be added to an ontology external to ENVO. See https://github.com/EnvironmentOntology/envo/pull/1184 for comments.
thermal nuclear reactor
A nuclear reactor in which the fission chain reaction is sustained by fast neutrons.
Fast neutrons are neutrons carrying energies above 0.5 MeV or greater, on average. They are defined as in opposition to thermal neutrons used in thermal-neutron reactors.
fast neutron reactor
A nuclear reactor which serves primarily as a neutron source for purposes other than power.
An example use of a research nucelar reactor is the production of radioisotopes for medicine and industry
Research reactors are simpler than power reactors and operate at lower temperatures. They need far less fuel, and far less fission products build up as the fuel is used
research nuclear reactor
A nuclear reactor which is used as a source of power.
nuclear power reactor
Soil which is located in a mangrove biome.
Mangrove soils are typically saline, anoxic, acidic and frequently waterlogged.
mangrove biome soil
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
fluid environmental material
A human construction which is used to process materials into forms that have increased value or utility in downstream processes.
refinery
A refinery which is capable of processing petroleum oil.
Petroleum processing is an industrial process in which crude oil is transformed and refined into useful products such as petroleum naphtha, gasoline, diesel fuel, asphalt base, heating oil, kerosene, liquefied petroleum gas, jet fuel and fuel oils.
petroleum oil refinery
A refinery which is capable of processing raw sugar. Raw sugar is processed from cane or beets into white refined sugar.
sugar refinery
A refinery which is capable of processing natural gas. Natural-gas processing encompasses a range of industrial processes designed to purify raw natural gas by removing impurities, contaminants and higher molecular mass hydrocarbons to produce what is known as pipeline quality dry natural gas
natural gas processing plant
A planned process which has the intention of producing, consuming, or transforming materials via the execution of chemical reactions.
chemical engineering process
A planned material transformation process which takes as input a material and removes impurities.
refinement process
A chemical engineering process that produces ammonia en masse via artificial nitrogen fixation.
This process is the primary synthetic means of producing fertilizer
Haber-Bosch process
A chemical engineering process which generates hydrogen gas.
hydrogen production process
A mineral deposit that contains uranium ore.
uranium deposit
A uranium deposit where self-sustaining nuclear chain reactions have occurred.
Oklo is the only known location for this in the world and consists of 16 sites at which self-sustaining nuclear fission reactions are thought to have taken place approximately 1.7 billion years ago, and ran for a few hundred thousand years, averaging probably less than 100 kW of thermal power during that time
natural nuclear fission reactor
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife.
desertification
A general and temporary condition of partial or complete inundation of normally dry land areas from the overflow of inland and/or tidal waters, and/or the unusual and rapid accumulation or runoff of surface waters from any source. A great flow along a watercourse or a flow causing inundation of lands not normally covered by water.
flooding
GEMET: http://www.eionet.europa.eu/gemet/concept/3301
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
A process by which thermal radiation from a planetary surface is absorbed by atmospheric greenhouse gases, and is re-radiated in all directions. Since part of this re-radiation is back towards the surface and the lower atmosphere, it results in an elevation of the average surface temperature above what it would be in the absence of the gases.
greenhouse effect
A process which diminishes the functioning of an ecosystem located on land.
An SDGIO request. Likely to be refined and revised.
This could include, for example, reducing soil health, pollinator activity, or an ecosystem's ability to sequester carbon.
A process which consists of all photosynthesis processes instantiated in an ecosystem.
A process which consists of all respiration processes instantiated in an ecosystem.
A biogeochemical process during which one or more chemical compounds are sequentially converted into a series of related compounds in a regularly repeating, periodic fashion.
A biogeochemical cycle which has carbon-bearing chemical entities as participants.
Establishment of a new forest by seeding or planting of nonforested land.
Prior to afforestation, the land cover of a region must not include forests.
An ecosystem process during which the flora and fauna belonging to a forest are removed or destroyed.
The planting of trees in areas in where forests have previously been cleared.
reforestation is reestablishment of forest where the forest recently existed[IPCC]
Adapted from GEMET:http://www.eionet.europa.eu/gemet/concept/6979
To be populated through inference. Do not use for annotation.
A process during which the populations in a community of algae in a marine or freshwater ecosystem undergo rapid growth, resulting in high concentrations of algal cells that occur only periodically and briefly in that ecosystem, relative to their concentrations through the majority of the planetary orbital period.
This class is under development. Note that cyanobacterial blooms are often confused with algal blooms. There is no globally recognised threshold beyond which community density enters a bloom state.
A process during which the rapid growth of algal populations that result in an algal bloom ceases, and cell densities begin to fall due to death, predation, and transport.
A process during which the algal cells constituting an algal bloom produce biomass from abiotic components during photosynthesis.
TODO; add axioms pointing to GO organismal process; Add axioms pointing to toxin role
accumulation of toxins from algal bloom process
degradation of toxins from algal bloom process
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
Relabel the obo foundry unique label to be generic process
anthropogenic modulatory intervention process
An environmental process which is driven by the action of humans.
An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited.
An erosional process in which bedrock is converted from its solid form into a solute by the action of some solvent.
A process during which chemicals that are involved in natural ecosystem processes are transported or transformed, and which impact the activity of biological entities
An environmental process which has water - in any of its states - as a participant.
This classes asserted subclasses will be moved away as it should be an inferred class.
A planned process during which human agents establish plant communities in ecosystems which have previously been, partially or wholly, stripped of existing plant communities.
Evapotranspiration is the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere.
Evaporation is a form of vaporisation which occurs when a portion of the surface layer of a liquid in contact with a gaseous material, which is not saturated with the evaporating substance, vaporises.
Transpiration is the process of water movement through a plant and its evaporation from aerial parts of that plant, such as from leaves but also from stems and flowers.
Needs a process part "water transport" or similar and some link to plants to be complete.
An environmental system process that results in the introduction of contaminants into an environment.
Pollutants may be material or immaterial (e.g. heat energy)
A pollution process during which particulates or other contaminants are released into a portion of air.
A pollution process during which contaminants are released into soil.
A pollution process during which contaminants are released into water.
A pollution process during which plastic contaminants are released into an environmental material.
An process in which environmental parameters and variables are continually assayed.
A planned process during which the amount of pollutants released into an environmental system is regulated.
A monitoring process that assays the level of environmental pollutants to determine the presence of effect of environmental pollution.
A pollution process that results in increased levels of pollutants in an urban environment.
Partially compacted granular snow, which has undergone several cycles of melting and refreezing while being compacted, usually found on the atmosphere-exposed surface of a glacier.
Névé that survives a full season of ablation turns into firn.
neve
Granular snow which contains a proportion of fused granules formed through melting and re-thawing while being compacted by the weight of overlying material and which contains interconnected gaseous pores.
Firn derives from névé which has survived a full season of ablation and has undergone a metamorphic transition.
firn
A material transformation process during which recently precipitated, powdery snow transitions into firn or névé through compaction and/or through cycles of freezing and thawing.
Often, the weight of material deposited on top of powdery snow by, for example, mass wasting, can lead to nivation.
nivation
Any water ice that is part of a glacier.
It is suggested that users complement this term with ice terms that are more descriptive of the ice itself, rather than its location/parthood.
glacial ice
Glacial ice which contains material liberated during a glacial erosion process.
erosionally enriched glacial ice
An erosion process during which the movement of a glacier across a terrestrial surface causes the removal of material from that surface.
glacial erosion process
Water ice containing little to no air bubbles resulting in a reduction of internal light scattering and, given sufficient volume, a blue appearance.
The blue 'appearance' is to be understood as that within the visual range of humans.
blue ice
A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together.
compaction process
A process during which the mass of one or more materials, present within a given site, increases.
Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process.
material accumulation process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
A material accumulation process during which the mass of an existing ice mass increases.
ice gain
A material transport process during which the snow and ice constituting a glacier, and anything contained within it, is transported down a slope by gravitation.
This must be differentiated from small ice masses simply falling or moving down slopes. In ENVO, this is a subclass of advective transport process, however, this may not be universally accepted by some which strictly limit advection to fluids.
glacial transport process
A small glacier contained within a cirque basin.
cirque glacier
A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed.
The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486
geographic basin
A process during which a mass composed of one or more environmental materials, present within a given site, decreases.
material decumulation process
A process during which the mass of ice constituting a glacier decreases.
glacial ice loss
A stream which is primarily composed of meltwater and which flows within a glacier or ice sheet.
englacial stream
A material transport process during which one or more environmental materials are transported by the action of wind.
aeolian transport process
Particulate environmental material which is composed primarily of carbon particles formed through the incomplete combustion of hydrocarbons.
soot
Water ice which contains material liberated during an erosion process.
erosionally enriched ice
Uncompacted snow containing trapped atmospheric gases.
Described as having a fluffy appearance.
powdery snow
A process during which the mass of ice constituting a glacier increases.
glacial ice gain
A process during which a part of a glacier breaks away from the main mass.
Calving is usually caused by the expansion of glaciers.
glacial ice calving process
A process during which a part of a glacier breaks away from the main mass as an iceberg.
iceberg calving process
A process during which a part of an iceberg breaks away from the main mass.
It would be ideal to express that the size of the icemass calved must be smaller than an iceberg.
calving of ice from an iceberg
Sediment which has been transported through the marine water column, settling on the seafloor.
Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.
marine sediment
Marine sediment soured from either terrestrial systems, marine organisms, seawater and or cosmogeneous sources, which is transported through the marine water column, and accumulates within shallow regions of the oceanic basin close to continents, such as the continental shelf, or continental slope.
In this definition we refer to sedimentation processes that occured above the shelf, however this should be relaxed to include the continental shelf and slope.
output of sedimentation process which occured in neritic zone biome
shallow marine sediment
A water body which is located in a depression within the surface of a glacier.
supraglacial lake
A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface.
sedimentation in a water body
An ablation zone which is part of a glacier.
This class is more fully defined as: "The part of the glacier, usually at lower elevations, where ablation exceeds accumulation in magnitude, that is, where the cumulative mass balance relative to the start of the mass-balance year is negative. Unless qualified, for example by giving a date within the year, references to the ablation zone refer to its extent at the end of the mass-balance year. The extent of the ablation zone can vary strongly from year to year. A synonym of ablation area." - GCW Terminology and Vocabulary Assessment Report 2018”, GCW report #23/2018
glacial ice ablation zone
SWEET asserts this to be a subclass of cryo:GlacialRegion, thus the lack of link to ice sheets.
Particulate environmental material which is composed primarily of dust, rock, and soot, as well as the microbial communities associated with these materials, deposited on an ice mass by an aeolian process.
This actually is formed as a result of an accumulation process involving the constituents of cryoconite. When their semantics are more stable, we can axiomatise this fully.
cryoconite deposit
A vertical thaw hole within an ice mass, formed as a result of ice melt associated with local temperature increases, due to increased absorption of solar radiation by cryoconite deposits.
The general semantics of depressions are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486
This class doesn't refer to the site but instead the depression or hole and therefore the adjacency to the cryoconite itself.
cryoconite hole
A water body which forms as a result of localised melting taking place on the surface of a glacier or a mass of sea ice and which is contained in the cavity formed by such melting.
melt pond
brine channel
A material accumulation process during which brine droplets, trapped between ice crystals formed during seawater freezing, form brine channels.
This process may be considered a material accumulation process as it is the accumulation of brine droplets which form the channels.
brine channel formation process
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A material transformation process during which seawater freezes into sea ice.
sea ice formation process
A material transformation process during which brine is formed due to the expulsion of salt during frazil formation or a seawater freezing process.
Expelled salt accumulates in brine droplets, which remain in a liquid state due to their increased salinity.
brine rejection from seawater
New ice which is composed frazil which has congealed into a thin sheet.
Typically 3 to 4 millimeters in diameter. These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.
frazil ice
A new ice formation process during which small, needle-like crystals consisting of nearly pure fresh water, form due to the freezing of open, turbulent, supercooled water.
frazil ice formation
A channel which traverses an ice mass floating on a water body and bridges the atmosphere to the underlying water through its internal cavity.
thaw hole
A melt pond which has a surface exposed to the atmosphere.
atmosphere-exposed melt pond
A melt pond which is completely encased in ice and thus not directly exposed to the atmosphere or underlying water.
In practice, there may be some openings which are small relative to the surface footprint of the meltpond.
ice-encased melt pond
A lake which is comprised of meltwater located underneath or within a glacier.
Add axioms to show that this is on the larger side in a size continuum between ice-encased meltponds and intraglacial lakes.
intraglacial lake
A process during which material entities are added to a landform or to a feature upon the landform.
depositional process
A desublimation process during which water vapour is frozen into water ice.
desublimation of water vapour into ice
An ice formation process during which water is frozen into a form of new ice such as frazil, grease ice, slush, or shuga.
Make this class the union of the following processes: frazil ice formation, grease ice formation process, slush formation process, and shuga formation process.
new ice formation process
A sea ice formation process during which new ice crystals freeze together, forming nilas, a thin, elastic, continuous, ice sheet of a transparent gray color.
nilas formation process
A sea ice formation process during which water freezes to the bottom of an existing nilas ice floe creating a thicker ice floe known as young ice.
young ice formation process
A sea ice formation process during which seawater freezes onto young ice during the cold season, forming first year ice.
First year ice that survives melting during spring and summer can transition to second year ice.
first year ice formation process
A sea ice formation process during which seawater freezes onto first year ice during the cold season, forming second year sea ice.
Second year ice forms from first year ice which has previously survived one melt season.
second year ice formation
A sea ice formation process during which seawater freezes into second year ice during the cold season, forming multiyear ice.
Multiyear ice forms from second year ice which has previously survived at least two melt seasons.
multiyear ice formation process
Water ice which is formed from freezing water and is suspended in a water body.
Currently the new ice classes are not specific to sea water as they may form in non marine systems, but it would be good to confirm this especially for frazil ice.
sea ice types include frazil, grease ice, slush, and shuga. These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.
new ice
An ice mass which forms a cohesive and contiguous sheet of water ice, floating upon the surface of a water body.
Ice floes can exist in sea ice, in rivers or lakes. The WMO offers the following extent-based classification. Floe giant: Over 10 km across. Floe vast: 2-10 km across. Floe big: 500-2000 m across. Floe medium: 100-500 m across. Floe small: 20-100 m across. Ice cake: Less than 20 m across. Small ice cake: Less than 2 m across.
ice floe
An ice floe which is formed from frozen sea water, and floats upon the surface of a marine water body.
sea ice floe
A sea ice floe which has a rounded or circular shape and raised rims.
pancake ice
A sea ice floe which is thin, elastic, continuous, and of a transparent gray color, which results from the freezing of new ice.
nilas
A sea ice floe which is inflexible and thicker than nilas.
young ice
Sea ice which has formed over a single freezing season.
Sea ice develops from young ice; thickness from 0.3 to 2 meters (1 to 6.6 feet). Sea ice be subdivided into thin first-year ice (white ice), medium first-year ice, and thick first-year ice. First-year ice is distinguished from older ice primarily by having a higher salinity. Undeformed first-year ice differs from older ice in that it is smoother and lacks refrozen melt ponds. Characteristically level where undisturbed by pressure, but where ridges occur, they distinguished by being larger, more angular, and more porous than multiyear ridges.
first year ice
First year ice which melts before the next freezing season is often referred to as seasonal ice. By definition, seasonal ice cannot become second year ice.
Sea ice which is thicker than first year ice, and has survived a seasonal melting process.
second year ice
Sea ice which is thicker than second year ice, and has survived more than two seasonal melting process.
multiyear ice
A layer which consists of a thin aggregate of frazil ice crystals, which float upon the surface of a water body.
Within a marine system, grease ice makes the ocean surface resemble an oil slick.
grease ice layer
New ice, which is spongy, lumpy and opaque, and forms from water which freezes in an agitated water body.
These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.
shuga
A slurry of frazil, snow, and liquid water.
slush ice
slush ice layer
A new ice formation process in which slush ice is formed.
slush formation process
A new ice formation process in which shuga is formed.
shuga formation process
A freshwater lake which fills a depression formed by the erosion of thermokarst caused by permafrost thaw.
Continued thawing of the permafrost substrate can lead to the drainage and eventual disappearance of thermokarst lakes, leaving only the landform, thermokarst depression behind.
thermokarst lake
A thermokarst lake through which methane gas released from thawing permafrost, or other methane stores, rises and escapes to the atmosphere.
On Earth, the bright blue appearance, in the light spectrum visible to humans, is due to increased abundances of microorganisms attracted to sulfur compounds associated with the methane release.
methane-releasing thermokarst lake
A geographic basin which is formed due to the erosion of thermokarst by meltwater released from thawing permafrost.
thermokarst depression
An irregular land surface which consists of marshy hollows, hummocks, thermokarst depressions and thermokarst lakes formed from the erosion of ice-rich thawing permafrost areas.
Thermokarst is usually found in Arctic or mountainous areas.
thermokarst
A permafrost thawing process during which water-based ice or snow present in permafrost is converted into meltwater.
ice-bearing permafrost thawing process
Permafrost which contains pockets of trapped methane gas.
It would probably be better to assert parthood between the permafrost and cavities filled with gas rather than the gases themselves.
Other hydrocarbon gasses such as carbon dioxide may also be present. These pockets can be sufficently large that the permafrost surface will undulate when pressure is applied.
methane-laden permafrost
A crater which is found in permafrost and formed as a result of an explosion fuelled by methane formerly contained in that permafrost.
permafrost crater derived from a methane explosion
A process during which a material entity undergoes a rapid increase in volume, releasing gasses and various forms of energy, often including thermal, light and sound energy.
Supersonic explosions are known as detonations and subsonic explosions as deflagrations.
explosion process
An explosion during which methane-rich gas trapped in permafrost combusts.
permafrost methane explosion
A material transport process during which a portion of gaseous environmental material is transported into the atmosphere.
gas emission process
A gas emission process during which a portion of hydrocarbon gas is transported into the atmosphere.
Some hydrocarbon gasses within the atmosphere contribute to the planetary green house gas effect by increasing absorption of solar energy.
hydrocarbon gas emission process
A hydrocarbon gas emission process during which a portion of methane gas is transported into the atmosphere.
Methane is emitted during the production and transport of coal, natural gas, and oil. Methane emissions also result from livestock and other agricultural practices and by the decay of organic waste in municipal solid waste landfills.
methane gas emission process
A process during which the intesity of stellar radiation received by a planet's surface varies in a cyclical regime due to the planet's orbital motion around the barycentre of a planetary system and/or the tilt of its rotational axis relative to its orbital plane.
The seasons that are generated by this process are divisions of time between warm (maximal radiation exposure) and cold (minimum radiation exposure) extremes. Depending on the planet's makeup, the resulting seasonal dynamics may include ecological and meteorological cycles which may form the basis for further divisions of the cycle (e.g. rainy season, dry season, wildfire season).
season generating process
A one-dimensional temporal region which is delimited by the occurrence of processes which serve as its delimiters.
Season could be implemented as a subclass of one-dimensional temporal region, however, this will need further thought and discussion with BFO editors.
season
A season during which the average temperature of a planetary part exceeds that of all other seasons it endures during a season generating process.
The boundaries of seasons are typically fiat and should be defined on a data/information layer. This also pertains to the amount of time included when averaging measured values of qualities like temperature.
warm season
A season during which the average temperature of a planetary part is below that of all other seasons it endures during a season generating process.
cold season
A material transformation process during which a material entity melts during a warm season.
seasonal melting process
A compaction process during which a material entity subjected to heat and/or pressure is compacted into a solid mass without undergoing melting.
We should add the subclass axiom: 'has output' some ('environmental material' and 'has quality' some 'decreased porosity') once PATO:decreased porosity is available see ENVO issue #497 Additional axioms could also refer to object aggregates becoming objects within an environmental material.
solid-phase sintering
A sintering process during which snow is compacted into glacial ice.
Axioms will probably need to be updated if the axiomatisation of solid-phase sintering changes.
glacial sintering
An aeolian transport process during which powdery snow is displaced and moved.
aeolian transport of snow
An accumulation process during which a powdery snow carried on the wind settles on a solid surface, forming a mound.
snow drift formation
A mass wasting process during which slab snow rapidly moves down a sloping surface.
Slab avalanches account for most back-country fatalities.
slab avalanche
An avalanche during which powdery snow rapidly flows down a sloping surface.
powdery snow avalanche
An avalanche during which a suspension of water and snow flows down a sloping surface.
Wet snow avalanches travel at a lower velocity than other types of avalanches.
wet snow avalanche
Snow which is cohesive, hard and overlies weaker snow.
slab snow
A solid astronomical body part which is primarily composed of a continuous mass of snow and/or ice.
Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported.
cryoform
snow mass
An accumulation of powdery snow which was transported and deposited via a snow drifting process.
snow drift
An accumulation of snow and firn which rests upon land.
snow patch
A snow patch which forms during a cold season and melts away during the succeeding warm season.
Need to find a way of expression the fact that it 'ends during' some 'warm season' (but not with that axiom as that is for processes not a material entity).
seasonal snow patch
A snow patch which persists through at least one seasonal cycle.
Need to find a way of expression the fact that it has survived two or more melt seasons.
A snow patch is defined as perennial if it survives two or more melt seasons.
perennial snow patch
A snow mass which is large enough, and persists long enough, to undergo compaction under its own weight, leading to layer-like structural differentiation.
Given that SWEET considers the term to be a thickness and ENVO currently considers it a mass of snow. We have mismatch with the SWEET class, however, in ENVO we will take this term to be a mass of environmental material not a quality based on the harmonized GCW definition. See https://github.com/ESIPFed/sweet/issues/236#issue-805822974.
snow pack
Snowpack is found in geographic regions experiencing cold weather for extended periods of time.
The GCW analysis of multiple glossaries found eight definitions of snowpack, with many commonalities but also disagreements. Please see the corresponding report "WMO GCW Nomenclature Assessment" for more information.
snowpack
A structure which traverses a mass of one or more environmental materials, and encloses a roughly tubular site.
Intended to be a top level class for wide variety of channel-like entities. It’s particulars may change once more subclasses are accumulated. This is distinct from 'channel of a watercourse', which is a depression.
channel
A melt pond which and is exposed to the atmosphere and to a lesser degree water underlying the ice mass which contains it.
It would be good to add an axiom such as 'continuous with' some 'water body'.
atmosphere and water column exposed melt pond
A melt pond which is formed close to that part of an ice mass which is in contact with some underlying water body, and which has channels connecting it to that water body.
water column exposed melt pond
A lake which is situated beneath a glacier.
subglacial lake
An erosion process during which rock or soil is removed or degraded due to alternative thawing and freezing of meltwater beneath and at the margins of snowbanks.
erosion through nivation
A fire which is planned and executed deliberately under human supervision.
Fire-stick farming was the practice of Indigenous Australians who regularly used fire to burn vegetation to facilitate hunting and to change the composition of plant and animal species in an area. Aboriginal people may have been able to aim the burning of the scrub to avoid growing areas. There may have been a ritual taboo against burning certain areas of jungle. This type of farming directly increased the food supply for Aboriginal people by promoting the growth of bush potatoes and other edible ground-level plants.
Planned burns are conducted for a variety of reasons such combating or preventing uncontrolled wildfires in order by reducing the fuel load in a wooded or similar areas with combustible vegetation. Alternatively planned burns, such as those practiced by various indigenous people, are conducted for a variety of reasons including facilitating agriculture, hunting and or traveling. As well as managing populations of parasitic species or game animals by decreasing or increasing the size of their habitats respectively.
planned burn
The concentration of nitrate and nitrite when measured in liquid water.
liquid water nitrate and nitrite concentration
concentration of nitrate and nitrite in liquid water
A water-based rainfall process during which water droplets with increased acidity fall towards a planetary surface.
On Earth, the acidity of raindrops is typically increased through interactions of water molecules with sulfur dioxide or nitrogen oxide, released into the atmosphere by natural or anthropogenic processes.
acid rainfall
Water-based rain which has increased acidity.
acidic water-based rain
A season during which changes in atmospheric circulation associated with the asymmetric heating of land and sea cause moisture to be brought inland by monsoon winds, leading to increased rainfall as moisture-laden air rises and cools over land.
Pending decision of placement of season as one-dimensional temporal region, we should add axioms cross linking to monsoon winds, as well as increased prevalence of water-based rainfall.
On Earth, monsoon seasons typically occur in West Africa, Asia and Australia.
monsoon season
An atmospheric wind during which air masses over an ocean flow towards a land mass, driven by disequilibria between land and ocean surface temperatures.
monsoon wind
A fire which occurs in a grassland, combusting biomass stored in grasses as its primary fuel.
grass fire
A woodland clearing which is large enough to starve land fires of fuel, impeding their progress through wooded areas.
Firebreaks are typically elongated in shape and may be artificially constructed or result from a naturally occurring obstacle to a fire. Such obstacles include naturally occurring astronomical body parts such as a as rivers, lakes or canyons, or alternatively anthropologically constructed features such as roads.
firebreak
An agricultural environmental material which 1) is composed of a mixture of materials such as peat, composted bark, sand, perlite, or compost, and 2) serves as a medium in which to grow plants.
Potting soil can be composed of a wide range of materials in varying ratios, often containing little or no actual soil.
agricultural potting mixture
A blizzard which 1) lasts at least 3 hours, 2) combines below freezing temperatures and very strong wind, laden with blowing snow.
Blizzards typically reduces visibility to less than 1 km
WMO blizzard
A blizzard which has 1) winds of 35 miles per hour (approximately 56 kilometers per hour), 2) lasts for a period of at least three hours, and 3) occurs in extremely cold temperatures.
The original definition has been edited to conform to ENVO's textual pattern. Subjective/observer-based differentia (e.g. visibility) have been moved to comments. The NSIDC definition notes that blizzards involve snow reducing visibility to less than one-quarter mile (0.4 km) and are associated with dangerous blizzard conditions.
NSIDC blizzard
A blizzard which occurs in winter.
The original definition has been edited to conform to ENVO's textual pattern. Subjective/observer-based differentia (e.g. visibility) have been moved to comments.
winter blizzard
A fog the droplets of which freeze upon contact with exposed objects, forming a coating of rime or glaze.
Freezing fog forms when the air temperature is below freezing and the water droplets in the fog become supercooled.
freezing fog
A particle which is 1) primarily compposed of water ice, 2) on the order of 1 milimeter or less, 3) has a white and opaque appearance, and 4) is formed as a result of water droplets freezing during precipitation.
Need to add a computable size constraint.
grain of snow
granule of snow
snow grain
snow granule
snow particle
granular snow
Precipitation in the form of very small, white opaque particles of ice; the solid equivalent of drizzle. They resemble snow pellets in external appearance, but are more flattened and elongated, and generally have diameters of less than 1 mm; they neither shatter nor bounce when they hit a hard surface. Descriptions of the physical structure of snow grains vary widely and include very fine, simple ice crystals; tiny, complex snow crystals; small, compact bundles of rime; and particles with a rime core and a fine glaze coating. It is agreed that snow grains usually fall in very small quantities, mostly from stratus clouds or from fog, and never in the form of a shower.
particle of snow
Fog which is composed of particles of ice.
In future will add computable renditions of size and temperature constraints. The synonyms of this class can be quite confusing, as they reference entities like frost (which requires a surface for deposition). Might need to add a new droxtal class see https://glossary.ametsoc.org/wiki/Droxtal.
frozen fog
ice-crystal fog
pogonip
air hoar
frost flakes
frost fog
rime fog
The suspended particles may be partly ice crystals 20 to 100 micron in diameter, but chiefly, especially when dense, droxtals 12-20 micron in diameter. Ice fog is formed by direct freezing of supercooled water droplets with little growth directly from the vapor. It occurs at very low temperatures, and usually in clear, calm weather in high latitudes. The sun is usually visible and may cause halo phenomena or luminous pillars. Ice fog is rare at temperatures warmer than -30 °C, and increases in frequency with decreasing temperature until it is almost always present at air temperatures of -45 °C in the vicinity of a source of water vapor. Such sources are the open water of fast-flowing streams or of the sea, herds of animals, volcanoes, and especially products of combustion for heating or propulsion. At temperatures warmer than -30 °C, these sources can cause steam fog of liquid water droplets, which may turn into ice fog when cooled.
ice fog
A climate which 1) has a mean temperature for the warmest month of less than 10°C (50°F), but higher than 0°C (32°F), 2) is not conducive to a permanent surficial cover of snow or ice, and 3) supports a tundra ecosystem.
Might need to add the Köppen climate classifications. Climate conditions might be obsoleted. Warmest month and mean temperature are operationally defined, will need to sort these out. Focusing on physical differential like surface cover would be preferable, (but maybe not practical).
In W. Köppen's 1936 climatic classification it is one of the polar climates, defined as having a mean temperature for the warmest month of less than 10°C (50°F) (in contrast to snow forest and temperate rainy climates) but higher than 0°C (32°F) (which is the limit of perpetual frost climate). Tundra is designated ET. Tundra climate appears as a temperature province in C. W. Thornthwaite's 1931 classification.
tundra climate
A cryospheric layer which is primarily composed of snow.
snow cover
Follows from the GCW's snow cover definition 2: In general, a layer of snow on the ground surface. Compare snowfield, snowpack. Given the SWEET terms location in its heirarchy I think only the 3rd definition is meant.
snow layer
A depth which inheres in a layer of liquid water derived from the complete melting a mass of snow contained in an area.
In an area of melted snow it's the thickness of acumulated water. This involves a processing step for measurement, may be more appropriate in OBI (if it extends beyond biomedicine).
The quantification of snow water equivalent can be done through direct melting of snow in a defined area, or through the derivation of such a value from the processing of remote sensing data of, e.g., snow density and coverage.
snow water equivalent
An astronomical body part which is composed primarily of environmental materials in their frozen form.
For the moment the definition links to liquid water but in the future we might need to link to other materials for other planets, e.g., Mars. Need to make this planet agnostic. Might want to not have the definition link to years as some astronomical body parts might not be in systems with years. Note that in a strict sense, rocks are also frozen but in a practical sense we use terms like "solidified". This maybe something to revist if we add more astrogelogical content.
The term generally refers to the portions of the Earth where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). Some definitions consider the cryosphere to include any area of Earth which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists." Definitions of Cryosphere come from several glossaries including: - PhysicalGeography.net http://physicalgeography.net/ - van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf] - American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017]. - EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary - IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link] - NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016]. - Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link] - UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link]
cryosphere
A cryosphere which is part of a planet.
Replacement for ENVO:01000818
planetary cryosphere
Land which is covered or partially covered by snow.
area of snow cover
land covered by snow
snow covered land
The threshold at which land is considered covered by snow varies. Please define such thresholds on the instance level, or request a subclass of this class if a threshold you know of is used by a large community of practice or in an official definition. This is one of three classes representing the idea of snow cover in the GCW glossary in addition to depth of snow and snow cover. In the GCW this refers to 1. The areal extent of snow-covered ground, usually expressed as percent of total area in a given region.
snow-covered land
A material transport process during which liquid water is circulated in the vicinity of a heat source in order to absorb thermal energy and transport it away form that source.
water cooling
The thickness of some snow.
snow thickness
thickness of snow
Please also see "snow cover" in ENVO which maps to an alternative snow cover in SWEET.
An area of tundra which is present in a region subject to alpine conditions.
area of alpine tundra
An area of tundra which is present in a region subject to polar conditions.
area of polar tundra
An area density which inheres in snow distributed over an area of a landmass or other substrate.
The superclass "area density" is somewhat awkward and this positioning requires further discussion.
1. The areal extent of snow-covered ground, usually expressed as percent of total area in a given region. 2. In general, a layer of snow on the ground surface. Compare snowfield, snowpack. 3. The depth of snow on the ground, usually expressed in inches or centimeters.
Snowfall which has an increased rate.
intense snowfall
heavy snow
intense snow
This generally means snowfall accumulating to 4 inches or more in depth in 12 hours or less; or snowfall accumulating to 6 inches or more in depth in 24 hours or less. In forecasts, snowfall amounts are expressed as a range of values, e.g., "8 to 12 inches." However, in heavy snow situations where there is considerable uncertainty concerning the range of values, more appropriate phrases are used, such as "...up to 12 inches..." or alternatively "...8 inches or more...".
heavy snowfall
An ice mass which is 1) transparent or translucent, 2) rounded, spherically, or cylindrically shaped, and 3) less than 5 milimetres in diameter.
grain of ice
ice grain
sleet
small hail
They may be spherical, irregular, or (rarely) conical in shape. Ice pellets usually bounce when hitting hard ground and make a sound upon impact. They can fall as continuous precipitation or in showers. Now internationally recognized, ice pellets includes two basically different types of precipitation, known in the United States as 1) sleet or grains of ice, generally transparent, globular, solid grains of ice that have formed from the freezing of raindrops or the refreezing of largely melted snowflakes when falling through a below-freezing layer of air near the earth's surface; and 2) small hail, generally translucent particles, consisting of snow pellets encased in a thin layer of ice. The ice layer may form either by the accretion of droplets upon the snow pellet or by the melting and refreezing of the surface of the snow pellet.
ice pellet
Snowfall which 1) is localized, 2) is convective, and 3) occurs as a result of a cold, dry air mass absorbing heat and moisture as it flows over a lake with warmer waters.
The factors involved in this process are complex, and expert input is needed to refine this. Similar input is needed to create bay-effect and ocean-effect snow. @Brandon: add axioms to relate this concept to proximity to a `lake`; perhaps using colocation and spatial region?
lake effect snow
lake-effect snow
The formation of lake-effect snow depends on multiple factors, effecting the thresholds of temperature needed in the air and water masses. In the United States this phenomenon is most noted along the south and east shores of the Great Lakes during arctic cold-air outbreaks.
lake-effect snowfall
A snowstorm during which intense lake-effect snowfall occurs.
Add axioms to nest the lake-effect snowfall process in this one
lake effect snow storm
Please see "lake-effect snowfall" for further definition. A lake effect snowstorm is a snowstorm occurring near or downwind from the shore of a lake resulting from the warming (destabilization) and moistening of relatively cold air during passage over a warm body of water.
lake-effect snow storm
A snowfall which occurs during springtime and is of low intensity.
Link this to spring once seasons are added to ENVO
Strictly, there is no increased rate of snowfall here, but of lamb death. We're not likely to add "lamb-death storm" to ENVO. Maybe AGRO would.
lamb storm
lamb-blasts
lamb-showers
This term is primarily used in England and refers to snowfall in lambing season. It is referred to as a "storm" as it may adversly affect or kill newborn lambs.
lambing storm
An object aggregate which is primarily composed of particles of water in liquid, frozen, or partially frozen states.
WMO METEOTERM notes that other regions define this as a sudden brief rainfall with wind and hail but they don't state what those other regions are. WMO, METEOTERM is available at https://www.wmo.int/pages/prog/lsp/meteoterm_wmo_en.html, Last accessed [26/01/2016].
falling sleet
Water-based rain which is composed of supercooled water droplets, which freeze on contact with surfaces.
Could make a freezing rain process class to mirror this in the process hierarchy as subclass to hydrological precipitation process.
There are communities which consider rain with droplets above the liquid-solid phase transition point of water to be freezing rain should they freeze on contact with a supercooled surface.
freezing rain
Precipitation which is composed primarily of hail stones.
Individual units of hail are called hailstones. Thunderstorms that are characterized by strong updrafts, large liquid water contents, large cloud-drop sizes, and great vertical height are favorable to hail formation. The destructive effects of hailstorms upon plant and animal life, buildings and property, and aircraft in flight render them a prime object of weather modification studies. In aviation weather observations, hail is encoded A. Smaller particles of similar origin, formerly called small hail, may be classed as either ice pellets or snow pellets.
hail
An ice mass which 1) occurs in a ball-shape or irregular lump, 2) has a minimum diameter of 5 millimeters (or 0.2 inches), and 3) is formed within convective clouds.
Nearly always formed within cumulonimbus clouds. Typically have a diameter ranging between 5 and 50 millimeters.
hail stone
An object aggregate which is composed primarily of snow falling through an atmosphere.
falling snow
A hydrological precipitation process during which water falls in both liquid and frozen form.
sleet fall
In nature, water-based precipitation will likely always have some liquid and solid/frozen components (especially in higher atmospheric layers) - sleet is generally composed of these phases in comparable proportions. Note that formation processes differ between sleet and other frozen precipitation. For example, hail, being larger in size than sleet or ice pellets, is formed by the accumulation of layers of freezing water in the clouds. Sleet, however, is formed due to temperature difference in the atmosphere
precipitation of sleet
An ice mass which is primarily composed of frozen or mostly frozen raindrops or refrozen partially melted snowflakes.
The size of sleet pellets are considered to be, at most, the size of a pea, although thresholds vary across cultures.
sleet pellet
An environmental zone which is covered or partially covered by ice.
area of ice cover
The depth of some water ice.
depth of water ice
A park which has been designed for the recreation of children.
playground
A park which is owned by a governmental or state entity and which is accessible by its citizenry (i.e. the public).
public park
A sports facility which has been constructed for sports that require large outdoor spaces and is owned by a governmental or state entity and which is accessible by its citizenry (i.e. the public).
public sports field
A constructed pavement which is intended for bicycle traffic
bike path
A material entity which has been discarded outside waste management systems by humans or their technologies.
basura antropogénica
rifiuti antropogenici
anthropogener Abfall
menschengemachter Abfall
Very large objects that are discarded are typically considered "debris", but this term is loosely defined and there are no standard size classifications which can be used to distinguish debris from litter.
anthropogenic litter
An anthropogenic environment in which populations of humans have limited acess to affordable and nutritious food.
food desert
An environment in which entities are exposed to either excessive or constant sound.
noisy environment
An environment in which humans have a low likelihood of being harmed or killed.
safe environment for human presence
An environment which includes components which are deemed to be aesthetically pleasing by a population of humans.
attractive environment
An environmental system which is shielded from direct stellar irradiation by material entities.
Requested a "shaded" quality in PATO: https://github.com/pato-ontology/pato/issues/285
Typically, the material entities which intercept the star's radiation are located far closer to the shaded environment than the star itself. For example, trees shading the understory or awnings shading restaurant seating.
shady environment
An environment in which humans are exposed to regularly occurring physical or emotional violence.
violent environment
An acoustic radiation process during which waves that transmit sound energy at frequencies above 20 kHz are emitted by a source.
An infrared radiation during which waves with frequencies between 30 THz and 120 THz and with wavelengths between 10 micrometers and 2.5 micrometers are emitted by a source.
An infrared radiation during which waves with frequencies between 120 THz and 400 THz and with wavelengths between 2.5 micrometers and 750 nanometers are emitted by a source.
An infrared radiation which consists of waves with frequencies between 300 GHz and 30 THz and with wavelengths between 1 mm and 10 micrometers are emitted by a source.
A merchant vessel which is used to carry passengers, vehicles, or cargo across a body of water.
ferry
An environmental system which is not sheltered.
outdoor environment
An industrial building made from steel and covered in polyethylene used for plant cultivation.
grow tunnel
high tunnel
hoop greenhouse
hoophouse
polyhouse
These tunnels are usually semi-circular, square or elongated in shape. These are not subclasses of ENVO:tunnel as they are not built underground or underwater.
polytunnel
A motor vehicle which is equipped with medical equipment and can be used to transport humans to treatment facilities.
ambulance
A boat which provides short-term residential and entertainment facilities to passengers.
cruise ship
recreational cruise ship
A transport boat which can be hired.
merchant ship
merchantman
trading vessel
merchant vessel
A vehicle which locomotes using rails and consists of a series of connected compartments used to transport passengers or cargo.
train
A train which is capable of and used for passenger transport.
passenger train
A passenger train which runs along an undergroud rail system.
subway
tube train
underground train
London Underground
SkyTrain
Tube
U-Bahn
Underground
metropolitana
subway train
A system which has components that have been constructed to allow the movement of people or goods.
constructed transport system
A constructed transport system which is owned by a government or other form of public representation.
public transport
public transportation
public transit system
A bus which is part of public infrastructure.
public autobus
public motorbus
public multibus
public omnibus
public bus
A ferry which is owned by a government or other form of public representation.
public ferry
A train which is owned by a government or other form of public representation.
public train
A subway train which is owned by a government or other form of public representation.
public subway train
A public transit system which is owned by a government or other form of public representation.
MRT
mass rapid transit
metro
heavy rail
light rail
medium-capacity rail
rapid transit system
A place where passengers and cargo are exchanged between vehicles or/and between transport modes.
transport interchange
transport hub
A transport hub which is part of public infrastructure.
public transport interchange
public transport hub
A research station in which food production and/or agribusinness research is performed.
AES
ARS
agricultural research station
research farm
agricultural experimental station
A farm which produces milk or products derived from milk.
dairy farm
A building part which is a narrow hall or passage in a building with rooms leading off it.
hall
passage
hallway
building corridor
A human construction with extended facilities from which aircraft flight operations take place.
aerodrome
airdrome
The "airport" term is usually associated with commercial air transport, while "militairy airport" and "airbase" cover militairy air force facilities.
airport
An industrial building in an airport where passengers transfer between facilities and vehicles.
airport terminal
An industrial building which provides travelers with access to airplanes.
airport concourse
A room in an airport where en-route passengers can wait between flights..
transit lounge
airport transit room
airport transit lounge
A building which is primarily used for Christian religious activities.
church
church house
church building
A building which accomodates conferences.
conference center
conference centre
conference venue
A room which accommodates conferences.
conference hall
meeting room
conference room
A human construction in which people are educated.
educational facility
An institutional building in which students are educated.
school
school building
An institutional building in which university services are performed.
campus building
university college building
university building
An institutional building in which firefighting apparati are stored, and which may include staff living spaces.
engine house
fire hall
fire house
firemen's hall
fire station
An institutional building which temporarily houses homeless people.
homeless shelter
A human construction in which healthcare is provided.
health facility
medical facility
healthcare facility
A healthcare facility which is used for short-term patient care.
ACC
ACF
acute care center
acute care facility
A healthcare facility in which patients are medically assessed.
CAC
clinical assessment centre
clinical patient assessment center
clinical patient assessment centre
clinical patient assessment facility
A healthcare facility which 1) is located in part of a hospital and 2) is used by an organizational unit within a hospital.
hospital ward
hospital unit facility
A hospital unit facility which is used for anaesthetic service provision.
anaesthesia unit
anaesthesia ward
anaesthetics unit facility
A hospital unit facility which is used for breast cancer screening.
breast assessment unit
breast screening ward
mammography unit
breast screening unit facility
A hospital unit facility which is used to provide nondemoninational religious services.
chaplain unit
chaplain's unit
chaplaincy unit facility
A hospital unit facility which is used to provide cardiac patient care.
CCU
CCW
CICU
cardiac care unit
cardiac care ward coronary care ward
cardiac intensive card ward
cardiac intensive care unit
coronary care unit facility
A hospital unit facility which is used to provide diagnostic imaging services.
diagnostic imaging ward
medical imaging unit
medical imaging ward
diagnostic imaging unit facility
A hospital unit facility which houses patients ready to leave the hospital facility.
discharge lounge
discharge ward
discharge unit facility
A hospital unit facility which is used to provide emergency medicine services.
A&E
accident & emergency department
casualty department
emergency department
emergency room
emergency ward
emergency unit facility
A room in which emergency medical care is provided.
A&E room
ER room
EW room
accident & emergency department room
casualty department room
emergency department room
emergency room room
emergency ward room
emergency unit room
A hospital unit facility which is used to provide gastroenterology medical services.
gastroenterology unit facility
A hospital unit facility which is used to provide surgical services.
general surgery ward
general surgical unit
general surgical ward
surgery unit
surgery ward
surgical unit
surgical ward
general surgery unit facility
A hospital unit facility which is used to provide geriatric medical services.
elderly unit
geriatric care ward
geriatric unit
geriatric ward
geriatric care unit facility
An intensive care unit facility which is used to provide care of critically ill elderly patients.
GICU
geriatric intensive care ward
geriatric intensive care unit facility
A hospital unit facility which is used to provide gynaecologic medical services.
gynaecology ward
gynaecology unit facility
A hospital unit facility which is used to provide haematological medical services.
haematology ward
hematology unit
hematology ward
haematology unit facility
A hospital unit facility which is used to provide intensive medical care.
Subclasses of this term are valid subclasses of their non-intensive care unit equivalents, e.g. psychiatric care unit. Equivalence axioms may resove this.
ICU
ICW
ITU
critical care unit
critical care ward
intensive care ward
intensive therapy unit
intensive treatment unit
intensive treatment ward
intensive care unit facility
An intensive care unit facility which is used to provide surgical services for critically ill patients.
SCCU
SICU
surgery critical care unit
surgery critical care ward
surgical critical care unit
surgical critical care ward
surgical intensive care ward
surgical intensive care unit facility
An intensive care unit facility which is used to provide medical care for trauma patients.
TICU
trauma intensive care unit
traumatic critical care unit
traumatic intensive care unit facility
A room in which intensive medical care is provided.
CCU room
CCW room
ICU room
ICW room
ITU room
critical care unit room
critical care ward room
intensive care ward room
intensive therapy unit room
intensive treatment unit room
intensive treatment ward room
intensive care unit room
A hospital unit facility which is used to provide materinity care.
materinity care unit
maternity ward
obstetrics unit
obstetrics ward
maternity unit facility
An ambulance which is equiped to enable intensive care service provision.
MICU
mobile ICU
mobile intensive care unit
mobile intensive unit
mobile intensive care ambulance
A hospital unit facility which is used to provide medical microbiology services.
clinical microbiology unit
clinical microbiology ward
microbiology ward
micobiology unit facility
A hospital unit facility which is used to provide neonatal medical services.
neonatal ward
neonatal unit facility
A hospital unit facility which is used to provide intensive neonatal medical care.
neonatal intensive care ward
neonatal intensive care unit facility
A hospital unit facility which is used to provide nephrological medical services.
general nephrology unit
general renal unit
general renal ward
generalnephrology ward
nephrology ward
renal unit
renal ward
nephrology unit facility
A hospital unit facility which is used to provide neurological medical services.
general neurology unit
general neurology ward
neurology ward
neurology unit facility
A hospital unit facility which is used to provide nutrition and dietetics services.
NDU
nutrition and dietetics ward
nutrition and dietetics unit facility
A hospital unit facility which is used to provide occupational therapy.
OT unit
OT ward
occupational therapy ward
occupational therapy unit facility
A hospital unit facility which provides treatment for cancer.
cancer unit
cancer ward
oncology ward
oncology unit facility
A hospital unit facility which is used to provide ophthalmological services.
ophthalmology ward
ophthalmology unit facility
A hospital unit facility in which orthopaedic medicine is performed.
orthopaedics ward
orthopedics unit
orthopedics ward
orthopaedics unit facility
A hospital unit facility which is used to provide pain management.
pain management unit facility
A hospital unit facility which is used to provide pediatric services.
children's unit
children's ward
pediatric ward
pediatric unit facility
A hospital unit facility which is used to provide pediatric intensive care.
pediatric intensive care unit facility
A hospital unit facility which is used to provide pharmacy services.
pharmacy ward
pharmacy unit facility
A hospital unit facility which is used to provide physiotherapy.
physiotherapy ward
physiotherapy unit facility
A hospital unit facility which is used to provide care for patients recovering from anesthesia.
PACU
PAR
post-anesthesia care ward
post-anesthesia recovery
post-anesthesia unit
post-anesthesia ward
post-anesthesia care unit facility
A hospital unit facility which is used to provide high dependency care.
HDU
high dependency ward
progressive care unit
progressive care ward
progressive intensive recovery unit
step-down unit
step-down ward
high dependency unit facility
A hospital unit facility which is used to provide psychiatric medicine.
psych unit
psych ward
psychiatric ward
psychiatric unit facility
A hospital unit facility which is used to provide intensive psychiatric care.
PICU
PsICU
psychiatric intensive care ward
psychiatric intensive care unit facility
A hospital unit facility which is used to provide radiation therapy.
radiation therapy unit
radiation therapy ward
radiotherapy ward
radiotherapy unit facility
A hospital unit facility which is used to provide rheumatic medical services.
rheumatology ward
rheumatology unit facility
A hospital unit facility which is used to provide urological medicine services.
urology ward
urology unit facility
A room which is used for patient care during a patient's visit or stay in a healthcare facility.
patient-care room
examination room
patient bed room
patient room
A hospital which is used to provide tertiary care.
tertiary care center
tertiary center
tertiary hospital
tertiary referral center
tertiary referral hospital
A facility which is used to provide treatment, remedial work, and/or instruction.
This sense of clinic does not necessarily involve medical services. For medical services see "medical clinic".
clinic
A healthcare facility which is used to provide outpatient health care services.
ambulatory care clinic
outpatient clinic
medical clinic
A medical clinic which is used to provide chiropractic services.
chiropractic office
chiropractor clinic
chiropractor office
chiropractic clinic
A medical clinic which is used to provide medical services focused on maintaining and improving the oral health of clients.
dental office
dentist clinic
dentist office
dental clinic
A medical clinic which is used to provide family medicine services.
GP clinic
GP office
family care clinic
family doctor clinic
family doctor office
family medicine clinic
family medicine office
general medicine clinic
general practice clinic
general practice office
family practice clinic
A medical clinic which is used to provide massage therapy services.
massage therapist clinic
massage therapist office
massage therapy office
massage therapy clinic
A medical clinic which is used to provide ophthalmology services.
ophthalmologist clinic
ophthalmologist office
ophthalmology office
ophthalmology clinic
A medical clinic which is used to provide optometry services.
eye doctor office
optometrist clinic
optometrist office
optometry clinic
A medical clinic which is used to provide pain management services.
pain management clinic
chronic pain clinic
pain clinic
A medical clinic which is used to provide physical therapy services.
physical therapy clinic
physical therapy office
physiotherapy office
physiotherapy clinic
A medical clinic which is used to provide services to walk-in patients.
walk-in centre
walk-in clinic
A healthcare facility which is used to prepare, dispense, or sell medical drugs.
apothecary
pharmacy
American Heritage Dictionary of the English Language, Fifth Edition. (2011). Retrieved August 11 2020 from https://www.thefreedictionary.com/pharmacy
A residential building which is used to provides long-term care for residents.
An equivalence axiom to show that this building is used for health care can be used to position this under health care facility.
LTC center
LTC centre
LTC facility
long-term care center
long-term care centre
long-term care facility
A long-term care facility which is used to provide care for people with disabilities or for adults who cannot or who choose not to live independently.
ALF
assisted living residence
assisted living facility
A long-term care facility which is used to provide care for people with complex health needs, and which typically has at least one caregiver in attendance twenty four hours a day.
residential care facility
group home facility
A building which is used by an organization which serves a long-established role in human society.
This term needs further consideration and development as semantics of institution are ambiguous at scale - e.g. are hotels institutional buildings?
institutional building
A market which is used for the sale and purchase of perishable goods.
wet market
A market which is used for the sale and purchase of durable goods.
dry market
An institutional building which is used to provide policing services.
station house
police station
A human construction which contains one or more polling stations
voting facility
polling place
A human construction which is that part of a polling place where voters cast their ballot
polling station room
polling station
A booth which enables a voter to vote confidentially.
voting booth
polling booth
A human construction which is used to forcibly confine humans.
correctional center correctional centre
correctional facility
detention centre
jail
lock-up
remand centre
prison facility
A prison facility which is owned and operated by a private corporation.
for-profit correctional center
for-profit correctional centre
for-profit correctional facility
for-profit detention center
for-profit detention centre
for-profit jail
for-profit lock-up
for-profit penitentiary
for-profit prison
for-profit remand center
for-profit remand centre
private correctional center
private correctional centre
private correctional facility
private detention center
private jail
private lock-up
private penitentiary
private remand center
private remand centre
private prison
A commercial building in which the majority of commerical activity occurs in shops occupying parts of the building.
shopping centre
shopping center
A shopping center in which a large indoor pedestrian promenade provides access to stores and other facilities.
mall
shopping mall
A manufactured product consisting of a duct opening which allows air to circulate.
vent
air vent
A poll which is attached to the head, foot, or side of a bed frame.
adult portable bed rail
assist bar
bed handle
bed rail
bed side rail
grab bar
half rail
hospital bed rail
safety rail
side rail
bedrail
A manufactured product consisting of a panel on which control or monitoring instruments are set.
console
control board
control unit
display board
display panel
indicator panel
instrument board
instrument panel
panel
control panel
A manufactured product consisting of a handle used to open or close a door.
door knob
door handle
A pole which provides stability or support when grasped by the hand.
rail, railing
hand rail
handrail
A switch which turns a light on or off.
switch, dimmer switch
lightswitch
light switch
A manufactured product which is a storage compartment with a lock.
lockable cabinet
lockable cupboard
locking cabinet
locking cupboard
locker
A switch which allows patients in health care settings to alert a nurse or other health care staff member.
nurse call cord
nurse call button
Steel which is composed primarily of a corrosion resistant alloy of iron and chromium.
inox steel
stainless
stainless steel
A paper product which is thin translucent paper.
tissue
Tissue paper is often used for wrapping or for protecting delicate articles.
tissue paper
A plumbing fixture which is bowl-shaped, part of a toilet fixture, and capable of contain human waste until it is disposed of.
lavatory bowl
toilet bowl
A manufactured product which is composed of one or more glass or other transparent or semi-transparent materials set inside a frame, and installed in wall, door, roof or vehicle surfaces to allow the passage of light, and sometimes air.
casement
casement window
pane
sash
sash window
windowpane
window
A manufactured product which is composed of a hinged, sliding, or revolving barrier which is installed at the entrance to a building, room, vehicle, or in the framework of a cabinet.
door
A restaurant which is of French cultural origin and which has a short menu and limited seating space.
bistrot
bistro
A type of restaurant which is of French cultural origin and which provides more service or food variety than a bistro.
brasserie
A restaurant which provides customers with cooked meat freshly sliced to order.
carvery
A restaurant which primarily serves coffee.
café
coffee shop
coffeehouse
A restaurant which is small, inexpensive, and typically specializing in fried foods and/or home-cooked meals.
greasy spoon
A restaurant which specializes in serving steaks and pork chops.
chophouse
steak house
steakhouse
A restaurant which is of Italian cultural origin and which is generally less formal than an Italian ristorante, but more formal than an osteria.
trattoria
A healthcare facility which is a temporary hospital or mobile medical unit that takes care of casualties on-site before they can be safely transported to more permanent facilities.
field hospital
A healthcare facility which provides palliative care for the terminally ill.
hospice
A commercial building which contains auditoria for viewing films.
cinema
cinema hall
picture house
movie theater
An industrial building which is used to store goods.
warehouse
An office building which is the chief administrative building of a city, town, or other municipality.
Rathaus (German)
city hall
civic centre
guildhall
town hall
A public building or site which provides facilities used by people to keep fit or relax.
leisure centre
An area of developed space which is reserved for office buildings.
office park
business park
A terrestrial environmental zone where wild animals live safely or are hunted in a controlled way for sport.
game park
wildlife preserve
game reserve
A hill which is small and usually separated from a larger group of hills such as a range.
knoll
Hillocks are similar in their distribution and size to small mesas or buttes.
hillock
A shore along a river.
riverfront
An island which is small, principally composed of rock, and usually too small for human habitation.
islet
skerry
A power plant which is a group of wind turbines in the same location used to produce electricity.
wind park
wind power plant
wind power station
wind farm
An island that is not permanently populated by humans.
uninhabited island
atoll
desert island
A store which is physically large and is part of a retail chain.
megastore
supercenter
superstore
big-box store
A bridge which is a truss bridge, pre-fabricated, and portable.
Bailey bridge
A bridge which is hinged and can be raised.
draw-bridge
drawbridge
A bridge designed solely for pedestrians.
pedestrian bridge
pedestrian overcrossing
pedestrian overpass
footbridge
A bridge which arches in the center, and has a span which is higher than the ramps on either side, forming a hump-like arrangement.
humpback bridge
A bridge which is used for transportaiton, and which crosses over another road or railway.
flyover
overbridge
overpass
A bridge which has its deck hung on vertical suspenders via suspension cables.
suspension bridge
A bridge which is movable and has a vertical locating pin as its primary structural support, and a support ring about which it can pivot horizontally.
swing bridge
A device that causes suction in order to remove debris from surfaces.
vacuum
hoover
vacuum cleaner
Poultry manure made of chicken feces.
chicken manure
A soft sulfate mineral composed of calcium sulfate dihydrate.
gypsum
A container for storing water.
water tank
An anthropogenic geographic feature consisting of a receptacle intended to provide drinking water to animals.
artificial watering point
water trough
A paper product which is a thin sheet material made of processed cellulose fibres.
paper
paper sheet
sheet of paper
An agricultural building used for crop storage or animal husbandry.
barn
An animal house where fowl are kept.
chicken coop
hen house
chicken house
Environmental material consisting of waste products that have been discarded at an unsuitable location.
litter
A manufactured product consisting of a table or desk used for sewing.
work table
sewing desk
sewing table
A manufactured product consisting of a disk-shaped material that rotates around an axle bearing placed through a hole in its center.
wheel device
wheel
A manufactured product consisting of a shallow platform designed for the carrying of items.
tray
A manufactured product which has been designed to 1) allow a human to do work more efficiently and 2) be used in a hand-held fashion.
hand tool
A tool with a flat, smooth rubber blade, used to remove or control the flow of liquid on a flat surface.
squilgee
squeegee
An indoor toilet that is available for public use.
public toilet
A device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action.
pump
A hand tool used to remove the outer layer of vegetables and fruit, consisting of a handle attached to a metal blade with a slot with a sharp edge.
vegetable scraper
peeler
A manufactured product which is a flat transport structure that supports goods in a stable fashion while being lifted and/or moved.
skid
pallet
A device used in packaging operations.
packing machine
packaging machine
A building or room that is part of a cathedral, monastery or collegiate church, in which larger meetings are held.
chapterhouse
chapter house
A building which is at the center of Islam's most important mosque, the Great Mosque of Mecca.
Kaaba
A building which is a place of worship for Muslims.
masjid
mosque
A building that has been placed on one of the four statutory lists maintained by Historic England in England, Historic Environment Scotland in Scotland, Cadw in Wales, and the Northern Ireland Environment Agency in Northern Ireland.
listed structure
protected structure
listed building
A residential building containing bunks or beds which are often not separated by walls.
bunkhouse
A commercial building where merchants trade grains.
grain exchange
corn exchange
A commercial building designed for kilning (drying) hops.
hop kiln
oast
oast house
A building that formed a very large fruit tree green house, or conservatory, on the grounds of fashionable residences from the 17th to the 19th centuries.
orangerie
orangery
A building which historically has at least 10 floors.
skyscraper
A residential building shared by multiple dwellings, typically with flats or apartments on each floor and with shared entrance stairway access.
tenement
A public building constructed as a external, free-standing monument enclosing the interment space or burial chamber of a deceased person or people.
mausoleum
A sports facility where bowling is played.
bowling arena
bowling center
bowling lounge
bowling alley
A transport feature consisting of a closed building structure to hold aircraft or spacecraft.
hangar
A device consisting of a continuous flexible band moved by a series of rollers to transport objects or material from one place to another.
belt conveyor system
conveyor
belt conveyor
conveyor belt
A device designed to remove water or humidity.
dryer
A dryer that is used to remove moisture from textiles.
tumble dryer
clothes dryer
A cow shed for baby cows/bulls.
calf house
calf-rearing shed
calfshed
calf shed
An animal house used for housing livestock.
livestock shelter
livestock structure
livestock house
A human construction specially designed for a specific purpose.
facility
A hand tool for making rotational adjustments.
spanner
wrench
A self-service shop offering a wide variety of food, beverages and household products, organized into sections.
supermarket
A part of an oven or a small stove used to broil food.
grill
broiler
A portable, box-type industrial storage product used for the storage and handling or parts and materials, that may collapse to conserve space when not in use.
storage bin
storage box
tote
tote box
tote bin
A large bag with parallel handles that emerge from the sides of its pouch.
bag
tote bag
A factory where raw or preprocessed materials are transformed into finished parts or products.
preprocessing factory
preprocessing plant
A factory where raw materials are treated or prepared for final processing.
processing factory
processing plant
A factory for processing, packaging, labelling, handling, and storing cheese.
cheese factory
cheese plant
cheese processing plant
A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products.
meat factory
meat plant
freezing works
meat packaging plant
packinghouse
slaughterhouse
meat processing plant
A bandage wrap used on the lower legs of a horse.
stable bandage
standing bandage
standing wrap
stable gauze
stall gauze
A stable bandage runs from just below the knee or hock, to the bottom of the fetlock joint, and protects the cannon bone, tendons of the lower leg, and fetlock joint.
A delicatessen which prepares and sells preserved meat products.
charcuterie
charcuterie shop
An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer.
animal manure
compost
farm slurry
green manure
liquid manure
Most manure consists of animal feces; other sources include compost and green manure.
manure
A building part consisting of a board covering the joint between the lowest part of an interior wall surface and the floor.
Its purpose is to cover the joint between the wall surface and the floor.
baseboard
Plant matter consisting of an impermeable buoyant material, the phellem layer of bark tissue.
cork
Macromolecules that are obtained naturally from plants or animals.
natural-based polymer
A thin, transparent sheet made of regenerated cellulose.
Plastic Wrap
Cellophane is used for food packaging.
cellophane
Synthetic plastic which is composed of a glossy, moistureproof membrane made of rubber hydrochloride.
pliofilm
A polyester film made from stretched polyethylene terephthalate (PET).
BoPET (Biaxially-oriented polyethylene terephthalate)
mylar
A solid environmental material that is hard, brittle, heat-resistant and corrosion-resistant, made by shaping and then firing a nonmetallic mineral at a high temperature.
ceramic
A human construction which is an enclosure or compartment designed for service provision.
"an enclosure or compartment that allows privacy or seclusion, for example when voting, broadcasting or recording sound, or making a phone call." OED I like this one more - except it doesn't fit "ticket booth", "gas station booth" etc.
booth
A device which can connect, disconnect, or divert current in an electrical circuit.
switch
An environmental system where environmental monitoring processes are in effect.
environmental monitoring area
An environmental monitoring area which is under observation by humans belonging to organisations with a legislative mandate to monitor the area.
environmental monitoring program area
An environmental monitoring program area within a food production facility.
food production environmental monitoring zone
An object aggregate which comprises objects whose surfaces are in contact with food during its processing in a food production facility
Zone 1
environmental monitoring zone 1
This can be axiomatised with "'has part' min 1 'food contact surface'" . This can also have the axiom "'part of' some 'food production environmental monitoring zone'"
food production environmental monitoring zone 1
An object aggregate which comprises objects whose surfaces are not in contact with food during its processing, but which are in close proximity to those in food production environmental monitoring zone 1.
Zone 2
This can be axiomatised with "'has part' min 1 'food contact surface'" . This can also have the axiom "'part of' some 'food production environmental monitoring zone'". The threshold for "close proximity" can vary based on local or national legislation. 'adjacent to' axioms may also be used for neighbouring zones.
food production environmental monitoring zone 2
An object aggregate which comprises a facility's set of more remote non-food-processing-contact surfaces that are in or near the processing areas (food productions environmental monitoring zones 1 and 2) and could lead to their contamination, especially through human movement.
Zone 3
food production environmental monitoring zone 3
An object aggregate which comprises objects in proximity to food production environmental monitoring zone 3.
Zone 4
food production environmental monitoring zone 4
An environmental system which is part of a food production facility and whose boundaries are defined by hygienic requirements.
hygienic zone
This class is more a convenience grouping class, but can be axiomatised if a hygienic assessment process is completed.
hygienic food production area
A hygienic food production area which is not an immediate part of a food manufacturing process area.
food prossessing non-production area
A hygienic food production area containing products having a low risk of contamination.
This class includes manufacturing areas in which raw materials and/or finished products (within their primary packaging) and packaging/labeling materials are received, sampled, or stored prior to dispatch.
food production low-risk contamination area
A hygienic food production area in which general food processing occurs.
This class includes areas in which raw materials are received, sorted, and sampled; areas within the plant where products susceptible to contamination and/or microbial growth are processed, treated, or handled; areas in which animal carcasses are cut into fresh meat products and areas in which vegetables and produce are packed. Food processing that prepares products for cooking by the consumer (e.g., raw meats, fish, and vegetables) or produces RTE products that are effectively preserved (e.g., canned or baked products) will require procesing in medium-risk hygiene areas.
food production medium-risk contamination area
A hygienic food production area containing food products that are not subjected to subsequent microbial decontamination, and where there is a risk of pathogen or microbial spoilage growth.
food production high-risk contamination area
An anthropogenic environment which provides long-term shelter for its inhabitants.
residential environment
A stable dispersion (emulsion) of polymer microparticles in an aqueous medium.
Natural rubber, India rubber, Gum elastic, Non-vulcanized rubber
Latex is made by some plants, but synthetic latexes can be manufactured as well.
latex
A boat which is used to transport cargo or carry passengers.
transport boat
A container which is typically made of glass or plastic and having a tapered neck, used primarily for holding liquids.
bottle
A hand tool for domestic use, especially in the kitchen.
utensil
An eating utensil with spikes used to put solid food into the mouth, or to hold food down while cutting.
fork
An eating utensil with a scooped end and a long handle.
spoon
A utensil which is a hand-sized container with an open top.
A cup may be used to hold liquids for pouring or drinking, or to store solids for pouring.
cup
An anthropogenic environment which is bounded by a healthcare facility in which health care services are provided by specialized staff and equipment.
healthcare environment
An anthropogenic environment which is the product of a particular human occupational acitivity.
work environment
occupational environment
An anthropogenic environment which is designed for child care.
childcare environment
day care environment
daycare environment
child care environment
A human construction in which child care services are provided to a human child by specialized staff and equipment.
childcare facility
day care facility
daycare facility
child care facility
A child care facility in which day care services are provided, by specialized staff and equipment, to a human child during the working day.
daycare
A human construction in which individuals or a group of people such as a congregation come to perform acts of devotion, veneration, or religious study.
place of worship
A building reserved in which religious or spiritual rituals and activities such as prayer and sacrifice are performed.
"The term typically used for such buildings belonging to all faiths where a more specific term such as church, mosque or synagogue is not generally used in English." [Wikipedia]
temple
A child care facility in which child care services are provided to young children and babies.
human nursery
An anthropogenic environment which is bounded by a human dwelling.
household environment
A public building in which health, recreation or other public services to a local community are provided.
community service centre
A healthcare facility which is used by a group of general practitioners and nurses to provide healthcare services to people in a certain area.
health center
healthcare center
cottage hospital
community health centre
A room which contains 1) a number of beds for sleeping and 2) often some other furniture and/or residential utilities.
A dormitory is often used to describe student and backpacker accommodation of this kind.
dormitory
A political entity which is defined by contract between the Canadian state ("the Crown") and a First Nations people.
"[First Nations reserves] are not to be confused with land claims areas, which involve all of that First Nations' traditional lands: a much larger territory than any other reserve." [Wikipedia]
first nations reserve
A human dwelling which may be unsustainable over the long term for an inhabitant because of financial, livability, overcrowding or other factors.
insecure housing
A human dwelling which is provided to one or more persons on a short-term basis.
temporary residence
An eating utensil which is a thin stick used in equal length pairs to manipulate food and bring it into a mouth.
chopstick
A building which 1) containing multiple dwellings of pre-furnished accomodation and 2) is rented on a short term and/or longer-term basis.
hotel
A healthcare facility which is used to provide healthcare services to animals.
veterinary facility
An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine.
plane
airplane
A healthcare facility which is the office of a physician.
doctor's office
doctor's practice
doctor's surgery
physician office
A constructed transport system which is designed to transport people or objects over land, but not water or air.
ground transport
An animal house which houses stray, lost, abandoned or surrendered animals.
animal shelter
pound
An animal rescue shelter typically houses mostly dogs and cats.
animal rescue shelter
A utensil used for consuming food.
cutlery utensil
eating utensil
A manufactured product which is an alloy of iron and which typically contains a few tenths of a percent of carbon.
steel
A prison facility which is owned by the state and operated by a private corporation.
public-private prison
A system which is composed of one or more machines that can continuously transport material from one location to at least one other location.
conveyor equipment
connveyor belt
A manufactured product which is capable of some manufacturing process.
A system which consists of manufacturing equipment that performs manufacturing processes in a linear fashion.
production line
A manufactured product which is a structural system on which equipment components are mounted.
A manufactured product which positions a piece of equipment above a surface.
A conveyor system which uses conveyer belt machines to transport material.
A manufactured product which is 1) an endless belt of flexible material stretched between two drums; 2) conveys material between drum locations.
A manufacturing equipment piece which is used to package material.
A conveyor system which is used to transport granular material vertically in open containers.
A conveyor system which consists of a helicoid flight mounted in a tube or shaft.
A conveyor system which transports dry bulk particulate or granular material through a pipeline by a stream of gas.
A manufactured product which is a cylindrical (or approximately cylindrical) item used under a heavy object to facilitate moving it.
Usually several conveyor rollers are organized in a linear fashion to convey an object between locations.
An interface layer which is formed where either two parts of a material entity or two separate material entities touch or are attached to one another along some length.
A liquid water which has no current or flow and is susceptible to contamination by pathogens or pathogenic vectors.
wet
Dust which is 1) generated when wood is processed and 2) composed primarily of cellulose, polyoses, and lignin.
Wood dust is typically generated through processes where wood is chipped, sawed, turned, drilled or sanded. The chemical composition of wood dust depends on the species of tree. Wood dust is not typically produced for specific uses. However, it is used commercially for wood composts. The primary routes of potential human exposure to wood dust are inhalation and dermal contact. It is known to be a human carcinogen.
wood dust
A hydraulic fluid which is 1) used in hydraulic brake and hydraulic clutch applications in vehicles to amplify braking force and 2) composed primarily of ethylene glycol, polyglycols, silicone fluids, and isobutyl alcohol.
brake fluid
Fluid used for valve operation, brake band friction, and gear lubrication within an automatic vehicle transmission.
automatic transmission fluid
An environmental system process during which populations have reduced access to food, causing increased hunger, malnutrition, and consequent mortality.
A medium by which power is transferred in hydraulic machinery.
Common hydraulic fluids are based on mineral oil or water.
hydraulic fluid
A lubricant for internal combustion engines which 1) reduces friction and wear 2) cleans the engine 3) neutralizes acids 4) improves sealing of piston rings, and 5) cools the engine.
motor oil
A liquid fuel used in diesel engines, whose fuel ignition takes place, without any spark, as a result of compression of the inlet air mixture and then injection of fuel.
diesel fuel
A clear petroleum-derived flammable liquid which is used as fuel in most spark-ignited internal combustion engines.
Gasoline consists mostly of organic compounds obtained by the fractional distillation of petroleum, enhanced with a variety of additives.
gasoline
A gas which results from the incomplete or complete combustion of diesel fuel.
diesel exhaust
A gas which results from the complete or incomplete combustion of gasoline fuel.
gasoline exhaust
A coloured substance that chemically bonds to the substrate to which it is being applied
dye
Pigments carried by solvents or water which are applied to leather to be absorbed into the pores of the leather to deposit coloration.
leather dye
Dyes used for the coloration or brightening of paper.
paper dye
Dyes utilized for coloring textiles such as wool or cellulose fibers.
Textile dyes may include acid dyes, substantive dyes, mordant dues, sulfur dyes, azoic dyes, and disperse dyes.
textile dye
A black or colored ink which is 1) used for writing, printing, and drawing and 2) made from fine soot (lampblack) and water.
India ink
A polysaccharide that functions as an emulsifier, stabilizer, and thickener in mixtures.
xanthan gum
A naturally occurring plant-based gum, which functions as a viscous, odorless, tasteless, water-soluble mixture of polysaccharides that absorbs water to become a gel/paste.
Tragacanth has many uses, including as an emulsifier, thickener, stabilizer, and texturant additive for foods, pharmaceuticals, and art materials.
tragacanth
Water based ink intended for use with fountain ink pens.
fountain pen ink
A solid or highly viscous plant or synthetic based substance that is typically convertible into polymers.
resin
A liquid, powder, spray, or granule used to remove dirt, including dust, stains, bad smells, and clutter on surfaces.
cleaning agent
A cleaning agent which 1) contains organic solvents and 2) dissolves oils and fats for the removal of grease.
degreaser
A clear transparent hard protective film or finish, primarily used for wood finishing applications.
Varnish is traditionally composed of a drying oil, a resin, and a thinner or solvent.
varnish
A varnish containing a natural, plant- or insect-derived substance dissolved in a solvent, called spirit varnish or solvent varnish.
resin (gum) varnish
A resin secreted by the female lac bug, which is dissolved in alcohol to be used as a brush-on colorant, food glaze, and wood finish.
shellac
A category of hard and potentially shiny (clear or colored) finishes which can be applied to materials including wood or metal.
lacquer
A solvent that can dissolve paint and reduce viscosity of paint or "thin" it.
Paint thinners can aid in removal of paint from brushes, rollers, or in spill cleanup.
paint thinner
A liquid, gel, or paste that can be mixed into acrylic paint to alter paint consistency and properties.
acrylic paint medium
A paint thinner specific for altering the viscosity of enamel paints.
enamel thinner
A solvent used to thin oil-based paints or clean up after their use.
oil paint thinner
A paint product which adheres to surfaces and forms a binding layer, preparing it to receive paint.
primer (paint)
A smooth, durable vitreous coating which is made by fusing powdered glass to a substrate.
Enamel can be used on metal, glass, ceramics, stone, or any material able to withstand the fusing temperature. Enamel is made by 1) firing, melting the powder and 2) allowing allowing it to flow across a surface to then harden.
vitreous enamel
A slow-drying paint that consists of particles of pigment suspended in a drying oil, commonly linseed oil.
oil-based paint
A water soluble, fast-drying paint made of pigment suspended in acrylic polymer emulsion.
acrylic paint
A paint that exhibits luminescence, giving off visible light through fluorescence, phosphorescence, or radioluminescence.
luminescent paint
A fluid obtained by the distillation of resin harvested from living trees, primarily used as a solvent.
turpentine
A flammable liquid hydrocarbon mixture produced from natural gas condensates, petroleum distillates, and the distillation of coal tar and peat.
Light and heavy varieties may consist of distinct quantities of carbon atoms per molecule.
naphtha
Dust which is composed of minerals and trace elements, generated by finely crushed rock.
Rock dust is widely used in mining to prevent coal dust explosions, or in agriculture for organic farming uses.
rock dust
Any material containing unstable atoms that emit ionizing radiation as it decays.
radioactive material
An environmental material which is primarily composed of cyanoacrolate.
Cyanoacrylates have industrial, medical, and household uses. A strong fast-acting adhesive which is an ester of cyanoacrylic acid.
volume of cyanoacrylate
A preparation with dye or pigment used to deposit coloration to a substrate.
stain
A stain which has colorants dissolved and/or suspended in a vehicle or solvent, used to add color to wood.
Wood stain is designed to add color to substrates, while still leaving some of the substrate visible.
wood stain
An environmental material which is composed of elastic polymers mixed in a solvent.
cow gum
Solvents typically used include acetone, hexane, heptane or toluene.
rubber cement
An environmental material which is 1) composed primarily of methyl cellulose and water, and 2) formulated to fix wallpaper to walls.
wallpaper adhesive
wallpaper paste
An environmental material which is 1) manufactured and 2) primarily composed of hydrogen peroxide and ammonia, and 3) when applied to hair, can alter the natural hair pigments for 6-8 weeks.
hair color
permanent hair dye
A colorant fluid which is 1) manufactured and 2) composed of alcohol, titanium dioxide, and propylene glycol.
pharmaceutical ink
A colorant fluid which is 1) manufactured and 2) composed of copper phthalocyanine, iron oxides, water, and biopolymers.
gel ink
A colorant fluid which is 1) manufactured and 2) primarily composed of soybean oil, as well as pigment, resin, and wax.
soy ink
A colorant fluid which is 1) manufactured, 2) primarily composed of water, as well as glycol, and dye, and 3) intended for use in inkjet printers.
aqueous inkjet printer ink
An environmental material which is composed primarily of gases and particles produced by the combustion of petroleum fuels.
emissions from petroleum combustion
A liquid environmental material which 1) contains at least one substance which can act as a chemical colorant.
colorant fluid
A function which is realised by a chemical when applied to a material, such that it alters the material's colour.
chemical colorant
Waste which contains toxic components (e.g., heavy metals or radiation) which can cause harm to organisms and/or the environment.
To be revised when we have information about the real definition. The definitions given by WMO cloud atlas are entered as comment, as these are not the defining features of the levels but the result of whatever it is that defines the levels (I assume temperature, density, etc. but have not yet found clear information about this). The german wikipedia page notes layers that coincide with the extent of the low étage, however, I have not yet seen further mention of them elsewhere and am thus hesitant about adding them.
low étage
A part of the troposphere which extends from the Earth's surface to 2 km (0 - 6500 ft) height.
low atmospheric level
To be revised when we have information about the real definition. The definitions given by WMO cloud atlas are entered as comment, as these are not the defining features of the levels but the result of whatever it is that defines the levels (I assume temperature, density, etc. but have not yet found clear information about this).
middle étage
A part of the troposphere which extends from 2 km to 4 km (6 500 – 13 000 ft) height in the polar region, from 2 km to 7 km (6 500 – 23 000 ft) height in the temperate region, and from 2 km to 8 km (6 500 – 25 000 ft) height in the tropical region.
middle atmospheric level
high étage
A part of the troposphere which extends from 3 km to 8 km (10 000 – 25 000 ft) height in the polar region, from 5 km to 13 km (16 500 – 45 000 ft) height in the temperate region, and from 6 km to 18 km (20 000 – 60 000 ft) height in the tropical region.
high atmospheric level
A part of a cloud.
This definition is practical but may need refinement.
cloud part
A cloud part which is closest to the surface of the astronomical body local to the cloud.
cloud base
A cloud part which is furthest from the surface of the astronomical body local to the cloud.
cloud top
A water droplet which exists at temperatures below 0°C (273.15K).
supercooled water droplet
A water ice crystal which is constituted by water molecules aligned in a hexagonal array.
snowflake
snow crystal
Snow crystals and snowflakes are often noted as synonyms, however, the term "snowflake" is generally used more loosely. Some sites mention that snow crystals refer to individual crystals of ice, while the term "snowflake" can refer both to an individual crystal of ice and to a bundle of snow crystals. Please see here [https://github.com/EnvironmentOntology/envo/issues/998#issuecomment-685649444]
A building part which is maintained such that the number of foreign particulates within it is controlled.
clean room
The cleanliness level of a cleanroom is quantified by the number of particles per cubic meter at a predetermined molecule measure. Cleanrooms are designed to maintain extremely low levels of particulates, such as dust, airborne organisms, or vaporized particles. Cleanroons are used in the manufacture of pharmaceutical items, integrated circuits, CRT, LCD, OLED and microLED displays.
cleanroom
Sediment which contains some chemical contaminant.
See https://github.com/EnvironmentOntology/envo/issues/1102 for a possible design pattern. Uses undesirability standard, compared to polluted river's ecological impact standard. What is the relation to ENVO:00002114 'chemically enriched sediment'? Does 'element' in the definition refer to something found in the periosic table (like selenium) or the member of some set, aka an entity?
chemically contaminated sediment
Liquid water which is a participant in a water cooling process.
Cooling water is commonly used for cooling automobile internal combustion engines and power stations.
cooling water
A pipeline network which is used to transport drinking water to consumers.
drinking water pipeline
drinking water pipeline network
An industrial building in which water undergoes a purification process to make it fit for human consumption.
CM: drinking water treatment plant should have an edge connecting to its function or a process MAM: Like some yet-to-be-created sibling of pollution control ENVO:02500042 ? Or sibling of environment control function OBI:0000401? Can't find suitable function currently in ENVO. Add term and add axioms later
drinking water treatment plant
A manufactured product which is capable of connecting or disconnecting the conducting path in an electrical circuit, interrupting the electric current or diverting it from one conductor to another.
electrical switch
A waste material which is primarily composed of uneaten food and removed from the food supply chain.
does FoodOn want this?
food loss
The causes of food waste or loss are numerous and can occur during production, processing, distribution, retail and consumption.
food waste
A fluid environmental material which is contained in geologic formations naturally.
assert contained in some child of astronmical body part? cavity? Parent class could use a better definition?
formation fluid
A building part which has been constructed to support the provision of intensive care medicine to patients with severe or life-threatening illnesses and injuries.
An ICU could be a part-of a hospital, but it would not be a subclass of a hospital. That's even reflected in the textual definition. THEREFORE parent class changed to building part. Could be in a hospital and related to some particular hospital department provides.
intensive care unit
Liquid water which occurs naturally within the pores of rocks and sediments.
interstitial water
A bioreactor which has a membrane as a part
It is widely used for municipal and industrial wastewater treatment. The membrane is usually used to perform microfiltration, ultrafiltration or osmosis, etc.
membrane bioreactor
A soil horizon which is primarily composed of mineral material.
ADDED 'composed primarily of' RO:0002473 mineral material 'ENVO:01000256'
Usually less than 20% organic carbon. The term mineral horizon refers to surface soil/topsoil and subsoil layer of the soil. When user does not/could not refer to the topsoil or subsoil specifically, the broader term, mineral horizon can be used.
mineral horizon
A pipeline network which is used to transport oil to consumers.
oil pipeline
oil pipeline network
An environmental material which consists of either loose sands or partially consolidated sandstone, containing a naturally occurring mixture of sand, clay, and water, soaked with a dense and extremely viscous form of petroleum.
TODO: create an astonomical body part 'bituminous sands" and assert composed primarily of realtionship. Xref https://github.com/EnvironmentOntology/envo/issues/1154. TREATED THIS as a material entity. could add something like "oil sands deposit" as a geospatial location later.
crude bitumen
oil sands
tar sands
bituminous sand
A human construction which is used to transport a material which is primarily composed of liquid or gas through a system of pipes.
Getting an example of use could be helpful. Are some environmental samples collected from the outside of a pipe or its fittings? Or taken from inside the pipe? Removing "transport" from the label may make the labels of sublasses more readable. However, "pipeline" alone could mean several unrelated things, like software pipelines. https://www.eia.gov/energyexplained/natural-gas/natural-gas-pipelines.php uses the term "pipeline network". ALSO could this be a transport feature? Xref https://github.com/EnvironmentOntology/envo/issues/1111.
Pipeline networks typically materials either from 1) a production area to a market area for consumption, 2) a production area to an area for waste disposal.
pipeline network
A river which has elevated levels of contaminants.
Uses 'adverse to ecosystem standard'. Compare to undesirability standard in 'contaminated sediment'. See also 'polluted lake'.
The contaminants may cause adverse changes in the ecosystems associated with it.
polluted river
Rock which is derived from bedrock through chemical weathering
add chemcical weathering term to improve axiomitization
saprolite
An environmental material which is composed of insoluble solid particles suspended in a liquid.
term requester also included <denser than water> and <usually suspended in water>, but they may only be found in wikipedia's definition
slurry
A soil horizon which is composed primarily of organic matter.
ADDED 'composed primarily of' RO:0002473 'soil organic matter' ENVO:04000008
soil organic layer
organic surface layer
The organic matter is this layer is genreally derived from biomatter.
organic horizon
Vinasse which is produced during the rectification and distillation of ethanol from sugar cane.
Might be nice to add an edge like 'derives from' RO:0001000 sugarcane or 'sugar cane plant' FOODON:03411378? Note that importing FOODON terms can bring in unexpected dependencies. Try again later!
sugarcane vinasse
An earth-filled dam which is used for the storage of mining operations byproducts, after separating the ore from the gangue.
dam is a functional label. we suggest distributing the terms in this definition. Might also want to define a new term gangue.
tailings dam
A human construction which is used as a storage area for mining tailings.
not placing under 'pond' class becasue contents may not be primarily be composed of water. consider revising 'pond' semantics
tailings pond
A manufactured product which is formed as a liquid byproduct generated during the rectification and distillation of ethanol.
Vinasse is produced by the sugar or ethanol industry and can be produced at volumes as high as 20-fold of ethanol. It is typically sulfur-rich, low pH, dark-colored and odorous.
vinasse
A soil layer which is parallel to the soil surface and which has roughly homogenous physical, chemical and biological properties relative to the soil layers above or beneath it.
soil horizon
An embankment dam which is primarily composed of compacted earth.
earthen dam
terrain dam
earth-filled dam
A dam which is created by the placement and compaction of a complex semi-plastic mound of various compositions of soil, sand, clay, or rock.
A yard which consists of land immediately adjacent to the back of a residential building
back yard
residential backyard
An island which is small, low in elevation, sandy, and located on the surface of a coral reef.
caye
key
cay
A room which is maintained at lower than ambient temperatures.
chiller room
cool room
refrigerating chamber
Cold rooms are generally used as walk-in storage facilities or to perform tasks requiring cooler ambient temperatures.
cold room
Soil which has properties that restrict a pathogen's ability to establish itself, persist, or cause disease that results in long-term harm.
disease-suppressive soil
The pathogenicity that is suppressed is typically directed towards plants, especially crops. Soils are typically classified as pathogen-suppressive if a pathogen 1) cannot establish itself or persist, 2) is able to establish itself, but causes little or no damage, or 3) is able to establishe itself, but only causes disease that does not result in long-term harm.
pathogen-suppressive soil
A pond which has nutrient-rich water.
eutrophic pond
A forest ecosystem which is designated for research.
experimental forest ecosystem
A pit which has been constructed for use in fermentation processes that will yield alcoholic spirits.
fermentation pit
A manufactured product which assists starting a fermentation process which is intended to prepare foods and alcoholic drinks.
Daqu
fermentation starter
A lake which is connected to a marine water body via tunnels or cracks in the soil.
marine lake
Liquid water which is either part of or was removed from a marine lake.
marine lake water
A pond which has layers of water that do not intermix.
meromictic pond
A farm which is managed using practices certified to be organic by a competent authority.
What qualifies as an organic farm varies significantly across nations and subnational entities. In general, however, organic farming involves the use of biological pest control, mixed cropping, natural fertilisers, and the fostering of insect predators. Further, organic certification often requires that synthetic pesticides and fertilisers are not used.
organic farm
A manufactured product which is designed to function as a container for growing plants.
plant pot
A manufactured product which is produced by curing, subsequent aging, slow oxidation and degradation of carotenoids in tobacco leaves.
processed tobacco
A pond which humans have constructed for the cultivation of algae.
algal pond
raceway pond
A manufactured product which is composed of flexible material and is intended to be hung such that it impedes the spray of water between a shower fixture and the rest of a room.
Shower curtains are typically made from plastic or another water resistant or waterproof material.
shower curtain
Processed tobacco which has been treated for use by placing it between the gum and cheek or lip, chewed, or sniffed, but not smoked.
smokeless tobacco
A spacecraft which is capable of supporting a human crew in orbit for an extended period of time.
orbital space station
orbital station
space station
A vehicle which is used for carrying cargo or passengers on a rail transport system.
train car
A manufactured product which is controls the flow of water.
water valve
water tap
An anthropogenic geographic feature which consists of land immediately adjacent to a building or a group of buildings.
yard
A manufactured product which is used to give input or control to an information processing system by touching a display screen with a special stylus or one or more fingers.
Touching the screen with multiple fingers is considered a multi-touch gesture.
touchscreen
Anthropogenic litter which consists of an abandoned ship's remains.
A shipwreck can be found beached on land or sunken to the bottom of a body of water.
shipwreck
A human construction which supplies drinking water by squirting it into a basin or jets water into the air for a decorative or dramatic effect.
fountain
A water well in which a long, 100–200 millimetres-wide, stainless steel tube or pipe is bored into an underground aquifer to lift water using a pump.
tube well
A sedimentary rock which is made of carbonate mud whose formation is mediated by microbes in the benthic zone.
microbialite
Water which comes from a spring.
spring water
A salt mass which consists of isometric crystals of sodium chloride (NaCl).
rock salt
Typically colorless or white. Halite may also occur in various color including light blue, dark blue, purple, pink, red, orange, yellow or gray depending on inclusion of other materials, impurities, and structural or isotopic abnormalities in the crystals.
halite
An intensive care unit (ICU) specializing in the care of ill or premature newborn infants.
ICN
NICU
intensive care nursery
neonatal intensive care unit
A geological fracture which is formed during winter months by a narrow or thin piece of ice.
The ice itself can measure up to 3–4 meters in length at ground level can extend downwards into the ground up to several meters.
ice wedge
An animal habitation which is built by alligators from plants and decomposing vegetation in order to protect their eggs from predators.
nest of alligator
An oceanic front in which mixing of river discharge and saline seawater occurs.
river plume
A feature which arises from a rapid multiplication of cyanobacteria, causing marked visible discoloration of the water.
cyanobacterial bloom
A planetary structural layer which consists of oceanic crust and the underlying upper mantle and has been uplifted and exposed above sea level.
Opholites are often emplaced onto continental crustal rocks
ophiolites
Land which has elevated levels of some contaminants or substances that are potentially hazardous to health or the environment.
contaminated land
An agricultural aquatic ecosystem in which fish, crustaceans, mollusks, aquatic plants and algae are cultivated.
aquaculture
aquafarming
aquaculture farm
An industrial building in which oil-bearing seeds or vegetable materials are crushed and pressed with a grinding mill in order to extract oils.
oil mill
A human construction which confines wastewater in a depression enclosed by earthen structures.
WSPs
stabilization ponds
waste stabilization lagoons
Presumably the waste is detained prior to treatment.
waste stabilization pond
A bioreactor which utilizes a light source to cultivate phototrophic microorganisms.
photobioreactor
An industrial building in which crude oil is transformed and refined into useful products.
The useful products include petroleum naphtha, gasoline, diesel fuel, asphalt base, heating oil, kerosene, liquefied petroleum gas, jet fuel and fuel oils. Oil refineries are typically large, sprawling industrial complexes with extensive piping running throughout, carrying streams of fluids between large chemical processing units, such as distillation columns.
oil refinery
A manufactured product which is used for cutting crops, vegetables, wood, metal, paper documents, etc into small pieces.
A shredder could more specifically be consered a machine.
shredder
A human construction which is used for the purpose of industrial development.
Industrial parks are usually located on the edges of, or outside, the main residential area of a city and that can be thought of as a more "heavyweight" version of a business park or office park, which has offices and light industry, rather than heavy industry.
industrial park
Fresh water which is harvested from cloud.
cloud water
Fluid environmental material which is present in the continental crust and dictates the nature and extent of crustal deformation.
The presence or absence of fluids exerts a fundamental control on rheology.
crustal fluid
A geological fracture, found near volacnoes in the final phase of thier activity, chiefly discharging carbon dioxide and possibly other vapors.
mofetta
An organic material which is derived from lichen mats.
lichen material
A manufactured product which floats in water and can be used a navigational marker among other purposes.
Buoy can be anchored (stationary) or allowed to drift with ocean currents.
buoy
A manufactured product which is used to remove contaminants from water impeding the flow of particles or solutes.
Fine physical barrier, a chemical process, or a biological process are applied in the water filter. Filters cleanse water to different extents for purposes such as providing agricultural irrigation, accessible drinking water, public and private aquariums, and the safe use of ponds and swimming pools.
water filter
A human construction which provides regulated climatic conditions for the growth of plants and whose walls and roof are made chiefly of transparent material, such as glass.
glasshouse
hothouse
greenhouse
A fermentation pit which is constructed to facilitate the fermentation of alcoholic substances.
Definition from 2021-08-05 call with Buttigieg, Duncan and Miller
A fermentation pit which is constructed from clay.
A pond which has been constructed by humans or their technologies.
A human construction that has intentionally been placed into orbit.
Not to be confused with a natural satellite like the earth's moon (https://en.wikipedia.org/wiki/Natural_satellite)
A water body which is created in a stream by local scour or impoundment and has some structural control.
pool
Pool water depth is above average for the stream. If if all the running water in the stream was shut off, areas in the stream that still hold water are pools. Pool water velocity is below average for the reach, causing fine sediments to deposit in pools. Pools are generally longer than they are wide (unless they are plunge pools), and are 1.5 x deeper at their maximum depth than they are at their crest
stream pool
A hydroform which is that part of a stream where water flows swiftly and uniformly with low surface water agitation.
run
stream run
A stream pool which is formed as a result of high-gradient, steep streams where water cascades over a rock or woody snag.
Due to the gradient and surrounding geology, this pattern continues down the stream: step (drop), pool, step, pool, etc.
step pool
Biofilm consisting of a mixture of algae, cyanobacteria, microbes, and detritus.
Periphytic biofilm coats the submerged surfaces in most bodies of water
periphytic biofilm
epilithon
epipelon
Periphyton colonizing surface of aquatic plants
epiphyton
epipsammon
epixylon
Water which is part of a stream.
stream water
A stream which is composed primarily of fresh water.
freshwater stream
A freshwater stream ecosystem which is undergoing climactic ecological succession.
freshwater stream biome
An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a freshwater stream.
freshwater stream ecosystem
Adfreezing is a freezing process during which two objects adhere to each other via ice.
adfreezing
Frost heaving is a process during which an upwards swelling of soil occurs due to freezing conditions caused by an increasing presence of ice as it grows towards the surface.
frost heaving process
A water temperature which inheres in water close to the surface of an ocean or sea.
The exact meaning of surface varies according to the measurement method used, but it is between 1 millimetre (0.04 in) and 20 metres (70 ft) below the sea surface.
temperature of sea surface
The concentration of carbon dioxide when measured in soil.
concentration of carbon dioxide in soil
The concentration of carbon dioxide when measured in air.
concentration of carbon dioxide in air
The concentration of carbon dioxide when measured in freshwater.
concentration of carbon dioxide in freshwater
The concentration of carbon dioxide when measured in seawater.
concentration of carbon dioxide in seawater
lake water
Organic material in soil, which consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms.
soil organic matter
A layer which is composed of ground that is 1) subject to annual thawing and freezing and 2) present in areas underlain by permafrost.
Potential synonyms are seasonal frost, frost zone, and mollisol. See issue #741 in GitHub for additional details. These synonyms should be validated in a cryohackathon.
active permafrost layer
A surface layer which is composed primarily of soil.
soil surface layer
A soil surface which is exposed to the troposphere, with no appreciable cover from vegetation or other material.
bare soil surface layer
Particulate environmental material which is composed primarily of organic material.
particulate organic matter
Particulate organic matter which is composed primarily of carbon.
particulate organic carbon
Particulate organic matter which is composed primarily of nitrogen.
particulate organic nitrogen
A material accumulation process during which atmospheric carbon dioxide is captured and stored.
carbon sequestration process
A carbon sequestration process during which atmospheric carbon dioxide is captured and stored by biological processes.
biotic carbon sequestration
A carbon sequestration process during which carbon dioxide is stored in underground geological formations.
geological carbon sequestration
A carbon sequestration process during which carbon dioxide is stored in the carbonate system of an ocean.
carbon sequestration by the ocean carbonate system
A disposition inhering in a bearer by virtue of that bearer's ability to, repeatedly, become plastic on heating and harden again on cooling.
termoplasticità
熱塑性
thermoplasticity
An environmental material which is capable of, repeatedly, becoming plastic when heated and hardening again when cooled.
thermoplastic material
A disposition which inheres in materials capable of becoming rigid when cured by heating.
熱固性
thermosetting disposition
A polymer which has been irreversibly hardened by heat-induced curing.
thermoset material
thermoset
thermoset plastic
Prior to curing, thermoset materials often occur as a soft solid or viscous liquid prepolymer or resin. In the literature, those are often referred to thermosetting resins. During curing process, well-defined and irreversible chemical networks form in three dimensions thus giving the thermosets a strong and rigid structure that can be added to other materials to increase strength.
thermoset polymer
A piece of plastic which has a matrix- or sponge-like structure with numerous, hollow internal spaces.
Plastikschaumstück
Schaumstoffstück
Depending on the type of plastic used and the organisation of the foam, a piece of plastic foam can show elastic properties (even if the plastic it is made out of does not have elastic properties).
piece of plastic foam
A piece of plastic which is flexible, thin, and planar.
Plastikfolie
pellicola di plastica
película de plástico
Kunststofffolie
plastic membrane
plastic sheet
The edge can be either smooth or angular.
plastic film
A piece of plastic which 1) is hard, 2) has an irregular shape, and 3) has broken off of a larger piece of plastic.
Plastikfragment
fragmento de plástico
frammento di plastica
plastic flake
plastic granule
To avoid ambiguity, we are being stricter with the "has broken off of a larger piece of plastic" aspect compared to the GESAMP report, which originally stated "having appearance of being broken down from a larger piece of litter".
plastic fragment
A piece of plastic which is linear and flexible.
plastic fibre
plastic filament
plastic strand
plastic line
A piece of plastic which is 1) hard, 2) has a smooth external surface, and 3) has a roughly spherical or granular shape.
mermaid's tears
pellet de plástico
pellet di plastica
resin bead
plastic pellet
A liquid astronomical body part which 1) vertically spans a water body and 2) has fiat boundaries approximating a columnar shape.
Wassersäule
colonna d'acqua
columna de agua
水層
water column
A collection of organisms which inhabits the same region, ecosystem, or time period.
This term is also requested on the PCO. Once it is added in PCO we will obsolete it in ENVO and replace it with the PCO terms.
Biota
biota
A biota which inhabits a marine ecosystem.
Meeresbiota
biota marino
marine life
ocean life
sea life
marine biota
A biological process during which a material entity is broken down.
Biodegradation
Biologischer Abbauprozess
biodegradación
biodegradazione
生物分解
biodegradation
A biodegradation process during which plastic is broken down.
Biologischer Plastikabbauprozess
biodegradación del plástico
biodegradazione della plastica
biological degradation of plastics
Biodegradation of plastic will lead to reduce molecular weight of that plastic.
biodegradation of plastic
A plastic which has a matrix- or sponge-like structure with numerous, hollow internal spaces.
cellular polymers
expanded polymers
geschäumter Kunststoff
plastic foam
foamed plastic
A physical quality which inheres in a liquid or solid bearer by virtue of that bearer trapping a gas in a colloidal suspension throughout its volume.
This term is also requested on the PATO. Once it is added in PATO we will obsolete it in ENVO and replace it with the PATO terms.
quality of a foam
A feeding behavior during which material is taken into the body of an organism.
(Nahrungs)aufnahme
Ingestion
ingestione
ingestión
攝食
Note that ingestion is not limited to materials which provide nutrition to an organism; indigestible or otherwise biologically inaccessible particles may also be ingested by organisms. Ingestion is also not limited to organisms with a mouth and digestive tract, as single-celled organisms like amoebae ingest material with their cell membrane. https://github.com/EnvironmentOntology/envo/pull/1153
ingestion
A material accumulation process during which material adheres to a solid or liquid surface.
Adsorption
adsorbimento
adsorción
吸附
adsorption
A material accumulation process during which material builds up on a solid surface such that a function of that surface, or the object it is a part of, is impaired.
Fouling
incrostazione
incrustación
Following BFO:function semantics, this suggests that the functions of the object of which the surface is a part are affected in their realisation in one or more processes.
fouling
A fouling process during which biological matter accumulates on a solid surface.
bio-incrostazione
bio-incrustación
biological fouling
Makrofouling
Mikrofouling
Bewuchs
The biological matter can be microscale (e.g. biofilms created by microorganism) and macroscale (created by macroorganism).
biofouling
An environmental system process during which two dissimilar materials attach to one another.
We'll relocate this in a hierarchy of similar processes later. We'll add different types of adhesion (mechanical, chemical, dispersive, diffusive, and electrostatic) as subclasses in later revisions.
The attachment is usually firm, and several mechanisms (mechanical, chemical, dispersive, diffusive, and electrostatic) have been proposed. This class is related to - but distinct from - those classes listed below: http://purl.obolibrary.org/obo/NCIT_C17597 http://purl.obolibrary.org/obo/GO_0022610 http://purl.obolibrary.org/obo/APO_0000288
adhesion
An environmental system process during which the molecules of similar materials are electrically attracted to one another, leading to the formation and maintenance of a microscopic structure holding the materials together.
cohesion
A piece of plastic foam which has a near-spherical or granular shape.
These granules are usually white or opaque but can be any color.
granule of plastic foam
An environmental system process during which a material entity breaks into pieces or parts.
Fragmentierung
fragmentación
frammentazione
fragmentation process
A fragmentation process which is caused by weathering.
Some example of materials that undergo fragmentation due to weathering are rocks and plastics.
fragmentation due to weathering
An environnmental material which 1) is composed primarily of polymers with high molecular mass and 2) once deformed does not spontaneously return to its original shape.
Plastik
plastica
塑膠
Kunststoff
"High molecular mass" can be ambiguous as it does not set a threshold for what is considered "high". Here we make no commitment to a threshold.
plastic
In German "Kunststoff" connotes those plastics which have intentionally been shaped by some art, thus "Kunst".
A piece of plastic which is greater than 1 metre in its longest dimension.
This classification is based on the thresholds detailed in GESAMP report # 99 on recommendation from the SDG 14 indicator team.
megaplastic particle
A piece of plastic which is between 25 and 1000 millimetres in its longest dimension.
This classification is based on the thresholds detailed in GESAMP report # 99 on recommendation from the SDG 14 indicator team. While the definition is in accordance with the common use of this term (as per GESAMP report # 99), alternative size classifications exist and are detailed in the same report. An alternative classification is a piece of plastic which is between 25 and 50 millimetres in its longest dimension.
macroplastic particle
A piece of plastic which is between 5 and 25 millimetres in its longest dimension.
This classification is based on the thresholds detailed in GESAMP report # 99 on recommendation from the SDG 14 indicator team. While the definition is in accordance with the common use of this term (as per GESAMP report # 99), alternative size classifications exist. Alternatives classifications are a piece of plastic which is less than 25 millimetres in its longest dimension, or a piece of plastic which is between 1 and 25 millimetres in its longest dimension.
mesoplastic particle
A piece of plastic which has a diameter less than 1 micrometre.
This classification is based on the thresholds detailed in GESAMP report # 99 on recommendation from the SDG 14 indicator team. While the definition is in accordance with the common use of this term (as per GESAMP report # 99), alternative size classifications exist. An alternative classification is a piece of plastic which has a diameter less than 100 nanometres. The GESAMP report states that it assumes a spherical shape for this size classification, which was understood to mean the generalised form of diameter, i.e. the largest distance between two points belonging to an object.
nanoplastic particle
A part of an astronomical body which includes, as parts, all the entities which are composed primarily of plastic and which are within the gravitational sphere of influence of that body.
Plastiksphäre
plastisfera
plastisphere
Anthropogenic litter which is present in the marine environment.
海洋廢棄物
marine anthropogenic litter
An anthropogenic environmental process during which waste is improperly disposed of into the environment.
littering
A role which 1) inheres in a material entity 2) is realised when that entity is discarded outside waste management systems by humans or their technologies.
litter role
A plastisphere which is composed primarily of manufactured plastic.
manufactured plastisphere
Plastic which is composed primarily of polymers produced by processes whose agents do not include humans or their technologies.
The corresponding subclass axiom will be added in the second phase of this project.
natural plastic
A plastic which is composed primarily of polymers produced by a manufacturing process.
manufactured plastic
synthetic plastic
A planned environmental usage process during which any number of fish are caught by humans or their technologies.
angeln
fischen
pesca
fishing
An anthropogenic environmental process during which abandoned, lost, or discarded fishing gear attracts and entangles organisms.
While not driven by humans directly, ghost fishing is a downstream result of their intentional actions.
ghost fishing
A manufactured product which is used for fishing.
Angelausrüstung
Angelzubehör
Fischereiausrüstung
attrezzo di pesca
equipo de pesca
fishing tackle
漁具
fishing gear
Abandoned fishing gear which was intentionally left unmaintained and uncontrolled by its custodian.
In the future some role semantics for "abandoned", "lost", and "discarded" could be set up.
entsorgte Angelausrüstung
equipo de pesca desechado
attrezzo di pesca scartato
weggeworfene Angelausrüstung
weggeworfene Fischerreiausrüstung
weggeworfenes Angelzubehör
In the literature, including GESAMP Report #99, this term is often referenced as part of abandoned, lost or otherwise discarded fishing gear (ALDFG).
discarded fishing gear
Fishing gear which is not under the control of or maintained by its custodian.
abandoned fishing gear
Abandoned fishing gear which was unintentionally left unmaintained and uncontrolled by its custodian.
attrezzo di pesca perso
equipo de pesca perdido
verschollene Angelausrüstung
lost fishing gear
A material transformation process during which the properties of a material are changed as a result of in situ exposure to atmospheric processes.
Verwitterung
meteorización
meteorizzazione
風化(作用)
The term "weathering" should not be confused with "erosion", which is the removal and transport of environmental material away from a site via exogenic processes.
weathering
An environmental system process during which material entities become entrapped, wrapped, twisted, entwined, or otherwise caught in one another.
Verfangen
Verhedderung
Verstrickung
proceso de enredamiento
processo di impigliamento
entanglement process
An entanglement process during which organisms become entrapped in anthropogenic marine debris.
We've added anthropogenic litter as an input, as the threshold between litter and debris is ambigious. See the notes on anthropogenic litter
Examples of marine debris include boating gear, or fishing gear (active or derelict). Marine debris may be in water or on land.
entanglement of organisms in marine debris
A polymer which is the output of a biological process.
biopolymer
A polymer which is the output of a manufacturing process.
synthetic polymer
Anthropogenic litter which is present in a coastal environment.
coastal anthropogenic litter
A manufacturing process which includes plastic as one of its specified outputs.
Plastikherstellung
plastic production
producción de plástico
produzione di plastica
plastic manufacturing process
Weathering during which plastic is worn or broken down.
weathering of plastic
A surface layer which is 1) part of a phreatic zone in contact with a vadose zone and 2) contains interstitial water with a pressure head equal to atmospheric pressure.
water table
Soil compaction is a compaction process during which the bulk density of soil increases and/or its porosity decreases due to externally or internally applied loads.
soil compaction process
An elevation which inheres in a water table by virture of its vertical distance from a land surface.
depth of the water table
depth to the water table
height of the water table
While called "depth", this is not the depth of the water table but rather how far it is below a reference plane, usually the soil surface. Thus, this is placed under PATO:elevation which allows for distance above and below a reference point.
water table depth
A rate which is characteristic of irradiance by photosynthetically active radiation by virtue of the number of photons received by an irradiated surface over time.
A best-guess at representing "density" of massless entities - likely to require further expert input and refinement.
PPFD
Often represented in micromoles of photons associated with photosynthetically active radiation per square meter per second.
photosynthetic photon flux density
A soil which has a high bulk density and/or a low porosity. A compacted soil has a reduced rate of both water infiltration and drainage
compacted soil
A rate which inheres in a soil percolation process.
percolation rate in soil
soil percolation rate
Liquid water which 1) flows over land and 2) is not absorbed or retained by the materials if flows over or through.
overland flow
surface runoff
Runoff often gathers debris and solutes from the materials it flows over or through, and often flows into a water body.
runoff
A flux which inheres in photosynthetically active radiation.
PPF
Often represented in micromoles of photons associated with photosynthetically active radiation per second.
photosynthetic photon flux
The number of days during which there is precipitation
The threshold at which a day is considered to be a rainy day is highly variable, and determined at the instance level.
rainy day count
The depth of the top part of a soil layer.
soil layer top depth
The depth of the bottom part of a soil layer.
soil layer bottom depth
A water flow process during which water occupies the pores or interstices of a solid or semi-solid material.
water infiltration
A water infiltration process during which water fills the pore space and interstices of soil.
soil water infiltration
water infiltration into soil
Albedo which inheres in soil.
soil albedo
Soil albedo which inheres in dry soil.
dry soil albedo
Soil albedo which inheres in moist soil.
This could be axiomatised with PATO:wet, but that isn't likely to map neatly to "moist".
moist soil albedo
An ion which is 1) adsorbed onto the surfaces of materials with an opposing charge, 2) are readily displaced by other ions, 3) may be displaced and absorbed by organisms.
Add an equivalence axiom to autopopulate this once we have ion exchange in as a process.
The exchangeable ion pool is the dominant storage pool for calcium, magnesium, and potassium ions. In soil, exchangeable ions are typically bound to the surface of clay and humus colloids.
exchangeable ion
A potassium ion which is capable of ion exchange.
This class will be moved under K+ once it has been imported from CHEBI
exchangeable K+
exchangeable potassium
Liquid water which is present in soils as discontinuous volumnes of water in contact with solid and gaseous components of the soil.
residual water in soil
A calcium ion which is capable of ion exchange.
This class will be moved under Ca2+ once it has been imported from CHEBI
exchangeable calcium
A physical quality which inheres in an environmental material by virtue of the material's ability to adsorb exchangeable cations.
CEC
In soils, these materials include clay and organic matter particles. Soil CEC is measured in millequivalents per 100 grams of soil (meq/100g). A meq is the number of ions which total a specific quantity of electrical charges. Common soil cations include: calcium (Ca++), magnesium (Mg++), potassium (K+), ammonium (NH4+), hydrogen (H+) and sodium (Na+).
cation exchange capacity
A drainage process during which liquid water is transported away from soil.
soil drainage
A cation exchange capacity which inheres in an environmental material by virtue of the material's ability to adsorb basic exchangeable cations.
The basic cation exchange capacity is often expressed as the percentage of the total exchangeable cations which are basic, known as the percentage base saturation. The percentage base saturation is expressed as follows: %BS = [(Ca2+ + Mg2+ + K+)/CEC] × 100
basic cation exchange capacity
Energy which has been absorbed by an astronomical body or its parts following that body's irradiation by shortwave radiation from a star.
absorbed shortwave radiation
Despite the label, this is not a shortwave radiation process, but the energy that is absorbed from one. This term is used to describe, e.g., the energy absorbed from insolation and stored by the Earth. Gross shortwave radiation would also include shortwave radiation reflected back into space by clouds, aerosols, and solid surfaces with high albedo.
net shortwave radiation
A layer that is composed primarily of soil.
soil layer
A planned process during which a soil profile is examined and the soil horizons that compose it are described.
soil profile characterization
Waste water which was converted into an effluent that can be either returned to the water cycle with minimal environmental issues or reused.
treated wastewater
Saline water from which minerals have been removed to produce fresh water suitable for human consumption or irrigation.
desalinated water
Texture which inheres in soil.
soil texture
Soil which is primarily composed of sand with silt and clay in progressively smaller proportions.
Some authorities consider this a soil type, composed of 70-86% of sand, 0-30% of silt and 0-15% of clay. Others consider this a soil material that contains at the upper limit 85 to 90% sand, and the percentage of silt plus 1.5 times the percentage of clay is not less than 15, at the lower limit it contains not less than 70 to 85% sand, and the percentage of silt plus twice the percentage of clay does not exceed 30.
loamy sand
Sand which is composed primarily of fine particles.
Thresholds for what particle size is considered "fine" vary by region and authority, as well as the tolerance for proportions of other particle sizes.
fine sand
Loam which has a high proportion of sand in its composition.
Some authorities consider sandy loam to be a soil composed of 50-70% sand, 0-50% silt, and 0-20% clay. Others, a soil material that contains either 20% or less clay, with a percentage of silt plus twice the percentage of clay that exceeds 30, and 52% or more sand; or less than 7% clay, less than 50% silt, and between 43% and 52% sand.
sandy loam
Loam which has a high proportion of silt in its composition.
Some authorities consider silt loam to be a soil composed of 20-50% of sand, 74-88% silt and 0-27% of clay.
silty loam
Clay loam which has a high proportion of sand in its composition.
Some authorities consider sandy clay loam to be a soil composed of 45-80% sand, 0-28% silt, and 20-35% clay.
sandy clay loam
Loam which has a high proportion of clay in its composition.
Interestingly, some instances of this class may not actually conform to the definition of loam, by having roughly unequal proportions of sand and silt and quite a large proportion of clay.
Some authorities consider clay loam to be a soil composed of 20-45% sand, 15-52% silt, and 27 to 40% clay.
clay loam
Clay loam which has a high proportion of silt in its composition.
Some authorities consider silty clay loam to be a soil composed of 0-20% of sand, 40-73 of silt and 27-40% of clay.
silty clay loam
Clay which has a high proportion of sand in its composition.
If this is a soil (in which case the differntia must be made clear) it should be moved (or a new class created) and labelled 'sandy clay soil'.
Some authorities consider sandy clay to be a soil composed of 45-65% of sand, 0-20% of silt and 35-55% of clay. If the proportion of sand exceeds that of clay, it is unclear whether this is still considered clay (due to other properties) or whether a new class "clay sand" should be created.
sandy clay
Clay which has a high proportion of silt in its composition.
If this is a soil (in which case the differntia must be made clear) it should be moved (or a new class created) and labelled 'silty clay soil'.
Some authorities consider this a soil composed of 0-20% of sand, 40-60% of silt and 40-60% of clay. If the proportion of silt exceeds that of clay, it is unclear whether this is still considered clay (due to other properties) or whether a new class "clay silt" should be created.
silty clay
A recycling process during which wastewater is treated
wastewater treatment process
A recycling process during which the dissolved mineral salts in water are removed
desalination process
A concentration of liquid water in soil arrived at after water which is not retained by the soil has drained away.
drained upper limit
The determination of field capacity is variable and multiple methods to do so exist. Even in a given soil, the value of field capacity is variable, but serves as a useful measure of its water-holding capacity. Field capacity is often characterized by measuring water content after wetting a soil profile, covering it (to prevent evaporation) and monitoring the change soil moisture in the profile. Water content when the rate of change is relatively small is indicative of when drainage ceases and is called field capacity, it is also termed drained upper limit (DUL). This measure of field capacity is well-correlated with field capacity determined by applying −33 kPa (or −0.33 bar) of hydraulic head or suction pressure (less in sandy soils) to a portion of soil and subsequently measuring the bulk water content it retains.Field capacity is usually naturally arrived at 2–3 days after rain or irrigation in pervious soils of uniform structure and texture.
field capacity
A concentration of liquid water in soil at or below which a plant will wilt and no longer recover its turgidity when placed in a water saturated atmosphere.
PWP
wilting point
The type of plant and soil are sources of variation for values of this concentration. The physical definition of the wilting point is conventionally measured as the water content at −1,500 kPa (−15 bar) of suction pressure, or negative hydraulic head.
permanent wilting point
Water-holding capacity which inheres in some soil.
soil water-holding capacity
water-holding capacity of soil
An environment that is determined by an axilla skin.
An environment that is determined by a mouth.
The solubility of a carbon atom when measured in environmental material.
environmental material carbon atom solubility
solubility of carbon atom in environmental material
The solubility of a carbon atom when measured in soil.
The solubility of a carbon atom when measured in water.
The amount of a carbon atom when measured in environmental material.
environmental material carbon atom amount
amount of carbon atom in environmental material
The amount of a carbon atom when measured in soil.
The amount of a carbon atom when measured in water.
The concentration of a carbon atom when measured in environmental material.
environmental material carbon atom concentration
concentration of carbon atom in environmental material
The concentration of a carbon atom when measured in soil.
The concentration of a carbon atom when measured in water.
The solubility of a nitrogen atom when measured in environmental material.
environmental material nitrogen atom solubility
solubility of nitrogen atom in environmental material
The solubility of a nitrogen atom when measured in soil.
The solubility of a nitrogen atom when measured in water.
The amount of a nitrogen atom when measured in environmental material.
environmental material nitrogen atom amount
amount of nitrogen atom in environmental material
The amount of a nitrogen atom when measured in soil.
The amount of a nitrogen atom when measured in water.
The concentration of a nitrogen atom when measured in environmental material.
environmental material nitrogen atom concentration
concentration of nitrogen atom in environmental material
The concentration of a nitrogen atom when measured in soil.
The concentration of a nitrogen atom when measured in water.
The concentration of a chloride when measured in water.
The concentration of a clay when measured in soil.
The concentration of a slit when measured in soil.
The concentration of a sand when measured in soil.
The concentration of a gravel when measured in soil.
The concentration of a liquid water when measured in soil.
soil moisture content
soil water content
The concentration of a salt when measured in soil.
The evaporation of a liquid water when measured in soil.
soil liquid water evaporation
evaporation of liquid water in soil
The rate of a hydrological evaporation when measured in soil.
soil hydrological evaporation rate
rate of hydrological evaporation in soil
The concentration of a soil organic matter when measured in soil.
concentration of soil organic matter in soil
The concentration of a pesticide when measured in surface water.
concentration of pesticide in surface water
The carbon atom in a dissolved state when measured in environmental material.
environmental material dissolved carbon atom
dissolved carbon atom in environmental material
The carbon atom in a dissolved state when measured in soil.
The carbon atom in a dissolved state when measured in water.
The nitrogen atom in a dissolved state when measured in environmental material.
environmental material dissolved nitrogen atom
dissolved nitrogen atom in environmental material
The nitrogen atom in a dissolved state when measured in soil.
The nitrogen atom in a dissolved state when measured in water.
The temperature of some environmental material.
The quality of a environmental system process.
The concentration of a ammonium when measured in soil.
The concentration of a nitrate when measured in soil.
soil pH
The concentration of a nitrate when measured in groundwater.
The speed of some soil water infiltration.
The amplitude of some temperature of air.
The pressure of some atmospheric water vapour.
A one-dimensional temporal region during which an entity is exposed to stellar radiation.
A hydrological precipitation process with a reduced rate relative to some historical average, typically resulting in ecosystemic perturbations.
Drought is often defined as a temporal period of below-average precipitation, however, representing it as a temporal entity seems insufficient.
drought
A gelatinous material primarily composed of exopolymeric compounds with colloidal properties, formed through the aggregation of marine snow particles, often found in large sheets, flocs, and clouds.
See issue #276. This class is complex as marine mucilage is quite complex. It will also requre new class creation in GO process for deeper semantics.
The formation of marine mucilage is often associated with conditions which stress marine microorganisms such as diatoms.
marine mucilage
A process in which carbohydrates are transported from the interior of an organism to its surroundings.
exudation of carbohydrates
A process which results in the formation of an island.
Addressing Issue #268. This top-level class may be converted to an inferred class.
island formation process
An island created when a continent is rifted.
"Examples are Madagascar and Socotra off Africa, the Kerguelen Islands, New Caledonia, New Zealand, and some of the Seychelles." https://en.wikipedia.org/wiki/Island
microcontinental island
An island formed by deposition of solid material such as sand or small rocks where a water current loses some of its carrying capacity.
depositional island
An island formed by the accumulation of sand deposited by sea currents on a continental shelves
barrier island
A manufactured product that is some mixture of chemicals created through some chemical engineering process
The portion of chemical products obtained by the distillation of a tar that remains heavier than water, notably useful for its anti-septic and preservative properties
A wastewater treatment plant that treates industrial wastewater. Industrial wastewater treatment covers the mechanisms and processes used to treat waters that have been contaminated in some way by anthropogenic industrial or commercial activities prior to its release into the environment or its re-use.
A wastewater treatment plant that treats agriculatural wastewater. Agricultural wastewater treatment relates to the treatment of wastewaters produced in the course of agricultural activities. Agriculture is a highly intensified industry in many parts of the world, producing a range of wastewaters requiring a variety of treatment technologies and management practices.
A feature that arises from a rapid increase or accumulation in the population of algae (typically microscopic) in an aquatic system.
An algal bloom that is located in freshwater. Freshwater algal blooms are the result of an excess of nutrients, particularly some phosphates.
An animal habitation constructed by termites. Termite workers build and maintain nests which house the colony. These are elaborate structures made using a combination of soil, mud, chewed wood/cellulose, saliva, and faeces. A nest has many functions such as providing a protected living space and water conservation (through controlled condensation).
charcoal that is used as a soil amendment.
A soft, brown, combustible, sedimentary rock formed from naturally compressed peat.
It is considered the lowest rank of coal due to its relatively low heat content. It has a carbon content around 60–70 percent.
a relatively soft coal containing a tarlike substance called bitumen or asphalt. It is of higher quality than lignite coal but of poorer quality than anthracite. It is an organic sedimentary rock formed by diagenetic and sub metamorphic compression of peat bog material.
A hard, compact variety of coal that has a submetallic luster. It has the highest carbon content, the fewest impurities, and the highest energy density of all types of coal and is the highest ranking of coal.
The generation of energy for use by humans
A disposition which is realized during the execution of work, the emission of heat, or the possession of mass.
Consider replacing with PATO class; note that PATO class is not a disposition. This should likely go into OBO Core and also have a physicist look at it.
Energy possessed by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors.
Energy which is realised through motion.
Energy which is the sum of 1) kinetic energy and 2) potential energy.
potential energy due to or stored in electric fields.
potential energy due to or stored in magnetic fields.
potential energy due to or stored in gravitational fields.
Potential energy which is stored in chemical bonds and realised through reactions which break them..
potential energy that binds an electron to its atom or molecule.
potential energy that binds nucleons to form the atomic nucleus (and nuclear reactions).
Potential energy due to the energy of the gluon-mediated field of the strong force, binding quarks together into hadrons.
potential energy due to the deformation of a material (or its container) exhibiting a restorative force.
Wave energy which inheres in an elastic material and is realised when a deformational wave passes through that material.
Mechanical wave energy which is realised when an acoustic wave propagates through a material.
Potential energy which is stored in the fields of propagated by electromagnetic radiation.
potential energy due to an object's rest mass.
Kinetic energy which is realised through the microscopic motion of particles.
A form of disordered mechanical energy.
Mechanical wave energy which inheres in an atmosphere and is realised during an atmospheric wind.
Thermal energy which propagates through a solid (typically rocky) astronomical body.
Often, this term is used specifically for thermal energy spreading from heat sources (e.g. magma chambers, the planetary core) within the Earth. However, it is also used for extraterrestrial bodies.
A power station which burns a fossil fuel such as coal, natural gas, or petroleum to produce electricity.
hydrocarbon-based environmental material
A biogeochemical cycle which has oxygen as participant.
An environment which is determined by an anatomical entity.
An environmental system determined by an intestine.
An environment determined by an area or zone of skin tissue.
A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths and frequencies which travel exclusively in a line-of-sight fashion and which may produce molecular rotation and torsion on contact with matter.
A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths ranging from millimetre to kilometer scales.
A radiation process during which electromagnetic waves or their quanta are emitted when molecules change their rotational-vibrational movements, usually at wavelengths between 760 nm and 1 mm.
A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths between 380 nm and 760 nm.
A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths between 10 nm and 400 nm.
A radiation process during which penetrating electromagnetic radiation is emitted by high-energy electrons as they fall into a lower state of energy.
A radiation process during which penetrating electromagnetic radiation is emitted from the radioactive decay (gamma decay) of atomic nuclei.
A radiation process during which electromagnetic waves or their quanta are emitted with sufficient energy to disrupt molecular bonds or alter the electron number of atoms.
The concentration of Adenosine 5-triphosphate when measured in liquid water.
liquid water Adenosine 5-triphosphate concentration
concentration of Adenosine 5-triphosphate in liquid water
The concentration of alloxanthine when measured in liquid water.
concentration of alloxanthine in liquid water
The concentration of alpha-carotene when measured in liquid water.
liquid water alpha-carotene concentration
concentration of alpha-carotene in liquid water
The concentration of ammonium when measured in liquid water.
concentration of ammonium in liquid water
The concentration of bacteriochlorophyll a when measured in liquid water.
liquid water bacteriochlorophyll a concentration
concentration of bacteriochlorophyll a in liquid water
The concentration of beta-carotene when measured in liquid water.
liquid water beta-carotene concentration
concentration of beta-carotene in liquid water
The concentration of carotene when measured in liquid water.
concentration of carotene in liquid water
The concentration of chlorophyll a when measured in liquid water.
liquid water chlorophyll a concentration
concentration of chlorophyll a in liquid water
The concentration of chlorophyll b when measured in liquid water.
liquid water chlorophyll b concentration
concentration of chlorophyll b in liquid water
The concentration of chlorophyllide a when measured in liquid water.
liquid water chlorophyllide a concentration
concentration of chlorophyllide a in liquid water
The concentration of dioxygen when measured in liquid water.
concentration of dioxygen in liquid water
The concentration of divinyl chlorophyll a when measured in liquid water.
liquid water divinyl chlorophyll a concentration
concentration of divinyl chlorophyll a in liquid water
The concentration of divinyl chlorophyll b when measured in liquid water.
liquid water divinyl chlorophyll b concentration
concentration of divinyl chlorophyll b in liquid water
The concentration of fucoxanthin when measured in liquid water.
concentration of fucoxanthin in liquid water
The concentration of Guanosine 5-triphosphate when measured in liquid water.
liquid water Guanosine 5-triphosphate concentration
concentration of Guanosine 5-triphosphate in liquid water
The concentration of hydrogen peroxide when measured in liquid water.
liquid water hydrogen peroxide concentration
concentration of hydrogen peroxide in liquid water
The concentration of hydrogen sulfide when measured in liquid water.
liquid water hydrogen sulfide concentration
concentration of hydrogen sulfide in liquid water
The concentration of lutein when measured in liquid water.
The concentration of methane when measured in liquid water.
concentration of methane in liquid water
The concentration of neoxanthin when measured in liquid water.
concentration of neoxanthin in liquid water
The concentration of nitrate when measured in liquid water.
concentration of nitrate in liquid water
The concentration of nitrite when measured in liquid water.
concentration of nitrite in liquid water
The concentration of nitrous oxide when measured in liquid water.
liquid water nitrous oxide concentration
concentration of nitrous oxide in liquid water
The concentration of peridinin when measured in liquid water.
concentration of peridinin in liquid water
The concentration of phosphate when measured in liquid water.
concentration of phosphate in liquid water
The concentration of silicate(4-) when measured in liquid water.
concentration of silicate(4-) in liquid water
The concentration of violaxanthin when measured in liquid water.
concentration of violaxanthin in liquid water
The concentration of zeaxanthin when measured in liquid water.
concentration of zeaxanthin in liquid water
The concentration of silicic acid when measured in liquid water.
concentration of silicic acid in liquid water
The concentration of chlorophyll when measured in liquid water.
concentration of chlorophyll in liquid water
The concentration of nitrate when measured in sea water.
The concentration of phosphate when measured in sea water.
The concentration of silicic acid when measured in sea water.
concentration of silicic acid in sea water
The concentration of ammonium when measured in sea water.
The concentration of nitrite when measured in sea water.
The concentration of carbon-13 atom when measured in sea water.
concentration of carbon-13 atom in sea water
The concentration of carbon atom when measured in sea water.
concentration of carbon atom in sea water
The concentration of chloroflurocarbon when measured in sea water.
sea water chloroflurocarbon concentration
concentration of chloroflurocarbon in sea water
The concentration of tritium when measured in sea water.
The concentration of helium-3 when measured in sea water.
The concentration of carbon-14 atom when measured in sea water.
concentration of carbon-14 atom in sea water
The concentration of sulfur hexafluoride when measured in sea water.
sea water sulfur hexafluoride concentration
concentration of sulfur hexafluoride in sea water
The concentration of calcium carbonate when measured in sea water.
sea water calcium carbonate concentration
concentration of calcium carbonate in sea water
The concentration of dioxygen when measured in sea water.
The concentration of bromine when measured in lake water.
The concentration of cerium when measured in lake water.
The concentration of cobalt when measured in lake water.
The concentration of dysprosium when measured in lake water.
concentration of dysprosium in lake water
The concentration of europium when measured in lake water.
The concentration of gadolinium when measured in lake water.
concentration of gadolinium in lake water
The concentration of lanthanum when measured in lake water.
concentration of lanthanum in lake water
The concentration of lithium when measured in lake water.
The concentration of methanesulfonic acid when measured in lake water.
lake water methanesulfonic acid concentration
concentration of methanesulfonic acid in lake water
The concentration of molybdenum when measured in lake water.
concentration of molybdenum in lake water
The concentration of neodymium when measured in lake water.
concentration of neodymium in lake water
The concentration of niobium when measured in lake water.
The concentration of praseodymium when measured in lake water.
concentration of praseodymium in lake water
The concentration of samarium when measured in lake water.
The concentration of silver when measured in lake water.
The concentration of thallium when measured in lake water.
The concentration of tin when measured in lake water.
The concentration of titanium when measured in lake water.
The concentration of yttrium when measured in lake water.
The concentration of bromine when measured in water ice.
The concentration of cerium when measured in water ice.
The concentration of cobalt when measured in water ice.
The concentration of dysprosium when measured in water ice.
concentration of dysprosium in water ice
The concentration of europium when measured in water ice.
The concentration of gadolinium when measured in water ice.
concentration of gadolinium in water ice
The concentration of lanthanum when measured in water ice.
The concentration of lithium when measured in water ice.
The concentration of methanesulfonic acid when measured in water ice.
water ice methanesulfonic acid concentration
concentration of methanesulfonic acid in water ice
The concentration of molybdenum when measured in water ice.
concentration of molybdenum in water ice
The concentration of neodymium when measured in water ice.
The concentration of niobium when measured in water ice.
The concentration of praseodymium when measured in water ice.
concentration of praseodymium in water ice
The concentration of samarium when measured in water ice.
The concentration of silver when measured in water ice.
The concentration of thallium when measured in water ice.
The concentration of tin when measured in water ice.
The concentration of titanium when measured in water ice.
The concentration of yttrium when measured in water ice.
The concentration of bromine when measured in snow.
The concentration of cerium when measured in snow.
The concentration of cobalt when measured in snow.
The concentration of dysprosium when measured in snow.
The concentration of europium when measured in snow.
The concentration of gadolinium when measured in snow.
The concentration of lanthanum when measured in snow.
The concentration of lithium when measured in snow.
The concentration of methanesulfonic acid when measured in snow.
concentration of methanesulfonic acid in snow
The concentration of molybdenum when measured in snow.
The concentration of neodymium when measured in snow.
The concentration of niobium when measured in snow.
The concentration of praseodymium when measured in snow.
The concentration of samarium when measured in snow.
The concentration of silver when measured in snow.
The concentration of thallium when measured in snow.
The concentration of tin when measured in snow.
The concentration of titanium when measured in snow.
The concentration of yttrium when measured in snow.
The concentration of urea when measured in liquid water.
The concentration of oxygen when measured in soil.
The concentration of manganese molecular entity when measured in soil.
soil manganese molecular entity concentration
concentration of manganese molecular entity in soil
The concentration of iron molecular entity when measured in soil.
soil iron molecular entity concentration
concentration of iron molecular entity in soil
The concentration of aluminium molecular entity when measured in soil.
soil aluminium molecular entity concentration
concentration of aluminium molecular entity in soil
The concentration of magnesium molecular entity when measured in soil.
soil magnesium molecular entity concentration
concentration of magnesium molecular entity in soil
The concentration of sodium molecular entity when measured in soil.
soil sodium molecular entity concentration
concentration of sodium molecular entity in soil
The concentration of organic nitrogen anion when measured in soil.
soil organic nitrogen anion concentration
concentration of organic nitrogen anion in soil
The concentration of organophosphorus compound when measured in soil.
soil organophosphorus compound concentration
concentration of organophosphorus compound in soil
The concentration of phosphorus molecular entity when measured in soil.
soil phosphorus molecular entity concentration
concentration of phosphorus molecular entity in soil
The concentration of potassium molecular entity when measured in soil.
soil potassium molecular entity concentration
concentration of potassium molecular entity in soil
The concentration of calcium carbonate when measured in soil.
concentration of calcium carbonate in soil
The concentration of organic molecular entity when measured in soil.
soil organic molecular entity concentration
concentration of organic molecular entity in soil
The concentration of tetraphosphorus decaoxide when measured in soil.
soil tetraphosphorus decaoxide concentration
concentration of tetraphosphorus decaoxide in soil
The concentration of sulfate when measured in soil.
The concentration of exchangeable potassium when measured in soil.
soil exchangeable potassium concentration
concentration of exchangeable potassium in soil
The concentration of residual water when measured in soil.
The concentration of exchangeable calcium when measured in soil.
concentration of exchangeable calcium in soil
An anatomical structure that forms all or part of a fungus.
orange juice (liquid)
Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products.
Damion Dooley
Foodon product type
The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations.
food product
The juice products which are made from the fermented sap of the maguey (agave) plant.
fermented agave juice
This food product type includes food products which are made from fermentation of juice extracted from pressed sugarcane.
fermenting sugar cane juice
fermenting elaeis palm sap food product
A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals.
mammalian meat food product
A processed meat food product that is made from a sausage.
sausage food product
SIREN DB annotation: * has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) * derives from 'liver' (http://purl.obolibrary.org/obo/UBERON_0002107)
liver paste
A hot dog is a moist sausage of soft, even texture and flavor, often made from advanced meat recovery or meat slurry. Most types are fully cooked, cured or smoked. It is often placed hot in a special purpose soft, sliced hot dog bun.
hotdog
frankfurter
hot dog
processed meat food product
milk formula food product
Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein.
cheese
cheese food product
A dairy product produced by bacterial fermentation of milk.
yoghourt
yoghurt
yougert
The bacteria used to make yogurt are known as yogurt cultures. The fermentation of lactose by these bacteria produces lactic acid, which acts on milk protein to give yogurt its texture and characteristic tart flavor.
yogurt food product
This class includes food products which are derived from or produced by a plant.
plant food product
Cabbage or headed cabbage (comprising several cultivars of Brassica oleracea) is a leafy green or purple biennial plant, grown as an annual vegetable crop for its dense-leaved heads.
cabbage food product
commercial yogurt
wort food product
beer wort food product
acifified beer wort food product
Cream component produced by churning and containing not less than 80% milkfat.
mammalian milk butter
pickled cabbage food product
camembert cheese food product
cheddar cheese food product
Brie cheese food product
gouda cheese food product
gorgonzola cheese food product
swiss cheese food product
emmenthal cheese food product
new zealand cheddar cheese food product
pont ieveque cheese food product
vacherin mont dor cheese food product
A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa).
pork
pork meat food product
cured meat food product
chicken meat food product
beef food product
ice cream
ice cream food product
A seafood product is a vertebrate or invertibrate organism from an aquatic environment.
Some of the subclasses are currently freshwater organisms.
animal seafood product
meshanger cheese food product
pork chop food product
A food product having tempeh as a defining ingredient
tempeh food product
fermented rice beverage
amasake food product
fermented dairy food product
fermented fish or seafood food product
sea water fish food product
A fine powder made from cereals or other starchy food sources.
flour food product
A food product derived from plant fruit.
plant fruit food product
fruit extract food product
Apple juice is a fruit juice made by the maceration and pressing of an apple.
apple juice
awamori food product
Any of certain cuts of meat taken from the sides, belly or back of a pig that may be cured and/or smoked.
bacon food product
fermented millet food product
millet beer food product
bottled beer food product
SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) * formed as a result of 'interior mold curing process' (http://purl.obolibrary.org/obo/FOODON_03460331)
blue cheese food product
buttermilk food product
fermented fruit food product
A food produced by fermenting rice, barley and/or soybeans, with salt and the mold koji-kin (Aspergillus oryzae).
SIREN DB annotation: * has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) * formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128) * formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) * formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104)
miso food product
A grape berry food product which is the juice of freshly pressed grapes that contains some amount of pulp, skins, stems, and seeds.
Grape pomace components typically comprises between 7 to 23 percent of the total weight of must. [https://en.wikipedia.org/wiki/Must]
grape must
vinegar food product
barley malt vinegar
mammalian milk (nonfat, dry)
Sake is a fermented rice beverage resulting from the fermentation of rice with the mold Aspergillus oryzae and, in parallel, with the yeast Saccharomyces cerevisiae [wikipedia:sake]
sake food product
salt pork meat food product
A food product having fermented soyabeans as a defining ingredient
fermented soybean food product
A food preserved by soaking and storing it in vinegar or brine.
pickled
subset_siren
SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190)
food (pickled)
tape kefan food product
Bondon cheese food product
bitter cheese food product
sugar condiment
kefir food product
A lipid material derived from plants. Physically, oils are liquid at room temperature.
vegetable oil food product
An oil used as a nutritional supplement and is a traditional European ethnic food, highly regarded for its nutty flavor.
flax oil
flax seed oil
linseed oil
Food-grade flaxseed oil is cold-pressed, obtained without solvent extraction, in the absence of oxygen, and marketed as edible flaxseed oil.[wikipedia]
flaxseed oil
corn flour food product
sour milk beverage
dried milk food product
A food product which is derived from or produced by an animal that has a vertibrae.
vertebrate animal food product
cereal grain food product
SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)
fermented beverage
fermented elaeis palm beverage
fermented sugar cane beverage
fermented apple beverage
apple beverage
SIREN DB annotation: * has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) * formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) * has substance added 'water addition process' (http://purl.obolibrary.org/obo/FOODON_03460148) * has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202) * has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)
orange fruit beverage
fermented grain beverage
This food product type includes beverage products which are made from the fermented sap of the maguey (agave) plant.
fermented agave beverage
This food product type includes food products which are made from eggs laid by the sea water fish.
sea water fish egg food product
A food product made from an avian egg.
avian egg food product
camelid dairy food product
bovine dairy food product
equine dairy food product
zebra dairy food product
cattle dairy food product
camelid milk beverage
equine milk beverage
caprine cheese food product
ovine cheese food product
bovine cheese food product
cow milk cheese
A very strong smelling, soft cow's milk cheese made by fermentation involving the bacterium Brevibacterium linens.
Limburger cheese food product
goat milk cheese food product
sheep milk cheese food product
A food product made from domesticated bird meat.
poultry meat food product
Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa.
porcine meat
swine food product
A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish.
condiment
condiment food product
bovine meat food product
distilled fermented grain beverage
distilled fermented beverage
A beverage product derived from leaves of the tea plant (Camellia sinensis).
"While fermentation is also referred to in the production of brewed teas, this is inaccurate. Some herbal teas on the market today include probiotic cultures alongside tea leaves to maintain gut health but the tea itself hasn't been fermented. Most dried teas however don't use live cultures at all during production. Instead, harvested tea leaves undergo a natural chemical process known as oxidation, which also changes the color, flavor and level of health benefits in the resulting brew." [https://eatcultured.com/blogs/our-awesome-blog/fermented-tea]
tea based beverage product
coffee and coffee products
coffee based beverage product
fruit juice food product
wheat food product
A food product deriving primarily from corn (maize).
maize food product
maize (corn) food product
tuber
solanaceous root food product
A food product derived from or produced by a plant root.
plant root food product
A potato food product is any product derived from potatoes.
potato food product
Food items that are rich in sugar, any one or type of which is called a confection. Modern usage may include substances rich in artificial sweeteners as well.
confectionery food product
cucurbit fruit food product
A citrus fruit is botanically classified as a type of berry called a hesperidium that has a thick, leathery rind, with numerous oil glands, and a large flesh portion composed of several wedge-shaped sections. Unlike pome fruit, such as the apple, the citrus fruit is derived from a superior ovary, an ovary completely separate from the calyx.
citrus
citrus fruit food product
The fleshy fruit (false berry) of a plant of the family Cucurbitaceae.
melon fruit food product
muskmelon (Cucumis melo) fruit food product
Citrullus lanatus is a plant species in the family Cucurbitaceae, a vine-like (scrambler and trailer) flowering plant originally from sub-Saharan Africa. It is cultivated for its fruit. The subdivision of this species into two varieties, watermelons (Citrullus lanatus (Thunb.) var. lanatus) and citron melons (Citrullus lanatus var. citroides (L. H. Bailey) Mansf.)
citrullus lanatus fruit food product
citrus fruit juice
pomaceous fruit juice beverage
pomes
pomaceous fruit food product
fermented pomaceous fruit beverage
pomaceous fruit extract
citrus fruit extract food product
grape extract
solanaceous fruit food product
A food product deriving from one or more tomatoes.
tomato food product
solanaceous food product
plant inflorescence food product
cruciferous food product
grape berry food product
cruciferous inflorescence food product
The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling.
nut food product
plant seed food product
plant lipid food product
plant stem food product
invertebrate animal food product
insect food product
honey food product
Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked.
prepared
prepared food product
cooked
food (cooked)
pickled cruciferous food product
bread food product
This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms.
algal food product
rice food product
buckewheat food product
sorghum food product
common oat food product
oat food product
rye food product
barley food product
quinoa food product
fonio food product
A product of the dry seeds of plants of the genus Pisum.
dry pea food product
A product of the dry seeds of Cajanus cajan.
pigeon pea (whole, dried)
A bambara groundnut food product is a product derived from fresh or dried beans of the bambara groundnut plant.
Bambara nut
Bambara-bean
Congo goober
earth pea
ground-bean
hog-peanut
bambara groundnut food product
A product of the dry seeds of plants of the genus Vicia.
dried fava bean
broad bean (whole, dried)
A product of the dry seeds of Cicer arietinum.
garbanzo bean food product
Bengal gram
Egyptian pea
gram
chickpea food product
A product of the dry seeds of Vigna unguiculata.
cowpea (pulse) food product
A dry bean food product refers to a bean product made from a Phaseolus species plant whose seeds are harvested at complete maturity.
kidney, haricot bean (Ph. vulgaris); lima, butter bean (Ph. lunatus); adzuki bean (Ph. angularis); mungo bean, golden, green gram (Ph. aureus); black gram, urd (Ph. mungo); scarlet runner bean (Ph. coccineus); rice bean (Ph. calcaratus); moth bean (Ph. aconitifolius); tepary bean (Ph. acutifolius)
FAO notes: "Only species of Phaseolus should be included, though several countries also include certain types of beans. Commonly classified as Vigna (angularis, mungo, radiata, aconitifolia). In the past, these species were also classified as Phaseolus."
dry bean food product
The winged bean food category covers beans of the winged bean plant
winged bean food product
A product of the dry seeds of Vicia sativa.
vetch seed (whole, dried)
Pachyrhizus erosus, commonly known as jicama Mexican yam bean, or Mexican turnip, is the name of a native Mexican vine, although the name most commonly refers to the plant's edible tuberous root. Jícama is a species in the genus Pachyrhizus in the bean family (Fabaceae). Plants in this genus are commonly referred to as yam bean, although the term "yam bean" can be another name for jícama. In contrast to the root, the remainder of the jícama plant is very poisonous; the seeds contain the toxin rotenone, which is used to poison insects and fish. FAO: The yam bean is a legume but unlike its close relatives the soybean and other beans, the yam bean is cultivated for its large, tuberous roots.
yam bean food product
A product of the dry seeds of Mucuna pruriens var. utilis.
velvet bean (whole, dried)
lupin seed food product
A dry seed of the jack-bean plant.
jack bean (whole, dried)
hyacinth bean food product
PULSES are annual leguminous crops yielding from one to 12 grains or seeds of variable size, shape and colour within a pod. They are used for both food and feed. The term "pulses" is limited to crops harvested solely for dry grain, thereby excludingcrops harvested green for food (green peas, green beans, etc.) which are classified as vegetable crops. Also excluded are those crops used mainly for oil extraction (e.g.soybeand and groundnuts) and leguminous crops (e.g. seeds of clover and alfalfa) that are used exclusively for sowing purposes.
pulse
pulses
pulse food product
wheat flour food product
pasta food product
pastry food product
A confection made from a concentrated solution of sugar in water, to which flavorings and colorants are added.
candy food product
A food product derived from Theobroma cacao.
cocoa and cocoa products
cacao food product
sweet cream
cream food product
mammalian milk beverage
bee food product
sausage (cooked, smoked)
sausage (smoked)
sausage (raw, smoked)
A sausage made from meats that have not been previously cured.
sausage (raw)
A cured sausage that is fermented and dried.
sausage (dried, fermented)
A sausage made with fresh meats, and then fully cooked.
sausage (cooked)
smoked meat food product
processed cheese food product
A product made from the seeds of a mustard plant (white or yellow mustard, Sinapis hirta; brown or Indian mustard, Brassica juncea; or black mustard, Brassica nigra).
mustard seed food product
creamy salad dressing
vinaigrette dressing food product
nut oil food product
mayonnaise food product
soy sauce food product
processed pork meat food product
A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment.
herb and spice
herb or spice
spice or herb
animal lipid food product
A brewed drink prepared from roasted seeds, commonly called coffee beans, of the coffee plant.
coffee beverage
A beverage prepared from the cured leaves of Camellia sinensis by combination with hot or boiling water.
tea beverage (liquid)
hot chocolate food product
mate food product
A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins).
fish food product
fish egg food product
avian food product
animal derived beverage
plant derived beverage
plant derived fermented beverage
nonfermented plant derived beverage product
A dairy food product has mammilian milk or a milk component as an ingredient.
dairy product
milk product
dairy food product
milk or milk based food product
Are all fermented foods considered preserved to some extent?
food (fermented)
non-fruit wine food product
Beer is a fermented cereal beverage resulting from the fermentation most commonly of malted barley (though wheat, corn, or rice may included), by a yeast, most commonly Saccharomyces cerevisiae, and flavored by dried flowers of hops, Humulus lupulus.
beer beverage
Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food.
vegetable food product
botanical fruit food product
A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995)
legume
legume food product
camel milk beverage
zebra milk beverage
Regarding American regulatory aspects of egg products, see this summary: https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077
egg food product
A hen egg food product is any food product consisting mainly of hen eggs or derivatives.
hen egg food product
Cider, hard apple cider, or hard cider in the US, is an alcoholic beverage made from the fermented juice of apples.
apple cider (alcoholic)
orange juice (unpasteurized)
cake food product
cake icing food product
chocolate food product
A food involving whipped and cooked milk, sugar and egg yolk mixtures.
sweet custard
custard dessert food product
A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese.
beef mince
ground beef
ground beef food product
A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants.
poultry food product
duck meat food product
goose meat food product
A turkey meat food product is any food product made predominantly of turkey parts.
turkey meat food product
Cantaloupe (also known as muskmelon (India and the United States), mushmelon, rockmelon (in Australian states and in New Zealand), sweet melon, spanspek (South Africa), or capuchin (Scotland) refers to a variety of the Cucumis melo species in the Cucurbitaceae family.
cantaloupe fruit food product
potato salad food product
A sauce for a salad.
salad dressing
clam food product
oyster food product
shellfish food product
goat milk cheese (unpasteurized)
A family of hard Italian cheeses made from sheep milk.
pecorino cheese
sheep milk cheese (unpasteurized)
unpasteurized camel milk beverage
apple condiment
apple food product
apple vinegar food product
bakery food product
barley flour food product
A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae.
Note, this was previously labelled "Bean (vegetable) food product". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope.
bean food product
berry food product
A broad bean food product is a product derived from the broad bean plant.
broad bean food product
cabbage juice food product
cattle cured meat food product
A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component.
food product component
cocoa beverage
common bean food product
cow milk based food product
cow milk dessert
cowpea vegetable food product
dairy dessert food product
fermented cereal beverage
food flavoring or seasoning product
linseed food product
flaxseed food product
food dressing product
frozen dairy dessert
frozen dairy food product
fruit salad food product
grain based vinegar food product
A food product made from legumes that are considered vegetables, such as immature raw legume pods or seeds.
leguminous vegetable food product
lupin
lupine bean food product
melon food product
milk dessert food product
millet food product
mollusk food product
mollusc food product
mustard food product
orange food product
A product containing primarily immature ripe pigeon peas.
pigeon pea vegetable food product
plant based bakery food product
plant-based candy
plant based refined or partially-refined food product
plant based salad food product
An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids.
plant fat or oil refined food product
A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product.
plant fruit as vegetable food product
plant product dressing
plant seed based bakery food product
plant seed vegetable food product
plant stem or spear vegetable food product
plant sweetener
preserved
food (preserved)
organ meat product
A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption.
prepared hen egg product
refined or partially-refined food product
salad food product
soft cheese food product
soybean condiment
soybean seed (field) food product
A soybean food product is a product derived from the soybean plant.
soy product
soybean food product
steeped beverage product
sweetener food product
pork cured meat food product
tomato juice food product
vegetable pickle food product
wine or wine-like food product
A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition)
food product by meal type
A food product consisting of food material derived primarily from a single organism.
food product by organism
Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience
food
foodstuff
nourishment
sustenance
This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/
food material
agave food product
multi-component honey product
A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process.
food product by quality
baked
baked food product
food (baked)
A food product consisting of food material derived from ingredients sourced from multiple organisms.
multi-ingredient
The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component?
multi-component food product
requires discussion
A preserved food, where the moisture levels in the food product have been reduced to low levels to improve shelf life.
https://orcid.org/0000-0002-8844-9165 | https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249
food (dessicated)
food (dehydrated)
A food product organized by the process which it results from.
food product by process
pork food product
A lipid food product is a food product made primarily of plant or animal fat or oil
fats and oils
oils and fats
lipid food product
A whole dried bean is a bean resulting from natural or mechanical air drying applied to a bean or bean pod.
dried bean
bean (whole, dried)
A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae).
Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet.
bean
bean (whole)
Cooked bean material is the bean material output of a cooking process applied to dry, rehydrated, or raw (fresh) beans.
bean (cooked)
A seed of a jack seed plant (Canavalia ensiformis).
jack bean
jack bean (whole)
jack-bean food product
A pigeon pea food product is a food product derived from the pigeon pea plant
pigeon pea food product
A seed of a pigeon pea plant (Cajanus cajan).
pigeon pea
pigeon pea (whole)
A seed of a velvet bean plant (Mucuna pruriens)
tericopelo bean
velvet bean
velvet bean (whole)
vetch food product
A seed of a vetch plant.
vetch seed
vetch seed (whole)
pea food product
A liver food product is a food product that derives from one or more liver organs.
liver food product
A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants.
bok choy vegetable food product
bomdong vegetable food product
broccolini vegetable food product
chinese cabbage vegetable food product
choy sum vegetable food product
collard greens vegetable food product
gai lan vegetable food product
komatsuna vegetable food product
mizuna vegetable food product
rutabaga vegetable food product
savoy cabbage vegetable food product
tatsoi vegetable food product
cole crop vegetable food product
cruciferous vegetable food product
brassica food product
multi-component wheat food product
A bean food product made from velvet bean.
velvet bean food product
A food product deriving from one or more animals.
animal food product
SIREN DB annotation: * has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)
sugar (granulated)
SIREN DB annotation: * has quality 'liquid, low viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430114) * derives from 'fruit, peel removed, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420229)
orange juice
A seed of a broad bean plant (Vicia faba).
Windsor bean
broad bean
broadbean
faba bean
fava bean
Horse bean
field bean
tic bean
tick bean
broad bean (whole)
SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)
vegetable juice food product
A bean substance is a substance made by processing seed from a bean plant.
Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc.
SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)
bean substance
A liquid prepared for consumption, or a product that can be combined with water or milk to make one.
beverage food product
SIREN DB annotation: * derives from 'part of animal' (http://purl.obolibrary.org/obo/FOODON_03420164)
animal-derived food
SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * derives from 'skeletal meat part, without bone or shell' (http://purl.obolibrary.org/obo/FOODON_03420125) * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)
beef (dehydrated)
desert preparation
dessert
SIREN DB annotation: * has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136)
dessert food
A cultured dairy product is a fermented dairy product in which a microbial starter was introduced to the fermentation process.
SIREN DB annotation: * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)
cultured dairy product
SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)
edible seed food product
SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) * has substance added 'honey added' (http://purl.obolibrary.org/obo/FOODON_03460149)
honey blend table syrup
SIREN DB annotation: * has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157)
sugar (refined)
SIREN DB annotation: * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)
food (dried)
SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)
fermented bean product
SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)
oil
processed food product
SIREN DB annotation: * has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)
pork (dehydrated)
SIREN DB annotation: * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913)
mammalian milk product
A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish.
SIREN DB annotation: * derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175)
fish product (unspecified species)
SIREN DB annotation: * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)
cocoa food product
juice
juice beverage
A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder.
sausage
SIREN DB annotation: * has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) * derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103) * has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)
sausage (whole)
SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103)
pate
SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * has quality 'heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440022) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) * formed as a result of 'steeping' (http://purl.obolibrary.org/obo/FOODON_03450036)
herbal infusion
SIREN DB annotation: * derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108)
sugar product
SIREN DB annotation: * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)
multi-component plant food product
SIREN DB annotation: * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)
vegetable fat food product
A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean).
SIREN DB annotation: * derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127)
meat (whole or parts)
Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog.
cheese or cheese product (us cfr)
Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products.
pie filling, fruit
fruit or fruit product (us cfr)
Food product having functional characteristics similar to milk or milk products, including cream product analogs, margarine, and milk analogs. Certain alternate ingredients are substituted for those components that are responsible for specific functional properties.
milk or milk product analog (us cfr)
Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*.
milk or milk product (us cfr)
Semisolid or jelled food prepared from fruit or fruit juice and other ingredients prescribed for the individual products (21 CFR 150).
fruit butter, jelly, preserve or related product (us cfr)
Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995]
dairy product (us cfr)
Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*).
natural cheese (us cfr)
Candy or other food product made with sweeteners and frequently containing nuts, fruits, starches, flavorings and other foods (21 CFR 170.3(n)(9). [FDA CFSAN 1995]
confectionery (us cfr)
Food product prepared by heating a mixture of sweeteners and other optional ingredients according to the specific formula for each subgroup.
candy (us cfr)
Jelled product made from one or more fruit juices and optional ingredients. Includes both fruit jelly, which may be sweetened with nutritive carbohydrate sweeteners, (21 CFR 150.140), and artificially sweetened fruit jelly (21 CFR 150.141). The finished fruit jelly must have a soluble solid content of no less than 65% and the ratio by weight of the fruit ingredient to sweetener in the starting mixture must be no less than 45:55. Artificially sweetened fruit jelly must contain no less than 55% fruit ingredient by weight.
fruit jelly (us cfr)
Soft candy prepared by boiling milk, sugar, salt and optional ingredients to the soft-ball stage (238 degrees F.).
fudge (us cfr)
Food product having functional characteristics similar to those of butter; it is in plastic form or liquid emulsion and contains not less than 80% fat whose origin is vegetable or rendered animal carcass fats or a mixture of these as well as other optional ingredients specified by 21 CFR 166.110.
margarine (us cfr)
Fruits and vegetables in all forms. [FDA CFSAN 1995]
fruit or vegetable product (us cfr)
Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995]
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
USA agency food product type
Candy prepared by cooking a mixture of water, sugars and optional ingredients to a temperature of 250 degrees F. or less.
soft candy (us cfr)
Food product having functional characteristics similar to a butter product; it may be nutritionally equivalent or inferior to the product it purports to resemble.
butter substitute
butter, imitation
imitation butter
butter product analog (us cfr)
Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008.
international agency food product type
European Union agency food product type
An agency food product type is a class of food product defined by an agency or consortium.
This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible.
agency food product type
Codex Alimentarius, Volume 2 - 1993, Section 2: Pesticide Residues in Food. The Codex Classification of food and animal feed commodities moving in trade and the description of the various items and groups of food and animal feedstuffs included in the present document have been developed by the Codex Committee on Pesticide Residues. It was first adopted by the 18th Session of the Codex Alimentarius Commission, (1989). The Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues. The Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set.
Codex Alimentarius classification of food and feed commodities
a. primary food commodities of plant origin (ccpr)
Vegetables are foods derived from many different kinds of plants mostly annual and usually cultivated, commonly known by custom and tradition as "vegetables". In several countries, some of these commodities grown on large areas are distinguished as "field crops" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables. Exposure to pesticides is dependent on the particular part of the plant used for food and the growing practices. Vegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods.
02 vegetables (ccpr)
Pulses are derived from the mature seeds naturally or artificially dried, of leguminous plants known as beans (dry) and peas (dry). The seeds in the pods are protected from most pesticides applied during the growing season except pesticides which show a systemic action. The dried beans and peas however are often exposed to post-harvest treatments. The dry pulses are consumed after processing or household cooking.
015 pulses (vd) (ccpr)
eurofir food classification
The group includes marine or freshwater fish, molluscs, crustaceans, and other fauna such as reptiles, insects or frogs not in the Meats group. The group also includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice.
seafood or related product (eurofir)
includes fish offal; a food product whose predominant constituent is fish (e.g. dried and salted fish, smoked fish, canned fish, pickled fish, restructured fish and fish analogues, surimi; fish paste, pâté).
seafood product (eurofir)
Alcoholic or non-alcoholic beverage; excludes milk and milk-based beverages.
beverage (non-milk) (eurofir)
Beverage containing no more than 0.5% alcohol; it may be flavoured, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices and vegetable juices.
non alcoholic beverage (eurofir)
Beverage prepared by extracting flavour and other components from food sources by percolation and/or immersion in water, usually at near-boiling temperature. The group includes coffee (e.g. instant coffee, coffee and chicory essence), tea, herbal tea (e.g. green tea, black tea, tisane), cocoa beverage and beverage powder.
infusion
steeped beverage
LanguaL curation note: Renamed from *COFFEE, TEA, COCOA (EUROFIR)* (LanguaL 2010).
coffee, tea, cocoa or infusion (eurofir)
EFG group 32, Eurocode-2 group 12.
LanguaL curation note: Use for foods and ingredients that could not fit into any of the above classes.
miscellaneous food product (eurofir)
This subgroup includes multicomponent meals, sauces, retail salads, desserts, soups, snacks and other foods where similarity of the product type is more significant than the source of the principal ingredient(s).
soup, sauce or miscellaneous food product
prepared food product (eurofir)
A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. Examples are egg and lemon soup, oxtail soup, fish soup, rice soup, lentil soup, minestrone, cherry soup.
soup (eurofir)
The Global System 1 (GS1) Global Product Classification (GPC) is a system that gives buyers and sellers a common language for grouping products in the same way, everywhere in the world.$br/$ The GS1 GPC classification in facet A is currently updated based on June 2017 release of GS1 GPC Standard for Food/Beverage/Tobacco, except for codes pertaining to tobacco. See the GS1 site for details [https://www.gs1.org/standards/gpc].
GS1 Global Product Classification (GPC)
50220000 - cereal/grain/pulse products (gs1 gpc)
50221200 - processed cereal products (gs1 gpc)
50190000 - prepared/preserved foods (gs1 gpc)
50192900 - pasta/noodles (gs1 gpc)
Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL.
U.S. code of federal regulations, title 21 food product type
polysaccharide-producing plant
plant used for producing extract or concentrate
starch-producing plant
carbohydrate-producing plant
amorphophallus konjac
amorphophallus rivieri
hydrosme rivieri
leopard palm
devils tongue plant
amorphophallus rivieri var. konjac
konjac plant
A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary.
sugar
Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide.
carbohydrate extract, concentrate, or isolate
Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture.
brown sugar
A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed.
Damion Dooley's note: Items in this branch will be merged into foodon food product branch.
extract, concentrate or isolate of plant or animal
The serum or watery part of milk that is separated from the thicker or more coagulable part or curd, espcially in the process of making cheese; it contains lactose, minerals and lactalbumin.
whey
mammalian milk whey
The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM
seed oil
A liquid that flows very easily at room temperature. Examples are: water, apple juice, sherry, acidophilus milk, whipping cream and some heavy liqueurs. The range of low viscosity liquid spans sucrose solutions between 0 and 45% solids (viscosity range from 1 to 10 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food.
liquid, thin
food (liquid, low viscosity)
A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*.
fluid
SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)
food (liquid)
This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred.
nut or seed added
LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance.
plant seed or nut food product
chocolate or cocoa added
LanguaL curation note: Used when chocolate or cocoa is added at any level or when chocolate is used as a coating.
chocolate or cocoa
A fat or oil derived from vegetable material
vegetable fat or oil added
This is a convenience class inherited from LanguaL
vegetable fat or oil
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
mitotic sister-chromatid adhesion release
The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
microtubule cytoskeleton organization and biogenesis
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
multicellular organismal polysaccharide catabolic process
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
A ribosome contained within a subcellular membrane-bounded organelle.
The joining of 2 or more lipid bilayer membranes that surround the nucleus.
The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.
The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
syncytium formation by plasma membrane fusion
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
A compact and highly condensed form of chromatin that is refractory to transcription.
The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets.
The developmental process in which the size or shape of a cell is generated and organized.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.
This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
blood vessel formation from pre-existing blood vessels
The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
Any process that modulates the frequency, rate, extent or direction of cell growth.
The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
branching involved in blood vessel morphogenesis
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
A process that results in a parallel arrangement of microtubules.
The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure.
A homeostatic process in which an organism modulates its internal body temperature.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%.
Cell migration that is accomplished by extension and retraction of a pseudopodium.
Note that this term refers to a mode of migration rather than to any particular cell type.
The nucleus of the female germ cell, a reproductive cell in females.
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation ternary complex assembly
formation of translation initiation ternary complex
The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.
embryonic development via the syncytial blastoderm
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
The formation of the ectoderm, mesoderm and endoderm during gastrulation.
The formation of ectoderm during gastrulation.
The formation of the endoderm during gastrulation.
The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The initial developmental process that will lead to the formation of an eye.
The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster.
The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell.
compound eye photoreceptor cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms.
The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes.
The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus.
Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus.
The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.
The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS5, embryo ; EMAP:23', 'TS5, inner cell mass ; EMAP:24' and 'TS5, trophectoderm; EMAP:28'.
The initial formation of a blastocyst from a solid ball of cells known as a morula.
See also the Anatomical Dictionary for Mouse Development ontology term 'TS3, compacted morula ; EMAP:9'.
The process in which a relatively unspecialized cell acquires specialized features of an inner cell mass cell.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14'.
The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19'.
The morphogenesis of trophectoderm cells.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'.
An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, blastocoelic cavity ; EMAP:17', 'TS5, blastocoelic cavity ; EMAP:27' and 'TS6, blastocoelic cavity ; EMAP:36'.
The proliferation of cells in the inner cell mass.
See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14' and 'TS5, inner cell mass ; EMAP:24'.
The proliferation of cells in the trophectoderm.
A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
mesenchymal cell differentiation from epithelial cell
The morphogenesis of an embryonic epithelium into a tube-shaped structure.
The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue.
The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system.
The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species.
defined as response to Saccharomycotina (true yeasts). This excludes fission yeast.
The progression of an endothelial cell over time, from its formation to the mature structure.
The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
Any process that modulates the frequency, rate, or extent of endothelial cell proliferation.
regulation of endothelial cell proliferation
Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
down regulation of endothelial cell proliferation
down-regulation of endothelial cell proliferation
downregulation of endothelial cell proliferation
inhibition of endothelial cell proliferation
negative regulation of endothelial cell proliferation
Any process that activates or increases the rate or extent of endothelial cell proliferation.
up regulation of endothelial cell proliferation
up-regulation of endothelial cell proliferation
upregulation of endothelial cell proliferation
activation of endothelial cell proliferation
stimulation of endothelial cell proliferation
positive regulation of endothelial cell proliferation
The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state.
Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter.
up regulation of neurotransmitter secretion
up-regulation of neurotransmitter secretion
upregulation of neurotransmitter secretion
activation of neurotransmitter secretion
stimulation of neurotransmitter secretion
positive regulation of neurotransmitter secretion
Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells.
An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division.
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
Any process that modulates the frequency or rate of heart contraction.
Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the rate of neuroblast proliferation.
up regulation of neuroblast proliferation
up-regulation of neuroblast proliferation
upregulation of neuroblast proliferation
positive regulation of neuroblast proliferation
The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
up regulation of mesenchymal cell proliferation
up-regulation of mesenchymal cell proliferation
upregulation of mesenchymal cell proliferation
activation of mesenchymal cell proliferation
stimulation of mesenchymal cell proliferation
positive regulation of mesenchymal cell proliferation
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
columnar/cuboidal epithelial cell differentiation
The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
columnar/cuboidal epithelial cell development
The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
glandular epithelial cell differentiation
The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell to attain its fully functional state. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
columnar/cuboidal epithelial cell maturation
The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
The developmental process, independent of morphogenetic (shape) change, that is required for a glandular epithelial cell to attain its fully functional state. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus.
optic cup morphogenesis involved in camera-style eye development
optic cup morphogenesis involved in camera-type eye development
Any process that prevents the activation of neuroepithelial cell differentiation. Neuroepithelial cell differentiation is the process in which epiblast cells acquire specialized features of neuroepithelial cells.
negative regulation of neural plate formation
repression of premature neural plate formation
inhibition of neuroepithelial cell differentiation
A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
regulation of respiratory gaseous exchange by neurological system process
regulation of respiratory gaseous exchange by nervous system process
The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters.
The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
haematopoietic progenitor cell differentiation
haemopoietic progenitor cell differentiation
hemopoietic progenitor cell differentiation
hematopoietic progenitor cell differentiation
An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues.
organ or tissue specific immune response
Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation.
The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages.
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
An immune response taking place in the liver.
Any process involved in the carrying out of an immune response by a leukocyte.
Any process involved in the carrying out of an immune response by a myeloid leukocyte.
myeloid leucocyte immune effector process
myeloid leukocyte immune effector process
The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
Any process that modulates the frequency, rate, or extent of an immune system process.
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
down regulation of immune system process
down-regulation of immune system process
negative regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
positive regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune effector process.
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process.
down regulation of immune effector process
down-regulation of immune effector process
downregulation of immune effector process
negative regulation of immune effector process
Any process that activates or increases the frequency, rate, or extent of an immune effector process.
up regulation of immune effector process
up-regulation of immune effector process
positive regulation of immune effector process
Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity.
regulation of immune cell mediated immunity
regulation of leucocyte mediated immunity
regulation of leukocyte mediated immunity
Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity.
down regulation of leukocyte mediated immunity
down-regulation of leukocyte mediated immunity
downregulation of leukocyte mediated immunity
negative regulation of immune cell mediated immunity
negative regulation of leucocyte mediated immunity
inhibition of leukocyte mediated immunity
negative regulation of leukocyte mediated immunity
Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity.
positive regulation of immune cell mediated immunity
positive regulation of leucocyte mediated immunity
up regulation of leukocyte mediated immunity
up-regulation of leukocyte mediated immunity
upregulation of leukocyte mediated immunity
activation of leukocyte mediated immunity
stimulation of leukocyte mediated immunity
positive regulation of leukocyte mediated immunity
Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation.
regulation of myeloid leukocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation.
down regulation of myeloid leukocyte differentiation
down-regulation of myeloid leukocyte differentiation
downregulation of myeloid leukocyte differentiation
inhibition of myeloid leukocyte differentiation
negative regulation of myeloid leukocyte differentiation
Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation.
up regulation of myeloid leukocyte differentiation
up-regulation of myeloid leukocyte differentiation
upregulation of myeloid leukocyte differentiation
activation of myeloid leukocyte differentiation
stimulation of myeloid leukocyte differentiation
positive regulation of myeloid leukocyte differentiation
The controlled release of a peptide from a cell or a tissue.
Any process that modulates the frequency, rate, or extent of peptide secretion.
Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion.
negative regulation of peptide secretion
Any process that activates or increases the frequency, rate, or extent of peptide secretion.
positive regulation of peptide secretion
Any process that modulates the frequency, rate, or extent of a response to biotic stimulus.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to biotic stimulus
Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus.
down regulation of response to biotic stimulus
down-regulation of response to biotic stimulus
downregulation of response to biotic stimulus
inhibition of response to biotic stimulus
negative regulation of response to biotic stimulus
Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus.
up regulation of response to biotic stimulus
up-regulation of response to biotic stimulus
upregulation of response to biotic stimulus
activation of response to biotic stimulus
stimulation of response to biotic stimulus
positive regulation of response to biotic stimulus
Any process that modulates the frequency, rate, or extent of myeloid leukocyte mediated immunity.
regulation of myeloid leukocyte mediated immunity
Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte mediated immunity.
down regulation of myeloid leukocyte mediated immunity
down-regulation of myeloid leukocyte mediated immunity
downregulation of myeloid leukocyte mediated immunity
inhibition of myeloid leukocyte mediated immunity
negative regulation of myeloid leukocyte mediated immunity
Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte mediated immunity.
up regulation of myeloid leukocyte mediated immunity
up-regulation of myeloid leukocyte mediated immunity
upregulation of myeloid leukocyte mediated immunity
activation of myeloid leukocyte mediated immunity
stimulation of myeloid leukocyte mediated immunity
positive regulation of myeloid leukocyte mediated immunity
The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move.
The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment.
A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring.
developmental process involved in reproduction
The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers.
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal.
The directed movement of sodium ions (Na+) by the renal system.
Any process that mediates the transfer of information from mesodermal cells to endodermal cells.
Any process that mediates the transfer of information from endodermal cells to mesodermal cells.
The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field.
The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis.
embryonic heart tube formation via epithelial folding
The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract.
The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum.
The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum.
The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation.
morphogenesis of an epithelial fold involved in embryonic heart tube formation
Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment.
The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat.
cardiac impulse conducting system development
The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system.
The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node.
The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle.
cardiac Purkinje fiber cell differentiation
The process in which the anatomical structures of veins of the heart are generated and organized.
The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart.
The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart.
The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart.
The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart.
The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The process in which the left cardiac atrium is generated and organized.
The process in which the right cardiac atrium is generated and organized.
The process in which the left cardiac ventricle is generated and organized.
The process in which the right cardiac ventricle is generated and organized.
The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts.
The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts.
The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts.
The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts.
The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized.
left ventricular myocardium morphogenesis
left ventricular cardiac muscle tissue morphogenesis
The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized.
right ventricle myocardium morphogenesis
right ventricular cardiac muscle tissue morphogenesis
The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized.
ventricular trabecula myocardium morphogenesis
The process in which the anatomical structures of cardiac left ventricular trabecular myocardium are generated and organized.
left ventricular trabecular myocardium morphogenesis
The process in which the anatomical structures of the right ventricular myocardium are generated and organized.
right ventricular trabecular myocardium morphogenesis
The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure.
atrial cardiac muscle tissue development
The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure.
ventricular cardiac muscle tissue development
The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.
Developmental growth that contributes to the shaping of the heart.
The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart.
cardiac muscle tissue growth involved in heart morphogenesis
The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle.
The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
cell migration involved in endocardial cushion formation
Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries.
apoptosis involved in outflow tract morphogenesis
apoptotic process involved in outflow tract morphogenesis
Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
apoptosis involved in endocardial cushion morphogenesis
apoptotic process involved in endocardial cushion morphogenesis
Any apoptotic process that contributes to the shaping of the heart.
apoptosis involved in heart morphogenesis
apoptotic process involved in heart morphogenesis
The progression of a cardiac septum over time, from its initial formation to the mature structure.
The progression of the ventricular septum over time from its formation to the mature structure.
The progression of the atrial septum over time, from its initial formation to the mature structure.
The process in which an endocardial cushion cell becomes a cell of a cardiac septum.
The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development.
The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart.
physiological cardiac muscle hypertrophy
The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic A cell. A pancreatic A cell is a cell in the pancreas that secretes glucagon.
The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin.
The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic polypeptide-producing cell. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide.
pancreatic polypeptide-producing cell differentiation
The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The process in which the anatomical structures of the heart rudiment are generated and organized.
The developmental process pertaining to the initial formation of the heart rudiment.
The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon.
The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin.
The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide.
The process in which an amino acid is transported across a membrane.
Note that this term is not intended for use in annotating lateral movement within membranes.
The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum.
The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme.
The process in which the anatomical structure of the pericardium is generated and organized.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell.
cardiac endothelial cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron, a neuron that secretes noradrenaline.
norepinephrine secreting neuron differentiation
The process whose specific outcome is the progression of a noradrenergic neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
norepinephrine secreting neuron development
The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord.
The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron that is part of the brainstem.
noradrenergic neuron differentiation involved in brainstem development
The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell.
establishment of cell polarity involved in ameboidal cell migration
Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell.
establishment or maintenance of cytoskeleton polarity involved in ameboidal cell migration
The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation.
establishment of cell polarity involved in gastrulation cell migration
Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell taking part in gastrulation.
establishment or maintenance of cytoskeleton polarity involved in gastrulation
The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation.
epithelial cell morphogenesis involved in gastrulation
The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.
The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.
The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.
The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye.
cell motility involved in camera-type eye morphogenesis
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.
chondrocyte differentiation involved in endochondral bone morphogenesis
The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized.
chondrocyte morphogenesis involved in endochondral bone morphogenesis
The increase in size or mass of an endochondral bone that contributes to the shaping of the bone.
The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone.
chondrocyte development involved in endochondral bone morphogenesis
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
This is the same as GO molecular function
gene product or complex activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the hydrolysis of ester linkages within nucleic acids.
Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
caspase-activated deoxyribonuclease activity
Long-range resection of DNA DSBs by EXO1 or DNA2
DNA nucleases unhook the interstrand crosslink (ICL)
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
ISGylation of protein phosphatase 1 beta (PP2CB)
Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
Nuclear VBC complex ubiquitinylates HIF-alpha
Ubiquitination of p130 (RBL2) by SCF (Skp2)
K63-linked ubiquitination of RIP1 bound to the activated TLR complex
Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling
Multiubiquitination of APC/C-associated Cdh1
Ubiquitination of Cyclin A by APC/C:Cdc20 complex
Ubiquitination of Securin by phospho-APC/C:Cdc20 complex
Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex
Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex
Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex
Ubiquitination of stimulated EGFR (CBL:GRB2)
CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix
CBL binds and ubiquitinates phosphorylated Sprouty
Ubiquitination of NOTCH1 by ITCH in the absence of ligand
CHIP (STUB1) mediates ubiquitination of ERBB2
NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1
Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling
Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex
SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7
Ubiquitination of DLL/JAG ligands upon binding to NOTCH2
Ubiquitination of SKI/SKIL by RNF111/SMURF2
Autoubiquitination of phospho-COP1(Ser-387 )
RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants
Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants
SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA
STING ubiquitination by TRIM32 or TRIM56
DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1
NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2
NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1
Cdh1:APC/C ubiquitinates EHMT1 and EHMT2
Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)
BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation
Parkin promotes the ubiquitination of mitochondrial substrates
SYVN1 ubiquitinates Hh C-terminal fragments
Hh processing variants are ubiquitinated
SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP
beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex
RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA
cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK
SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2
SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2
TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains
The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1
RIP2 induces K63-linked ubiquitination of NEMO
DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3
VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
Ubiquitination of DLL/JAG ligands upon binding to NOTCH3
Auto-ubiquitination of TRAF3 within activated TLR3 complex
RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS
Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2
Activated TRAF6 synthesizes unanchored polyubiquitin chains
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation
Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation
Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer
BRCA1:BARD1 heterodimer autoubiquitinates
TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex
Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane
MIB2 ubiquitinates RIPK1 at K377, K604, K634
STUB1 ubiquitinates RIPK1 at K571, K604, K627
SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex
Transfer of Ub from E2 to substrate and release of E2
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
Virion-associated M2 protein mediated ion infusion
SMAD7:SMURF1 complex is exported to the cytosol
Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group.
amine/polyamine transmembrane transporter activity
amino acid-polyamine transmembrane transporter activity
amine transmembrane transporter activity
Enables the transfer of acetylcholine from one side of a membrane to the other. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.
acetylcholine transmembrane transporter activity
Loading of acetylcholine in synaptic vesicles
Enables the transfer of dicarboxylic acids from one side of a membrane to the other. A dicarboxylic acid is an organic acid with two COOH groups.
sodium:dicarboxylate/tricarboxylate symporter activity
dicarboxylate (succinate/fumarate/malate) antiporter activity
dicarboxylic acid transmembrane transporter activity
Sulfate is exported to the cytosol in exchange for dicarboxylate
SLC25A10 mediates exchange of malate and phosphate
Enables the directed movement of lipids into, out of or within a cell, or between cells.
ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex
ABCA12 transports lipids from cytosol to extracellular region
Defective ABCA12 does not transport lipids from cytosol to extracellular region
Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body
ABCA3 transports PC, PG from ER membrane to lamellar body
TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane
ABCA5 transports CHOL from lysosomal lumen to cytosol
MTTP lipidates APOB-100, forming a pre-VLDL
Enables the directed movement of a neurotransmitter into, out of or within a cell, or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
neurotransmitter transmembrane transporter activity
Noradrenaline clearance from the synaptic cleft
Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage.
organic acid transmembrane transporter activity
Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other.
lactose/glucose efflux transporter activity
galactose/glucose (methylgalactoside) porter activity
glucose transmembrane transporter activity
Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2
SLC2A1 tetramer transports Glc from cytosol to Golgi lumen
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
Any triple helical collagen trimer that forms fibrils.
A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes.
A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer.
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
cell nucleus
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
The volume enclosed within the vacuolar membrane.
A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
Note that this definition includes vesicles that are transiently associated with the Golgi.
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules.
Any microtubule in the nucleus of a cell.
Any microtubule in the cytoplasm of a cell.
non-spindle-associated astral microtubule
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.
A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
multicellular organismal polysaccharide metabolic process
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
regulation of glycogen biosynthetic process
The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
regulation of glycogen catabolic process
The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.
The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.
The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
The chemical reactions and pathways resulting in the breakdown of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.
The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways involving acetate, the anion of acetic acid.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
regulation of carbohydrate metabolic process
Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
regulation of glucose biosynthetic process
regulation of gluconeogenesis involved in cellular glucose homeostasis
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
DNA fragmentation involved in apoptotic nuclear change
endonucleolytic DNA catabolic process involved in apoptosis
DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA.
establishment or maintenance of chromatin architecture
DNA replication-independent chromatin assembly
DNA replication-independent chromatin organization
DNA replication-independent nucleosome organisation
DNA replication-independent nuclesome assembly
transcription-coupled nucleosome assembly
The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
A process in which RNA is transported to, or maintained in, a specific location.
establishment and maintenance of RNA localization
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
Any process that modulates the frequency, rate or extent of translational initiation.
Any process that modulates the frequency, rate, extent or accuracy of translational elongation.
Any process that modulates the frequency, rate or extent of translational termination.
The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
cellular amino acid and derivative metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.
regulation of cellular amino acid metabolic process
The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
cellular biogenic amine metabolic process
The chemical reactions and pathways resulting in the breakdown of acetylcholine, the acetic acid ester of the organic base choline.
The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.
The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular aromatic compound metabolic process
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate-containing compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.
di-, tri-valent inorganic cation transport
The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
mitochondrial sodium/calcium ion exchange
sodium channel auxiliary protein activity
The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems.
The directed movement of acetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of acetate across a plasma membrane.
The transport of substances that occurs outside cells.
The directed extracellular movement of amino acids.
The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
copper-induced intracellular protein transport
A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.
The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
Golgi to plasma membrane vesicle-mediated transport
The directed movement of substances from the Golgi to the vacuole.
Golgi to vacuole vesicle-mediated transport
The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo.
Fusion of the membrane of a transport vesicle with its target membrane.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
cellular component disassembly involved in apoptotic process
cellular component disassembly involved in apoptosis
cellular component disassembly involved in execution phase of apoptosis
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
Any process that modulates the frequency, rate or extent of muscle contraction.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
Any process that modulates the frequency, rate or extent of smooth muscle contraction.
A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope.
Any process that modulates the frequency, rate or extent of striated muscle contraction.
regulation of striated muscle contraction
The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
nuclear envelope organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
plasma membrane organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cytoskeletal organization and biogenesis
cytoskeleton organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
regulation of actin filament localization
Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
The removal of tubulin heterodimers from one or both ends of a microtubule.
microtubule depolymerization during nuclear congression
The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
down regulation of microtubule depolymerization
down-regulation of microtubule depolymerization
downregulation of microtubule depolymerization
negative regulation of microtubule disassembly
inhibition of microtubule depolymerization
negative regulation of microtubule catastrophe
negative regulation of microtubule depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme.
negative regulation of microtubule depolymerization in axoneme
negative regulation of axonemal microtubule depolymerization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
The directed movement of substances into, out of or within a vacuole.
The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.
protein catabolic process in the vacuole
The aggregation, arrangement and bonding together of a set of components to form a junction between cells.
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis.
Any process that modulates the frequency, rate or extent of mitosis.
The directed movement of the nucleus to a specific location within a cell.
establishment of cell nucleus localization
establishment of localization of nucleus
A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins.
A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline.
Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiotic nuclear division; GO:0140013'.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
establishment and/or maintenance of cell polarity
establishment and/or maintenance of cell polarization
establishment or maintenance of cell polarity
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission.
A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin.
The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
Note that this term was 'developmental process'.
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction.
Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster.
The synthesis, deposition, and organization of the materials in a cell of an ovary; where the cell can then undergo meiosis and form an ovum. An example of this is found in Drosophila melanogaster.
Any process that modulates the rate or extent of progress through the mitotic cell cycle.
modulation of mitotic cell cycle progression
regulation of mitotic cell cycle progression
regulation of progression through mitotic cell cycle
A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron.
Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts.
down regulation of neuroblast proliferation
down-regulation of neuroblast proliferation
downregulation of neuroblast proliferation
negative regulation of neuroblast proliferation
The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the ectodermal digestive tract over time, from its formation to the mature structure. The ectodermal digestive tract includes those portions that are derived from ectoderm.
The process in which the anatomical structures of the foregut are generated and organized.
The process in which the anatomical structures of the hindgut are generated and organized.
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
The establishment of the sex of an organism by physical differentiation.
The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
respiratory gaseous exchange by respiratory system
The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
The controlled release of a fluid by a cell or tissue in an animal.
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
locomotory behavioral response to stimulus
locomotory behavioural response to stimulus
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
Enables the transfer of monocarboxylic acids from one side of a membrane to the other. A monocarboxylic acid is an organic acid with one COOH group.
prostaglandin/thromboxane transporter activity
monocarboxylic acid transmembrane transporter activity
SLC5A8 transports monocarboxylates from extracellular region to cytosol
SLC16A3,7,8 cotransport monocarboxylates, H+ from extracellular region to cytosol
Defective SLC16A1 does not cotransport monocarboxylates, H+ from extracellular region to cytosol
SLC16A1:BSG cotransports monocarboxylates, H+ from extracellular region to cytosol
The directed movement of organelles or molecules along microtubules in neuron projections.
Any process in which a protein is transported to, or maintained in, a specific location.
establishment and maintenance of asymmetric protein localization
establishment and maintenance of protein localization
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
A biological process is an evolved process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms.
The directed movement of sulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
Any process that activates or increases the rate or extent of cell proliferation.
positive regulation of cell proliferation
positive regulation of cell population proliferation
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
negative regulation of cell proliferation
negative regulation of cell population proliferation
The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
The chemical reactions and pathways resulting in the formation of acetylcholine, the acetic acid ester of the organic base choline.
Enables the transfer of a protein from one side of a membrane to the other.
protein transmembrane transporter activity
TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space
TIMM23 PAM translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix
Monoubiquitinated N-myristoyl GAG polyprotein is targeted to the late endosomal vesicle membrane by the ESCRT-I complex
Pink1 is recruited from the cytoplasm to the mitochondria
pagA(197-794):ANTRX2 oligomer transports cya and lef (target cell endosome to cytosol)
pagA(197-794):ANTRX1 oligomer transports cya and lef (target cell endosome to cytosol)
tetX HC transports tetX LC from target cell endosome membrane into cytosol
AP4 transports APP from trans-Golgi network to endosome lumen
botB HC transports botB LC from target cell synaptic vesicle membrane into cytosol
botA HC transports botA LC from target cell synaptic vesicle membrane into cytosol
botE HC transports botE LC from target cell synaptic vesicle membrane into cytosol
botC HC transports botC LC from target cell synaptic vesicle membrane to cytosol
botD HC transports botD LC from target cell synaptic vesicle membrane into cytosol
botF HC transports botF LC from target cell synaptic vesicle membrane into cytosol
botG HC transports botG LC from target cell synaptic vesicle membrane into cytosol
DT fragment B transports DT fragment A from target cell endosome membrane
SecA2 transports SapM from cytoplasm to cytosol
Enables the transfer of cation from one side of a membrane to the other.
cation transmembrane transporter activity
transmembrane cation transporter activity
monoatomic cation transmembrane transporter activity
The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.
The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
Enables the transfer of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), from one side of a membrane to the other.
monoamine transmembrane transporter activity
Loading of dopamine into synaptic veiscles
SLC6A3 cotransports DA, Na+ from extracellular region to cytosol
loading of Serotonin in synaptic vesicles
VMAT1/2 can mediate the transport of biogenic amines
Defective SLC6A3 does not cotransport DA, Na+ from extracellular region to cytosol
Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
organic anion transmembrane transporter activity
Growing HA is extruded from the cell by ABCC5
OAT1-3 transport organic anions with antiport of dicarboxylic acids
SLC22A8 transports Cipro into renal cell
The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster.
The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
cellular amino acid biosynthetic process
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
multicellular organismal catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
multicellular organismal macromolecule catabolic process
cellular macromolecule catabolic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
multicellular organismal biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues.
The controlled release of proteins from a cell.
protein secretion during cell fate commitment
protein secretion resulting in cell fate commitment
The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
response to electromagnetic radiation stimulus
Note that 'radiation' refers to electromagnetic radiation of any wavelength.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
catechol-containing compound metabolic process
The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent.
catechol-containing compound biosynthetic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
Any process that modulates the frequency, rate or extent of asymmetric cell division.
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
embryo development ending in birth or egg hatching
The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
The chemical reactions and pathways resulting in the breakdown of alkaloids, nitrogen containing natural products not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
negative regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
negative regulation of organismal metabolism
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
negative regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
positive regulation of metabolic process
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
negative regulation of catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
positive regulation of catabolic process
The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis.
The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
anterior/posterior pattern specification
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
negative regulation of signaling pathway
negative regulation of signalling pathway
negative regulation of signal transduction
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete.
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell.
The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
Compaction of chromatin structure prior to meiosis in eukaryotic cells.
chromosome condensation involved in meiotic cell cycle
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
process resulting in tolerance to organic substance
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
The division of the zygote into two daughter cells that will adopt developmentally distinct potentials.
The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues.
The process in which the anatomical structures of the soma are generated and organized.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.
Any process that modulates the frequency, rate or extent of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
negative regulation of cell fate commitment
Any process that activates, maintains or increases the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
positive regulation of cell fate commitment
The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
regulation of mesenchymal cell proliferation
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals.
Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells.
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis.
The movement of substances between cells.
Any process that modulates the frequency, rate or extent of membrane disassembly.
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule biosynthetic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule biosynthetic process
Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
regulation of glycoprotein biosynthetic process
Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
positive regulation of glycoprotein biosynthetic process
Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
negative regulation of glycoprotein biosynthetic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
positive regulation of phosphorus metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
negative regulation of phosphorus metabolic process
Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
regulation of cellular ketone metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells.
regulation of ketone biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells.
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
posttranscriptional regulation of gene expression
post-transcriptional regulation of gene expression
Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
regulation of cardiac muscle hypertrophy
Any process that modulates the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
positive regulation of cardiac muscle hypertrophy
Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
negative regulation of cardiac muscle hypertrophy
Any process that increases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
positive regulation of cardiac muscle adaptation
Any process that decreases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
negative regulation of cardiac muscle adaptation
The activation of endogenous cellular processes that result in the death of a cell as part of its development.
programmed cell death involved in development
This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure.
programmed cell death involved in cell development
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation.
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
positive regulation of organelle organisation
positive regulation of organelle organization and biogenesis
positive regulation of organelle organization
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
negative regulation of organelle organisation
negative regulation of organelle organization and biogenesis
negative regulation of organelle organization
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of cell communication
Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
negative regulation of muscle cell apoptosis
negative regulation of muscle cell apoptotic process
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations.
A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
regulation of muscle cell apoptotic process
Any process that increases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death.
positive regulation of muscle cell apoptosis
positive regulation of muscle cell apoptotic process
Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
regulation of striated muscle cell apoptosis
regulation of striated muscle cell apoptotic process
Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
positive regulation of striated muscle cell apoptosis
positive regulation of striated muscle cell apoptotic process
Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
down regulation of striated muscle cell apoptosis
down-regulation of striated muscle cell apoptosis
downregulation of striated muscle cell apoptosis
inhibition of striated muscle cell apoptosis
negative regulation of striated muscle cell apoptosis
negative regulation of striated muscle cell apoptotic process
Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
regulation of cardiac muscle cell apoptosis
regulation of cardiac muscle cell apoptotic process
Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
positive regulation of cardiac muscle cell apoptosis
positive regulation of cardiac muscle cell apoptotic process
Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
down regulation of cardiac muscle cell apoptosis
down-regulation of cardiac muscle cell apoptosis
downregulation of cardiac muscle cell apoptosis
inhibition of cardiac muscle cell apoptosis
negative regulation of cardiac muscle cell apoptosis
negative regulation of cardiac muscle cell apoptotic process
The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate.
Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine.
negative regulation of norepinephrine secretion
Any process that increases the frequency, rate or extent of the regulated release of norepinephrine.
positive regulation of norepinephrine secretion
Any process that modulates the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.
regulation of collagen catabolic process
Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.
down regulation of collagen catabolic process
down-regulation of collagen catabolic process
downregulation of collagen catabolic process
negative regulation of collagen breakdown
negative regulation of collagen catabolism
negative regulation of collagen degradation
inhibition of collagen catabolic process
negative regulation of collagen catabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
regulation of collagen metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
negative regulation of collagen metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
positive regulation of collagen metabolism
positive regulation of collagen metabolic process
Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
regulation of extracellular matrix breakdown
regulation of extracellular matrix degradation
regulation of extracellular matrix disassembly
Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
down regulation of extracellular matrix disassembly
down-regulation of extracellular matrix disassembly
downregulation of extracellular matrix disassembly
negative regulation of extracellular matrix breakdown
negative regulation of extracellular matrix degradation
inhibition of extracellular matrix disassembly
negative regulation of extracellular matrix disassembly
Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
regulation of epithelial to mesenchymal transition
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
positive regulation of epithelial to mesenchymal transition
Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
negative regulation of epithelial to mesenchymal transition
Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of sodium ion transport
Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of sodium ion transport
Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
positive regulation of cell morphogenesis
Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
negative regulation of cell morphogenesis
Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action.
Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of glucose transmembrane transport
Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of glucose transport
positive regulation of glucose transmembrane transport
Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of glucose transport
negative regulation of glucose transmembrane transport
Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
positive regulation of myotube differentiation
Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
negative regulation of myotube differentiation
The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
Any process in which a lipid is transported to, or maintained in, a specific location.
Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
positive regulation of steroid biosynthetic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
negative regulation of steroid biosynthetic process
Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
positive regulation of glucose metabolism
positive regulation of glucose metabolic process
The cellular component assembly that is part of the initial shaping of the component during its developmental progression.
cellular component assembly involved in morphogenesis
Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization.
regulation of cytoplasmic microtubule depolymerization
The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule.
cytoplasmic microtubule depolymerization
Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
negative regulation of cell cycle process
Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
regulation of glucan biosynthetic process
Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.
The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity.
establishment of localization by movement along microtubule
Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
regulation of neuron projection development
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
positive regulation of neurite biosynthesis
positive regulation of neurite development
positive regulation of neurite formation
positive regulation of neuron projection development
Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
negative regulation of neurite biosynthesis
negative regulation of neurite development
negative regulation of neurite formation
negative regulation of neuron projection development
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
The lipid bilayer surrounding any membrane-bounded vesicle in the cell.
The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others.
Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia.
Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia.
Any process that activates or increases the frequency, rate or extent of gliogenesis, the formation of mature glia.
The process in which a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts.
The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron.
The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube.
The formation of a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts.
The formation of a thickened region of the neurectoderm that is roughly triangular in cross section. The neural keel develops from the neural plate and develops into the neural rod. Neural keel formation occurs during primary neurulation in teleosts.
The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column.
The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell.
Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change.
Any process that activates or increases the frequency, rate or extent of neuron maturation.
positive regulation of neuron maturation
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron maturation.
negative regulation of neuron maturation
The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS).
acetylcholine secretion, neurotransmission
Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine.
regulation of acetylcholine secretion, neurotransmission
Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine.
up regulation of acetylcholine secretion
up-regulation of acetylcholine secretion
positive regulation of acetylcholine secretion, neurotransmission
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine.
down regulation of acetylcholine secretion
down-regulation of acetylcholine secretion
downregulation of acetylcholine secretion
negative regulation of acetylcholine secretion, neurotransmission
Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine.
Any process that modulates the frequency, rate or extent of the regulated release of serotonin.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin.
positive regulation of serotonin release
negative regulation of serotonin secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin.
positive regulation of serotonin secretion
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells.
Any process in which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
regulation of skeletal muscle plasticity
regulation of skeletal muscle adaptation
The enlargement or overgrowth of all or part of an organ due to an increase in size (not length) of individual muscle fibers without cell division. In the case of skeletal muscle cells this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils.
Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hypertrophy.
negative regulation of muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of muscle hypertrophy.
positive regulation of muscle hypertrophy
Any process that modulates the frequency, rate or extent of muscle hypertrophy.
Any process that activates or increases the frequency, rate or extent of muscle adaptation.
positive regulation of muscle plasticity
positive regulation of muscle adaptation
Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle adaptation.
negative regulation of muscle plasticity
negative regulation of muscle adaptation
Any process in which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
Any process that modulates the frequency, rate or extent of somitogenesis.
Any process that modulates the frequency, rate or extent of skeletal muscle contraction.
regulation of skeletal muscle contraction
A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the intestine. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The intestine is the section of the alimentary canal from the stomach to the anal canal. It includes the large intestine and small intestine.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract).
gastro-intestinal system smooth muscle contraction
Any process that modulates the frequency, rate or extent of skeletal muscle contraction by variation of the pattern of stimulation by nervous system.
regulation of skeletal muscle contraction by neural stimulation via neuromuscular junction
The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle.
The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population.
Any process that modulates the frequency, rate or extent of skeletal muscle cell proliferation.
regulation of skeletal muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of skeletal muscle cell proliferation.
positive regulation of skeletal muscle cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle cell proliferation.
negative regulation of skeletal muscle cell proliferation
The regulated release of neurotransmitter into the synaptic cleft involved in skeletal muscle contraction. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin.
neurotransmitter secretion involved in control of skeletal muscle contraction
neurotransmitter secretion involved in regulation of skeletal muscle contraction
Any process that modulates the frequency, rate or extent of skeletal muscle contraction by depolarization of muscle membrane and ionic fluxes.
regulation of skeletal muscle contraction via membrane action potential
regulation of skeletal muscle contraction via regulation of action potential
The process whose specific outcome is the progression of the skeletal myofibril over time, from its formation to the mature structure. A skeletal myofibril is a myofibril specific to skeletal muscle cells.
The process resulting in the physical partitioning and separation of a myoblast into daughter cells. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. This occurs as part of the regulation of muscle adaptation.
response to stimulus involved in regulation of muscle plasticity
response to stimulus involved in regulation of muscle adaptation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. This process occurs as part of the regulation of muscle adaptation.
response to electrical stimulus involved in regulation of muscle plasticity
response to electrical stimulus involved in regulation of muscle adaptation
The series of events by which an electrical stimulus is received and converted into a molecular signal. This occurs as part of the regulation of muscle adaptation.
detection of electrical stimulus involved in regulation of muscle adaptation
The process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors.
Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
The enlargement or overgrowth of all or part of an organ due to an increase in size of its smooth muscle cells without cell division. Physiological hypertrophy is a normal process during development, and can also occur in mature structures on demand. In the uterus, smooth muscle cells undergo hypertrophy during pregnancy.
The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy.
The enlargement or overgrowth of all or part of an organ due to an increase in size of muscle cells without cell division. In the case of striated muscle, this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils.
The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an ion from one side of a membrane to the other.
monoatomic ion transmembrane transporter activity
Enables the transfer of sodium ions (Na+) from one side of a membrane to the other.
sodium ion transmembrane transporter activity
Enables the transfer of organic cations from one side of a membrane to the other. Organic cations are atoms or small molecules with a positive charge that contain carbon in covalent linkage.
organic cation transmembrane transporter activity
abacavir [extracellular] => abacavir [cytosol]
OCT1 transports organic cations into hepatic cells
OCT2 mediates tubular uptake of organic cations in the kidney
OCT3 mediates renal clearance of organic cations
OCT1 transports organic cations out of hepatic cells
OCT2 mediates tubular secretion of organic cations in the kidney
OCT3 mediates renal uptake of organic cations
SLCO1A2 transports Cipro(1+) into the cytosol
SLC22A1 transports Cipro into renal cell
SLC22A1 transports Cipro into hepatic cell
Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage.
inorganic anion transmembrane transporter activity
Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-.
bicarbonate transmembrane transporter activity
BESTs transport cytosolic HCO3- to extracellular region
Enables the transfer of phosphate (PO4 3-) ions from one side of a membrane to the other.
phosphate transmembrane transporter activity
phosphate ion transmembrane transporter activity
Enables the transfer of sulfate ions, SO4(2-), from one side of a membrane to the other.
sulfate transmembrane transporter activity
Defective SLC26A2 does not cotransport extracellular SO4(2-), H+ to cytosol
SLC26A1,2 cotransport SO4(2-), H+ from extracellular region to cytosol
SLC26A11 transports SO4(2-) from extracellular region to cytosol
Enables the transfer of acetate from one side of a membrane to the other. Acetate is the 2-carbon carboxylic acid ethanoic acid.
acetate transmembrane transporter activity
Enables the transfer of bile acid from one side of a membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
bile acid transmembrane transporter activity
SLCO1B3 transports ALB:(GCCA, TCCA) from extracellular region to cytosol
SLCO1B1 transports ALB:(GCCA,TCCA) from extracellular region to cytosol
Transport (influx) of bile salts and acids by OATP-A
Defective SLCO1B1 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)
Defective SLCO1B3 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)
SLC51A:SLC51B transports bile salts from cytosol to extracellular region
Enables the transfer of bilirubin from one side of a membrane to the other. Bilirubin is a linear tetrapyrrole produced in the reticuloendothelial system from biliverdin and transported to the liver as a complex with serum albumin. In the liver, bilirubin is converted to bilirubin bisglucuronide, which is excreted in the bile.
bilirubin transmembrane transporter activity
Defective ABCC2 does not transport BMG,BDG from cytosol to extracellular region
ABCC2 transports BMG,BDG from cytosol to extracellular region
ABCG2 tetramer transports BMG,BDG from cytosol to extracellular region
Enables the transfer of carbohydrate from one side of a membrane to the other.
carbohydrate transmembrane transporter activity
Enables the transfer of a monosaccharide from one side of a membrane to the other.
monosaccharide transmembrane transporter activity
Enables the transfer of a hexose sugar, a monosaccharide with 6 carbon atoms, from one side of a membrane to the other.
hexose transmembrane transporter activity
SLC2A2 tetramer transports Fru, Gal, Glc from cytosol to extracellular region
Defective SLC2A2 does not transport Fru, Gal, Glc from cytosol to extracellular region
Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
polysaccharide transmembrane transporter activity
Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group.
amino acid/choline transmembrane transporter activity
hydroxy/aromatic amino acid permease activity
amino acid transmembrane transporter activity
SLC6A18 transports Gly from extracellular region to cytosol
SLC6A6-mediated uptake of taurine and beta-alanine
SLC6A12 (BGT-1)-mediated uptake of GABA and betaine
SLC6A20 cotransports L-Pro, Na+ from the extracellular region to cytosol
SLC43A1 (LAT3)-mediated uptake of large neutral amino acids
SLC43A2 (LAT4)-mediated uptake of large neutral amino acids
SLC38A2 (ATA2)-mediated uptake of neutral amino acids
SLC38A1 (ATA1)-mediated uptake of neutral amino acids
SLC38A4 (ATA3)-mediated uptake of arginine and lysine
SLC16A10-mediated uptake of aromatic amino acids
SLC38A3-mediated uptake of glutamine, histidine, asparagine, and alanine
SLC38A5-mediated uptake of glutamine, histidine, asparagine, and serine
SLC7A8-mediated uptake of neutral amino acids
SLC7A5:SLC3A2 transports neutral amino acids from extracellular region to cytosol
SLC1A4-mediated exchange of extracellular serine for cytosolic alanine, threonine, or cysteine
SLC1A4-mediated exchange of extracellular cysteine for cytosolic alanine, serine, or threonine
SLC1A4-mediated exchange of extracellular alanine for cytosolic serine, threonine, or cysteine
SLC1A4-mediated exchange of extracellular threonine for cytosolic alanine, serine, or cysteine
SLC1A5-mediated exchange of alanine and glutamine across the plasma membrane
SLC1A5-mediated exchange of glutamine and alanine across the plasma membrane
SLC36A2 cotransports Gly, L-Pro with H+ from extracellular region to cytosol
SLC36A1-mediated uptake of glycine, proline, and alanine
SLC6A19 cotransports neutral amino acids, Na+ from extracellular region to cytosol
SLC6A14 cotransports SLC6A14 ligands, Cl-, 2Na+ from extracellular region to cytosol
SLC7A2, isoform B (CAT-2B)-mediated uptake of cationic amino acids
SLC7A3 (CAT-3)-mediated uptake of cationic amino acids
SLC7A1 (CAT-1)-mediated uptake of cationic amino acids
SLC7A2, isoform A (CAT-2A)-mediated uptake of cationic amino acids
SLC7A10-mediated uptake of small neutral amino acids
SLC7A11-mediated exchange of extracellular cysteine and cytosolic glutamate
SLC7A7:SLC3A2 exchanges L-Arg for L-Leu, Na+ across the plasma membrane
SLC7A6 (y+LAT2)-mediated exchange of extracellular leucine for cytosolic arginine
SLC7A9:SLC3A1 exchanges L-Arg, CySS-, L-Lys for L-Leu
Defective SLC36A2 does not cotransport Gly, L-Pro with H+ from extracellular region to cytosol
Defective SLC3A1 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu
Variant SLC6A14 cotransports SLC6A14 ligands, Cl-, 2Na+ from extracellular region to cytosol
Defective SLC6A19 does not cotransport neutral amino acids, Na+ from extracellular region to cytosol
Defective SLC6A18 does not transport Gly from extracellular region to cytosol
Variant SLC6A20 does not cotransport L-Pro, Na+ from extracellulare region to cytosol
Defective SLC7A9 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu
Defective SLC7A7 does not exchange L-Arg for L-Leu, Na+ across the plasma membrane
Loading of GABA into clathrin sculpted GABA transport vesicle lumen
SLC38A9 transports L-Arg from lysosomal lumen to cytosol
Enables the transfer of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acidfrom one side of a membrane to the other.
nucleobase transmembrane transporter activity
Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon.
inorganic solute uptake transmembrane transporter activity
inorganic molecular entity transmembrane transporter activity
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage.
The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage.
The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of bilirubin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom.
The directed movement of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.
The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine.
The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
nucleobase, nucleoside, nucleotide and nucleic acid transport
nucleobase-containing compound transport
Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other.
nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity
nucleobase-containing compound transmembrane transporter activity
energy derivation by oxidation of reduced inorganic compounds
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
energy derivation by oxidation of organic compounds
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
multicellular organism lipid catabolic process
multicellular organismal lipid catabolic process
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
non-developmental growth of a unicellular organism
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
catabolic carbohydrate metabolic process
multicellular organismal carbohydrate catabolic process
single-organism carbohydrate catabolic process
The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.
Hyperpolarization (vertebrates) or depolarization (invertebrates) of the photoreceptor cell membrane via closing/opening of cation specific channels as a result of signals generated by rhodopsin activation by a photon.
changes in polarization state of photoreceptor cell membrane
regulation of membrane potential in photoreceptor cell
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
Any process that modulates the frequency, rate or extent of striated muscle development.
regulation of striated muscle tissue development
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female.
Formation and maintenance of a polarized microtubule array originating from a microtubule-organizing center (MTOC) in the oocyte. An example of this is found in Drosophila melanogaster.
oocyte microtubule cytoskeleton organisation
oocyte microtubule cytoskeleton organization
The process in which the anatomical structures of embryonic epithelia are generated and organized.
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.
Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum.
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
Partial proteolysis of antigen in phagolysosomes
Production of AA by iPLA2 upon FCGR activation
Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate
Catalysis of the hydrolysis of any ester bond.
hydrolase activity, acting on ester bonds
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid
Butyrylcholinesterase hydrolyzes acyl Ghrelin
Platelet-activating factor acetylhydrolase (PLA2G7) hydrolyzes acyl Ghrelin
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insecticide stimulus. Insecticides are chemicals used to kill insects.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells.
The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
down regulation of protein biosynthetic process
down-regulation of protein biosynthetic process
downregulation of protein biosynthetic process
negative regulation of protein anabolism
negative regulation of protein biosynthesis
negative regulation of protein biosynthetic process
negative regulation of protein formation
negative regulation of protein synthesis
inhibition of protein biosynthetic process
protein biosynthetic process inhibitor activity
Any process that modulates the frequency, rate or extent of exocytosis.
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.
Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds.
phenol-containing compound metabolic process
The specific behavior of an organism that is associated with reproduction.
reproductive behavior in a multicellular organism
multicellular organism reproductive behavior
Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids.
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
regulation of nucleobase-containing compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
An action potential that occurs in a neuron.
The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the formation of hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
anaerobic respiration, using ammonium as electron donor
aerobic respiration, using nitrite as electron donor
The chemical reactions and pathways resulting in the breakdown of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.
phenol-containing compound catabolic process
aerobic respiration, using ammonia as electron donor
aerobic respiration, using carbon monoxide as electron donor
aerobic respiration, using ferrous ions as electron donor
aerobic respiration, using hydrogen as electron donor
The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid.
aerobic respiration, using sulfur or sulfate as electron donor
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The chemical reactions and pathways involving a protein. Includes protein modification.
protein metabolic process and modification
multicellular organismal protein metabolic process
The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent.
catechol-containing compound catabolic process
Any process involved in the maintenance of an internal steady state at the level of the cell.
The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
The directed movement of one-carbon compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
The formation of the prechordal plate. The prechordal plate is a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells.
The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate.
ventral spinal cord interneuron differentiation
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output.
The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate.
spinal cord motor neuron differentiation
The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of somatic motor neurons. Somatic motor neurons innervate skeletal muscle targets and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube.
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The multiplication or reproduction of cells, resulting in the expansion of a cell population in the hindbrain.
The orderly movement of a cell that will reside in the hindbrain.
The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
The process whose specific outcome is the progression of the rhombomere over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The regionalization process that gives rise to the midbrain-hindbrain boundary. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate.
midbrain-hindbrain boundary biosynthesis
The process whose specific outcome is the progression of the pons over time, from its formation to the mature structure. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process whose specific outcome is the progression of the medulla oblongata over time, from its formation to the mature structure. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process in which the anatomical structure of the midbrain-hindbrain boundary is generated and organized. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate.
midbrain-hindbrain boundary morphogenesis
The process that gives rise to the central nervous system. This process pertains to the initial formation of a structure from unspecified parts. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
A developmental process, independent of morphogenetic (shape) change, that is required for the hindbrain to attain its fully functional state. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
The process in which the anatomical structure of the medulla oblongata is generated and organized. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process that gives rise to the medulla oblongata. This process pertains to the initial formation of a structure from unspecified parts. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
A developmental process, independent of morphogenetic (shape) change, that is required for the medulla oblongata to attain its fully functional state. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate.
The process in which the anatomical structure of the pons is generated and organized. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process that gives rise to the pons. This process pertains to the initial formation of a structure from unspecified parts. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
A developmental process, independent of morphogenetic (shape) change, that is required for the pons to attain its fully functional state. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum.
The process in which the anatomical structure of the rhombomere is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The process that gives rise to the rhombomere. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates.
The process in which the anatomical structure of the cranial nerves are generated and organized. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
The process that gives rise to the cranial nerves. This process pertains to the initial formation of a structure from unspecified parts. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
A developmental process, independent of morphogenetic (shape) change, that is required for a cranial nerve to attain its fully functional state. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
A developmental process, independent of morphogenetic (shape) change, that is required for the central nervous system to attain its fully functional state. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
A developmental process, independent of morphogenetic (shape) change, that is required for the trigeminal nerve to attain its fully functional state. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process in which the anatomical structure of the trigeminal nerve is generated and organized. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process that gives rise to the trigeminal nerve. This process pertains to the initial formation of a structure from unspecified parts. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
The process that gives rise to a rhombomere boundary. This process pertains to the initial formation of a boundary delimiting a rhombomere. Rhombomeres are transverse segments of the developing rhombencephalon that are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order.
The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
A developmental process, independent of morphogenetic (shape) change, that is required for a nerve to attain its fully functional state.
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.
The process whose specific outcome is the progression of the locus ceruleus over time, from its formation to the mature structure. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process in which the anatomical structure of the locus ceruleus is generated and organized. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process that gives rise to the locus ceruleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
A developmental process, independent of morphogenetic (shape) change, that is required for the locus ceruleus to attain its fully functional state. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic.
The process whose specific outcome is the progression of the superior olivary nucleus over time, from its formation to the mature structure. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
The process in which the anatomical structure of the superior olivary nucleus is generated and organized. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
The process that gives rise to the superior olivary nucleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
A developmental process, independent of morphogenetic (shape) change, that is required for the superior olivary nucleus to attain its fully functional state. The superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound.
A developmental process, independent of morphogenetic (shape) change, that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate.
The process whose specific outcome is the progression of a salivary nucleus over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the superior salivary nucleus over time, from its formation to the mature structure.
The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the neural tube is divided into specific regions along the rostrocaudal axis.
anterior-posterior neural tube patterning
The process whose specific outcome is the formation of the hindbrain-spinal cord boundary.
hindbrain-spinal cord boundary formation
The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system.
central nervous system neuron differentiation
The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
central nervous system neuron development
The formation of the flat, thickened layer of ectodermal cells known as the neural plate. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system.
The process that regulates the coordinated growth and differentiation that establishes the non-random anterior-posterior spatial arrangement of the neural plate.
neural plate anterior/posterior pattern formation
neural plate anterior/posterior regionalization
Generation of cells within the nervous system.
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier.
The movement of a cell within a rhombomere. This process is known to occur as an early step in the generation of anatomical structure from a rhombomere.
The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure.
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
A cellular process that results in the breakdown of a cellular component.
cellular component disassembly at cellular level
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
reproductive cellular process in multicellular organism
cellular process involved in reproduction in multicellular organism
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
regulation of anatomical structure morphogenesis
Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
negative regulation of cell shape and cell size
positive regulation of cell shape and cell size
The aggregation, arrangement and bonding together of a cellular component.
cellular component assembly at cellular level
The process in which the anatomical structures of a gland are generated and organized.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
ribonucleoprotein complex biogenesis and assembly
A process that results in the breakdown of the extracellular matrix.
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction.
active transmembrane transporter activity
Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction.
active ion transmembrane transporter activity
active monoatomic ion transmembrane transporter activity
Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
substrate-specific transmembrane transporter activity
uptake transmembrane transporter activity
Egress of internalized antigen to the cytosol via sec61
Defective SLC2A9 does not transport Fru, Glc, urate
Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA
An unknown carrier transports cytosolic glyoxylate to the peroxisome
An unknown carrier transports mitochondrial glyoxylate to the cytosol
Enables the transfer of a macromolecule from one side of a membrane to the other.
macromolecule transmembrane transporter activity
Enables the transfer of inorganic cations from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage.
di-, tri-valent inorganic cation transmembrane transporter activity
divalent inorganic cation transmembrane transporter activity
monovalent inorganic cation transmembrane transporter activity
trivalent inorganic cation transmembrane transporter activity
inorganic cation transmembrane transporter activity
Any process that modulates the frequency, rate or extent of transmembrane transporter activity.
regulation of transmembrane transporter activity
Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
regulation of gene expression as a consequence of signal transmission
signal transduction involved in regulation of gene expression
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
negative regulation of signaling process
negative regulation of signalling process
The process in which a signal is secreted or discharged into the extracellular medium from a cellular source.
The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The specification and formation of anisotropic intracellular organization or cell growth patterns.
bud site selection/establishment of cell polarity
The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organization and biogenesis
cell surface structure organization and biogenesis
Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
actin cytoskeleton organization and biogenesis
Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins.
Movement of a vesicle along an actin filament, mediated by motor proteins.
A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.
The regulated release of a peptide hormone from a cell.
The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
constitutive secretory pathway transport vesicle
Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'.
A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'.
The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
multicellular organismal protein catabolic process
This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.
The process in which a relatively unspecialized cell acquires specialized features of a neuron.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
extracellular matrix organization and biogenesis
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
Formation of myofibrils, the repeating units of striated muscle.
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis.
The compaction of chromatin during apoptosis.
The breakdown of the nucleus into small membrane-bounded compartments, or blebs, each of which contain compacted DNA.
nuclear fragmentation involved in apoptotic nuclear change
Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
negative regulation of bone biosynthesis
Any process that activates or increases the frequency, rate, extent or direction of cell growth.
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract.
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
Any process that modulates the frequency, rate or extent of cell migration.
Any process that activates or increases the frequency, rate or extent of cell migration.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
The controlled breakdown of any cell membrane in the context of a normal process such as autophagy.
A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards.
The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins.
microtubule cytoskeleton-dependent nuclear positioning
microtubule cytoskeleton-dependent nucleus positioning
microtubule-dependent nuclear positioning
microtubule-dependent nucleus positioning
transport of nucleus, microtubule-mediated
The contractile fiber of smooth muscle cells.
The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile.
bile acid 7alpha-dehydroxylation pathway
The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
The lipid bilayer surrounding a transport vesicle.
constitutive secretory pathway transport vesicle membrane
The lipid bilayer surrounding a cytoplasmic vesicle.
The lipid bilayer surrounding a vesicle associated with the Golgi apparatus.
The lipid bilayer surrounding a secretory granule.
The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
cytoskeleton-dependent intracellular transport
Directed movement of the oocyte, following its specification, from its original central position in the cyst to a posterior position relative to the nurse cells of the egg chamber, and its maintenance in this posterior location. This is the first sign of anterior-posterior asymmetry in the developing egg chamber.
establishment and maintenance of oocyte localization in egg chamber
establishment and maintenance of oocyte position during oogenesis
oocyte localisation involved in germarium-derived egg chamber formation
oogenesis, establishment and maintenance of oocyte localization
oocyte localization during germarium-derived egg chamber formation
oocyte localization involved in germarium-derived egg chamber formation
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
Any process that modulates the frequency, rate or extent of epithelial cell differentiation.
regulation of epithelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation.
down regulation of epithelial cell differentiation
down-regulation of epithelial cell differentiation
downregulation of epithelial cell differentiation
inhibition of epithelial cell differentiation
negative regulation of epithelial cell differentiation
Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation.
up regulation of epithelial cell differentiation
up-regulation of epithelial cell differentiation
upregulation of epithelial cell differentiation
activation of epithelial cell differentiation
stimulation of epithelial cell differentiation
positive regulation of epithelial cell differentiation
The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).
The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages.
isthmomesencephalic boundary development
midbrain-hindbrain orgainizer development
Any collagen trimer that passes through a lipid bilayer membrane.
Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures.
establishment or maintenance of microtubule cytoskeleton polarity
Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures.
establishment or maintenance of cytoskeleton polarity
A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.
Note that we deem cilia and microtubule-based flagella to be equivalent.
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones.
The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells.
The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins.
nuclear migration, microfilament-mediated
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments.
actomyosin structure organization and biogenesis
Note that this term is a child of 'actin cytoskeleton organization and biogenesis ; GO:0030036' because the actin cytoskeleton is defined as actin filaments and associated proteins.
Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.
The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule.
microtubule polymerization or depolymerization
Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule.
regulation of microtubule polymerization or depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization.
down regulation of microtubule polymerization or depolymerization
down-regulation of microtubule polymerization or depolymerization
downregulation of microtubule polymerization or depolymerization
inhibition of microtubule polymerization or depolymerization
negative regulation of microtubule polymerization or depolymerization
Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization.
up regulation of microtubule polymerization or depolymerization
up-regulation of microtubule polymerization or depolymerization
upregulation of microtubule polymerization or depolymerization
activation of microtubule polymerization or depolymerization
stimulation of microtubule polymerization or depolymerization
positive regulation of microtubule polymerization or depolymerization
Any process that modulates the frequency, rate or extent of microtubule polymerization.
regulation of microtubule polymerization
Any process that modulates the frequency, rate or extent of microtubule depolymerization.
regulation of microtubule depolymerization
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
down regulation of microtubule polymerization
down-regulation of microtubule polymerization
downregulation of microtubule polymerization
inhibition of microtubule polymerization
negative regulation of microtubule polymerization
Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
up regulation of microtubule polymerization
up-regulation of microtubule polymerization
upregulation of microtubule polymerization
activation of microtubule polymerization
stimulation of microtubule polymerization
positive regulation of microtubule polymerization
Any process that activates or increases the frequency, rate or extent of microtubule depolymerization.
positive regulation of microtubule disassembly
up regulation of microtubule depolymerization
up-regulation of microtubule depolymerization
upregulation of microtubule depolymerization
activation of microtubule depolymerization
positive regulation of microtubule catastrophe
stimulation of microtubule depolymerization
positive regulation of microtubule depolymerization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
cytoplasmic microtubule organization and biogenesis
A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder).
The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
The area of a motile cell closest to the direction of movement.
The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
The portion of the plasma membrane surrounding the leading edge of a motile cell.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
negative regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
positive regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
down regulation of cellular biosynthetic process
down-regulation of cellular biosynthetic process
downregulation of cellular biosynthetic process
negative regulation of cellular anabolism
negative regulation of cellular biosynthesis
negative regulation of cellular formation
negative regulation of cellular synthesis
inhibition of cellular biosynthetic process
negative regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
activation of cellular biosynthetic process
stimulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
regulation of cellular catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
down regulation of cellular catabolic process
down-regulation of cellular catabolic process
downregulation of cellular catabolic process
negative regulation of cellular breakdown
negative regulation of cellular catabolism
negative regulation of cellular degradation
inhibition of cellular catabolic process
negative regulation of cellular catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
positive regulation of cellular breakdown
positive regulation of cellular catabolism
positive regulation of cellular degradation
up regulation of cellular catabolic process
up-regulation of cellular catabolic process
upregulation of cellular catabolic process
activation of cellular catabolic process
stimulation of cellular catabolic process
positive regulation of cellular catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
down regulation of protein complex assembly
down-regulation of protein complex assembly
downregulation of protein complex assembly
negative regulation of protein complex assembly
negative regulation of protein-containing complex assembly
Any process that activates or increases the frequency, rate or extent of protein complex assembly.
up regulation of protein complex assembly
up-regulation of protein complex assembly
upregulation of protein complex assembly
positive regulation of protein complex assembly
positive regulation of protein-containing complex assembly
Any process that modulates the frequency, rate or extent of vesicle fusion.
Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion.
Any process that activates or increases the frequency, rate or extent of vesicle fusion.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
regulation of cell projection organisation
regulation of cell projection organization and biogenesis
regulation of cell projection organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
down regulation of cell projection organization
down-regulation of cell projection organization
downregulation of cell projection organization
negative regulation of cell projection organisation
inhibition of cell projection organization
negative regulation of cell projection organization and biogenesis
negative regulation of cell projection organization
Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
positive regulation of cell projection organisation
up regulation of cell projection organization
up-regulation of cell projection organization
upregulation of cell projection organization
activation of cell projection organization
stimulation of cell projection organization
positive regulation of cell projection organization and biogenesis
positive regulation of cell projection organization
A vesicle found in the cytoplasm of a cell.
A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
establishment and maintenance of protein complex localization
cellular protein-containing complex localization
establishment and maintenance of cellular protein complex localization
The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system.
regulation of neurological system process
regulation of neurophysiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process.
negative regulation of neurological process
negative regulation of neurological system process
negative regulation of neurophysiological process
negative regulation of nervous system process
Any process that activates or increases the frequency, rate or extent of a neurophysiological process.
positive regulation of neurological process
positive regulation of neurological system process
positive regulation of neurophysiological process
positive regulation of nervous system process
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.
The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope.
The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.
A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.
The volume enclosed by the nuclear inner membrane.
Any small, fluid-filled, spherical organelle enclosed by membrane.
Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
locomotion involved in locomotory behavior
Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
positive regulation of insulin secretion
Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress.
down regulation of translation initiation in response to stress
down-regulation of translation initiation in response to stress
downregulation of translation initiation in response to stress
inhibition of translation initiation in response to stress
negative regulation of translational initiation in response to stress
Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress.
up regulation of translation initiation in response to stress
up-regulation of translation initiation in response to stress
upregulation of translation initiation in response to stress
activation of translation initiation in response to stress
stimulation of translation initiation in response to stress
positive regulation of translational initiation in response to stress
A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
regulation of deoxyribonuclease activity
Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
negative regulation of nuclease activity
Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
positive regulation of nuclease activity
Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
down regulation of deoxyribonuclease activity
down-regulation of deoxyribonuclease activity
downregulation of deoxyribonuclease activity
inhibition of deoxyribonuclease activity
negative regulation of deoxyribonuclease activity
Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
up regulation of deoxyribonuclease activity
up-regulation of deoxyribonuclease activity
upregulation of deoxyribonuclease activity
activation of deoxyribonuclease activity
stimulation of deoxyribonuclease activity
positive regulation of deoxyribonuclease activity
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
regulation of response to external stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
down regulation of response to external stimulus
down-regulation of response to external stimulus
downregulation of response to external stimulus
inhibition of response to external stimulus
negative regulation of response to external stimulus
Any process that activates, maintains or increases the rate of a response to an external stimulus.
up regulation of response to external stimulus
up-regulation of response to external stimulus
upregulation of response to external stimulus
activation of response to external stimulus
stimulation of response to external stimulus
positive regulation of response to external stimulus
The lipid bilayer surrounding a dense core granule.
Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine.
regulation of synaptic transmission, cholinergic
Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine.
down regulation of synaptic transmission, cholinergic
down-regulation of synaptic transmission, cholinergic
downregulation of synaptic transmission, cholinergic
inhibition of synaptic transmission, cholinergic
negative regulation of synaptic transmission, cholinergic
Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine.
up regulation of synaptic transmission, cholinergic
up-regulation of synaptic transmission, cholinergic
upregulation of synaptic transmission, cholinergic
activation of synaptic transmission, cholinergic
stimulation of synaptic transmission, cholinergic
positive regulation of synaptic transmission, cholinergic
Any process that modulates the frequency, rate or extent of the assembly of actin filament bundles.
regulation of actin filament bundle formation
regulation of actin filament bundle assembly
Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles.
down regulation of actin filament bundle formation
down-regulation of actin filament bundle formation
downregulation of actin filament bundle formation
inhibition of actin filament bundle formation
negative regulation of actin filament bundle assembly
Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
up regulation of actin filament bundle formation
up-regulation of actin filament bundle formation
upregulation of actin filament bundle formation
activation of actin filament bundle formation
stimulation of actin filament bundle formation
positive regulation of actin filament bundle assembly
Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
regulation of nucleobase-containing compound transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
inhibition of nucleobase, nucleoside, nucleotide and nucleic acid transport
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
negative regulation of nucleobase-containing compound transport
Any process that activates or increases the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
activation of nucleobase, nucleoside, nucleotide and nucleic acid transport
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport
positive regulation of nucleobase-containing compound transport
Any process in which a secretory granule is transported to, and/or maintained in, a specific location within the cell.
Any process in which a dense core granule is transported to, and/or maintained in, a specific location within the cell.
Any process that modulates the frequency, rate or extent of the process of creating protein polymers.
Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers.
down regulation of protein polymerization
down-regulation of protein polymerization
downregulation of protein polymerization
negative regulation of protein polymerization
Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers.
positive regulation of protein polymerization
Any process that modulates the frequency, rate or extent of chondrocyte differentiation.
regulation of chondrocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
down regulation of chondrocyte differentiation
down-regulation of chondrocyte differentiation
downregulation of chondrocyte differentiation
inhibition of chondrocyte differentiation
negative regulation of chondrocyte differentiation
Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
up regulation of chondrocyte differentiation
up-regulation of chondrocyte differentiation
upregulation of chondrocyte differentiation
activation of chondrocyte differentiation
stimulation of chondrocyte differentiation
positive regulation of chondrocyte differentiation
The directed movement of lipids within cells.
Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells.
regulation of intracellular lipid transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells.
down regulation of intracellular lipid transport
down-regulation of intracellular lipid transport
downregulation of intracellular lipid transport
inhibition of intracellular lipid transport
negative regulation of intracellular lipid transport
Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells.
up regulation of intracellular lipid transport
up-regulation of intracellular lipid transport
upregulation of intracellular lipid transport
activation of intracellular lipid transport
stimulation of intracellular lipid transport
positive regulation of intracellular lipid transport
Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells.
down regulation of intracellular transport
down-regulation of intracellular transport
downregulation of intracellular transport
negative regulation of intracellular transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells.
up regulation of intracellular transport
up-regulation of intracellular transport
positive regulation of intracellular transport
Any process that modulates the activity of a transporter.
Any process that stops or reduces the activity of a transporter.
negative regulation of transporter activity
Any process that activates or increases the activity of a transporter.
positive regulation of transporter activity
Any process that modulates the activity of an ion transporter.
regulation of ion transmembrane transporter activity
regulation of monoatomic ion transmembrane transporter activity
Any process that stops or reduces the activity of an ion transporter.
down regulation of ion transporter activity
down-regulation of ion transporter activity
downregulation of ion transporter activity
negative regulation of ion transporter activity
negative regulation of ion transmembrane transporter activity
Any process that activates or increases the activity of an ion transporter.
positive regulation of ion transporter activity
up regulation of ion transporter activity
up-regulation of ion transporter activity
upregulation of ion transporter activity
positive regulation of ion transmembrane transporter activity
An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a microvillus.
regulation of microvillus organization and biogenesis
A process that modulates the formation of a microvillus.
The portion of the plasma membrane surrounding a neuron projection.
The directed movement of a protein from one location to another within a lipid bilayer.
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
double-stranded RNA biosynthetic process
Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue.
The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-).
The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection.
plasma membrane bounded cell projection cytoplasm
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion.
Any process that modulates the frequency, rate or extent of the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
regulation of establishment or maintenance of cell polarity
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
regulation of cellular protein localisation
regulation of cellular protein localization
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides.
regulation of polysaccharide metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides.
regulation of polysaccharide biosynthetic process
Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton.
Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of organic acid transport
down-regulation of organic acid transport
downregulation of organic acid transport
negative regulation of organic acid transport
Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of organic acid transport
The controlled release of a substance by a cell.
The controlled release of a substance by a tissue.
The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form.
peripheral blood mononuclear cell proliferation
Any process that modulates the frequency, rate or extent of mononuclear cell proliferation.
regulation of peripheral blood mononuclear cell proliferation
regulation of mononuclear cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation.
negative regulation of PBMC proliferation
negative regulation of peripheral blood mononuclear cell proliferation
negative regulation of mononuclear cell proliferation
Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation.
up regulation of mononuclear cell proliferation
up-regulation of mononuclear cell proliferation
upregulation of mononuclear cell proliferation
activation of mononuclear cell proliferation
positive regulation of PBMC proliferation
positive regulation of peripheral blood mononuclear cell proliferation
stimulation of mononuclear cell proliferation
positive regulation of mononuclear cell proliferation
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
regulation of actin cytoskeleton organisation
regulation of actin cytoskeleton organization and biogenesis
regulation of actin cytoskeleton organization
The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
regulation of collagen biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
negative regulation of collagen anabolism
negative regulation of collagen biosynthesis
negative regulation of collagen formation
negative regulation of collagen synthesis
negative regulation of collagen biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
positive regulation of collagen anabolism
positive regulation of collagen biosynthesis
positive regulation of collagen formation
positive regulation of collagen synthesis
positive regulation of collagen biosynthetic process
Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton.
regulation of actin filament-based process
The disaggregation of a protein-containing macromolecular complex into its constituent components.
cellular macromolecule complex disassembly
The disaggregation of a protein-DNA complex into its constituent components.
The disaggregation of a protein-RNA complex into its constituent components.
The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system.
cellular anatomical entity morphogenesis
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
A macromolecular complex containing both protein and DNA molecules.
Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.
The expansion of a muscle cell population by cell division.
The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
The chemical reactions and pathways leading to the breakdown of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
Any process that modulates the frequency, rate, or extent of myeloid cell apoptotic process.
regulation of myeloid cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
down regulation of myeloid cell apoptosis
down-regulation of myeloid cell apoptosis
downregulation of myeloid cell apoptosis
negative regulation of myeloid cell apoptosis
negative regulation of myeloid cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of myeloid cell apoptotic process.
positive regulation of myeloid cell apoptosis
positive regulation of myeloid cell apoptotic process
Any process in which a macromolecule is transported to, or maintained in, a specific location.
Any process in which a polysaccharide is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
regulation of organelle organization and biogenesis
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome.
regulation of chromosome organization and biogenesis
Any process that modulates the frequency, rate or extent of sister chromatid segregation.
regulation of sister chromatid segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation.
negative regulation of sister chromatid segregation
Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis.
regulation of mitotic sister chromatid segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis.
negative regulation of mitotic sister chromatid segregation
The deposition or aggregation of coloring matter in a cell.
Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
regulation of intracellular protein transport
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines.
regulation of cellular amine metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines.
negative regulation of cellular amine metabolic process
negative regulation of amine metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines.
positive regulation of cellular amine metabolic process
positive regulation of amine metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.
regulation of cellular amine catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.
negative regulation of amine degradation
negative regulation of cellular amine catabolic process
negative regulation of amine catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines.
positive regulation of amine degradation
positive regulation of amine catabolic process
The multiplication or reproduction of cells, resulting in the expansion of a cell population in the midbrain.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion.
secretory granule organization and biogenesis
A process in which a protein is transported to, or maintained in, a location within an organelle.
A process in which a protein is transported to, or maintained in, a location within a secretory granule.
protein localisation in secretory granule
protein localization in secretory granule
protein localization to secretory granule
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine.
down regulation of catecholamine secretion
down-regulation of catecholamine secretion
downregulation of catecholamine secretion
negative regulation of catecholamine secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine.
up regulation of catecholamine secretion
up-regulation of catecholamine secretion
positive regulation of catecholamine secretion
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
A process in which a ribosome is transported to, and/or maintained in, a specific location.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus.
establishment of protein localisation to Golgi
establishment of protein localization in Golgi
establishment of protein localization to Golgi
establishment of protein localization to Golgi apparatus
Any process of regulating the production and elimination of erythrocytes within an organism.
The process in which a carbohydrate is transported across a membrane.
A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
ATP hydrolysis coupled ion transmembrane transport
Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
negative regulation of syncytium formation by plasma membrane fusion
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides.
regulation of cellular amide metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides.
negative regulation of cellular amide metabolic process
negative regulation of amide metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides.
positive regulation of cellular amide metabolic process
positive regulation of amide metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.
regulation of cellular amide catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.
negative regulation of cellular amide catabolic process
negative regulation of amide degradation
negative regulation of amide catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.
positive regulation of cellular amide catabolic process
positive regulation of amide degradation
positive regulation of amide catabolic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus.
A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix.
Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
glial cell programmed cell death by apoptosis
programmed cell death of glia by apoptosis
programmed cell death of glial cells by apoptosis
Any process that modulates the frequency, rate, or extent of glial cell apoptotic process.
regulation of glial cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process.
negative regulation of glial cell apoptosis
negative regulation of glial cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of glial cell apoptotic process.
positive regulation of glial cell apoptosis
positive regulation of glial cell apoptotic process
Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels.
programmed cell death of smooth muscle cells by apoptosis
programmed cell death, smooth muscle cells
smooth muscle cell programmed cell death by apoptosis
Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process.
regulation of smooth muscle cell apoptosis
regulation of smooth muscle cell apoptotic process
Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
down regulation of smooth muscle cell apoptosis
down-regulation of smooth muscle cell apoptosis
downregulation of smooth muscle cell apoptosis
inhibition of smooth muscle cell apoptosis
negative regulation of smooth muscle cell apoptosis
negative regulation of smooth muscle cell apoptotic process
Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
up regulation of smooth muscle cell apoptosis
up-regulation of smooth muscle cell apoptosis
upregulation of smooth muscle cell apoptosis
activation of smooth muscle cell apoptosis
positive regulation of smooth muscle cell apoptosis
stimulation of smooth muscle cell apoptosis
positive regulation of smooth muscle cell apoptotic process
The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The process in which a solute is transported from one side of the vacuolar membrane to the other.
The process in which an amino acid is transported from one side of the vacuolar membrane to the other.
vacuolar amino acid transmembrane transport
Any process in which a protein is transported to, or maintained at, a specific location on a chromosome.
A process in which a protein transports or maintains the localization of another protein to the nucleus.
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
nucleobase-containing compound catabolic process
Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
down regulation of transmembrane transport
down-regulation of transmembrane transport
downregulation of transmembrane transport
negative regulation of membrane transport
negative regulation of transmembrane transport
Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
positive regulation of membrane transport
up regulation of transmembrane transport
up-regulation of transmembrane transport
positive regulation of transmembrane transport
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
regulation of ion transmembrane transport
regulation of transmembrane ion transport
regulation of monoatomic ion transmembrane transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
negative regulation of ion transmembrane transport
down regulation of transmembrane ion transport
down-regulation of transmembrane ion transport
downregulation of transmembrane ion transport
negative regulation of ion membrane transport
negative regulation of transmembrane ion transport
inhibition of transmembrane ion transport
negative regulation of monoatomic ion transmembrane transport
Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
positive regulation of ion transmembrane transport
positive regulation of ion membrane transport
positive regulation of transmembrane ion transport
up regulation of transmembrane ion transport
up-regulation of transmembrane ion transport
upregulation of transmembrane ion transport
activation of transmembrane ion transport
stimulation of transmembrane ion transport
positive regulation of monoatomic ion transmembrane transport
The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion.
Note that this term has no relationship to 'membrane disassembly ; GO:0030397' because the basement membrane is not a lipid bilayer.
The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual.
The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent.
The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch.
The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal.
Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
lumen formation in an anatomical structure
The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex.
Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
programmed cell death of ectopic germ cells
programmed cell death, ectopic germ cells
The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals.
The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function.
Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes.
Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system.
The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis.
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
A process in which a protein is transported to, or maintained at, a microtubule.
Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
The process in which acetate is transported across a membrane. Acetate is the 2-carbon carboxylic acid ethanoic acid.
The process in which a phosphate is transported across a membrane.
The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.
cell migration involved in vasculogenesis
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
intracellular signal transduction pathway
signal transmission via intracellular cascade
The directed movement of a protein to a specific location within the extracellular region.
establishment of protein localisation in extracellular region
establishment of protein localization in extracellular region
establishment of protein localization to extracellular region
The progression of the intrahepatic bile ducts over time, from their formation to the mature structure. Intrahepatic bile ducts (bile ducts within the liver) collect bile from bile canaliculi in the liver, and connect to the extrahepatic bile ducts (bile ducts outside the liver).
The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct.
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the intestine.
intestinal smooth muscle cell differentiation
enteric smooth muscle cell differentiation
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.
intraciliary transport involved in cilium morphogenesis
intraflagellar transport involved in cilium morphogenesis
intraciliary transport involved in cilium assembly
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis.
cell proliferation involved in compound eye morphogenesis
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells).
angioblastic mesenchymal cell differentiation
A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development.
The chemical reactions and pathways involving an indole alkaloid, an alkaloid containing an indole skeleton.
The chemical reactions and pathways resulting in the formation of an indole alkaloid, an alkaloid containing an indole skeleton.
The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates.
The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.
Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone.
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system.
The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell.
vascular smooth muscle cell differentiation
vascular associated smooth muscle cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta.
aortic smooth muscle cell differentiation
The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
The progression of the ascending aorta over time, from its initial formation to the mature structure. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.
The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
The regulated release of any steroid that acts as a hormone into the circulatory system.
The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates.
The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force.
The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts.
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues.
The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population.
A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
The portion of the plasma membrane surrounding a muscle cell projection.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen.
This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'response to hypoxia ; GO:0001666'.
Any biological process involved in the maintenance of the steady-state number of hepatocytes within a population of cells. Hepatocytes are specialized epithelial cells of the liver that are organized into interconnected plates called lobules.
Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells.
The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance.
The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon.
The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane.
membrane fusion involved in Golgi reassembly
The increase in size or mass of an entire organism, a part of an organism or a cell.
See also the biological process term 'cell growth ; GO:0016049'.
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
Self-propelled movement of a cell or organism from one location to another.
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
regulation of multicellular organism growth
Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size.
negative regulation of multicellular organism growth
The first few specialized divisions of an activated animal egg.
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
positive regulation of multicellular organism growth
Any process that activates or increases the frequency, rate or extent of embryonic development.
positive regulation of embryonic development
Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes.
Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and the rate at which this time point is reached.
regulation of development, heterochronic
The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia.
Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines.
regulation of catecholamine metabolic process
The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.
intraflagellar transport involved in cilium organization
intraflagellar transport involved in microtubule-based flagellum organisation
Note that we deem cilium and microtubule-based flagellum to be equivalent.
The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression).
The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes.
Any process that modulates the frequency, rate or extent of cell proliferation.
regulation of cell population proliferation
The continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane.
nuclear membrane-endoplasmic reticulum continuum
nuclear envelope-endoplasmic reticulum continuum
nuclear envelope-endoplasmic reticulum network
nuclear outer membrane-endoplasmic reticulum membrane network
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
regulation of cellular protein breakdown
regulation of cellular protein catabolic process
regulation of cellular protein catabolism
regulation of cellular protein degradation
Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process.
down regulation of cellular protein breakdown
down regulation of cellular protein catabolic process
down regulation of cellular protein catabolism
down regulation of cellular protein degradation
down regulation of protein catabolic process
down-regulation of cellular protein breakdown
down-regulation of cellular protein catabolic process
down-regulation of cellular protein catabolism
down-regulation of cellular protein degradation
down-regulation of protein catabolic process
downregulation of cellular protein breakdown
downregulation of cellular protein catabolic process
downregulation of cellular protein catabolism
downregulation of cellular protein degradation
downregulation of protein catabolic process
negative regulation of cellular protein breakdown
negative regulation of cellular protein catabolic process
negative regulation of cellular protein catabolism
negative regulation of cellular protein degradation
negative regulation of protein breakdown
negative regulation of protein catabolism
negative regulation of protein degradation
inhibition of cellular protein breakdown
inhibition of cellular protein catabolic process
inhibition of cellular protein catabolism
inhibition of cellular protein degradation
negative regulation of protein catabolic process
The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
The aggregation, arrangement and bonding together of the mature ribosome and of its subunits.
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
cellular biogenic amine biosynthetic process
The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
cellular biogenic amine catabolic process
The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
The chemical reactions and pathways resulting in the breakdown of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
The chemical reactions and pathways resulting in the breakdown of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton.
indole-containing compound metabolic process
The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton.
indole-containing compound biosynthetic process
The chemical reactions and pathways resulting in the breakdown of compounds that contain an indole (2,3-benzopyrrole) skeleton.
indole-containing compound catabolic process
Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light.
Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
Any process that modulates the frequency, rate or extent of eye photoreceptor development.
regulation of eye photoreceptor development
regulation of eye photoreceptor cell development
Any process that activates or increases the frequency, rate or extent of eye photoreceptor development.
positive regulation of eye photoreceptor development
up regulation of eye photoreceptor cell development
up-regulation of eye photoreceptor cell development
upregulation of eye photoreceptor cell development
activation of eye photoreceptor cell development
stimulation of eye photoreceptor cell development
positive regulation of eye photoreceptor cell development
Any process that stops, prevents, or reduces the frequency, rate or extent of eye photoreceptor development.
down regulation of eye photoreceptor cell development
down-regulation of eye photoreceptor cell development
downregulation of eye photoreceptor cell development
negative regulation of eye photoreceptor development
inhibition of eye photoreceptor cell development
negative regulation of eye photoreceptor cell development
A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state.
A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme.
The lipid bilayer surrounding a zymogen granule.
Any biological process involved in the maintenance of an internal steady state.
negative regulation of homeostatic process
positive regulation of homeostatic process
Any complex of actin, myosin, and accessory proteins.
The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell.
The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur.
The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, from one side of a membrane to the other.
amide transmembrane transporter activity
Any process that modulates the occurrence or rate of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
A prolongation or process extending from a cell, e.g. a flagellum or axon.
Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
regulation of Golgi to plasma membrane protein transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
down regulation of Golgi to plasma membrane protein transport
down-regulation of Golgi to plasma membrane protein transport
downregulation of Golgi to plasma membrane protein transport
inhibition of Golgi to plasma membrane protein transport
negative regulation of Golgi to plasma membrane protein transport
Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
up regulation of Golgi to plasma membrane protein transport
up-regulation of Golgi to plasma membrane protein transport
upregulation of Golgi to plasma membrane protein transport
activation of Golgi to plasma membrane protein transport
stimulation of Golgi to plasma membrane protein transport
positive regulation of Golgi to plasma membrane protein transport
The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane.
Golgi to plasma membrane protein transport
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching.
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.
extracellular structure organization and biogenesis
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
positive regulation of apoptotic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
negative regulation of apoptotic process
Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
regulation of non-apoptotic programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
positive regulation of non-apoptotic programmed cell death
positive regulation of programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
down regulation of programmed cell death
down-regulation of programmed cell death
negative regulation of non-apoptotic programmed cell death
negative regulation of programmed cell death
The nucleus of a germ cell, a reproductive cell in multicellular organisms.
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
down-regulation of metalloenzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
negative regulation of metalloenzyme activity
negative regulation of catalytic activity
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine.
Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine.
Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location.
establishment and maintenance of translational machinery localization
establishment and maintenance of translational protein localization
regulation of translation by machinery localisation
regulation of translation by machinery localization
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
multicellular organismal macromolecule metabolic process
The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-enclosed organelle
intracellular non-membrane-bounded organelle
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
down regulation of protein complex disassembly
down-regulation of protein complex disassembly
downregulation of protein complex disassembly
inhibition of protein complex disassembly
negative regulation of protein complex disassembly
negative regulation of protein-containing complex disassembly
Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
up regulation of protein complex disassembly
up-regulation of protein complex disassembly
upregulation of protein complex disassembly
activation of protein complex disassembly
stimulation of protein complex disassembly
positive regulation of protein complex disassembly
positive regulation of protein-containing complex disassembly
Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
regulation of protein complex disassembly
regulation of protein-containing complex disassembly
A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state.
Any process that modulates the frequency, rate or extent of protein complex assembly.
regulation of protein-containing complex assembly
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates.
regulation of carbohydrate biosynthetic process
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell.
extracellular non-membrane-enclosed organelle
extracellular non-membrane-bounded organelle
Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of monoatomic ion transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of monoatomic ion transport
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alkaloid stimulus. Alkaloids are a large group of nitrogenous substances found in naturally in plants, many of which have extracts that are pharmacologically active.
Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
enucleate red blood cell differentiation
A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus.
A developmental process, independent of morphogenetic (shape) change, that is required for a nucleate erythrocyte to attain its fully functional state. A nucleate erythrocyte is an erythrocyte with a nucleus.
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte with a nucleus, as found in non-mammalian vertebrates such as birds.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
response to polypeptide hormone stimulus
The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon.
regulation of secondary metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances.
regulation of generation of precursor metabolites and energy
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates.
regulation of carbohydrate catabolic process
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals.
Any process that modulates the frequency, rate or extent of muscle adaptation.
Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
regulation of apoptosis of neuronal cells
regulation of neuron programmed cell death
regulation of neuronal cell programmed cell death
regulation of programmed cell death of neuronal cells
regulation of programmed cell death, neurons
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
negative regulation of programmed cell death, neurons
negative regulation of neuron apoptotic process
Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
positive regulation of programmed cell death, neurons
positive regulation of neuron apoptotic process
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
aerobic respiration, using arsenite as electron donor
Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment.
regulation of respiratory gaseous exchange
The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-).
The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups.
The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups.
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state.
ossification involved in skeletal development
ossification involved in bone maturation
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex subunit organisation
macromolecular complex subunit organization
protein-containing complex subunit organization
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.
Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity.
Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system.
regulation of respiratory system process
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
cellular component biogenesis at cellular level
Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
regulation of cellular component biogenesis
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole.
Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
positive regulation of cellular component biogenesis
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole.
positive regulation of vacuole organisation
positive regulation of vacuole biogenesis
positive regulation of vacuole organization
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane.
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
negative regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation (ternary) complex
The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas.
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways resulting in the breakdown of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.
Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
A process in which a protein is transported to, or maintained in, a location within the cytoskeleton.
Any process evolved to enable an interaction with an organism of a different species.
interspecies interaction between organisms
interspecies interaction with other organisms
biological process involved in interspecies interaction between organisms
The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon.
secondary metabolite biosynthetic process
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
microtubule-based flagellum organization
The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion.
development of primary sexual characteristics
The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate.
Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created.
Signaling at long or short range between cells that results in the commitment of a cell to a certain fate.
cell fate commitment, cell-cell signaling
cell fate commitment, cell-cell signalling
cell-cell signaling during in cell fate commitment
cell-cell signaling resulting in cell fate commitment
cell-cell signalling during cell fate commitment
cell-cell signalling resulting in cell fate commitment
cell-cell signalling involved in cell fate specification
cell-cell signaling involved in cell fate commitment
The directed movement of a protein to a specific location.
Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system.
establishment and/or maintenance of neuroblast cell polarity
establishment or maintenance of neuroblast polarity
The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system.
establishment of neuroblast cell polarity
The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
cell-cell junction assembly and maintenance
intercellular junction assembly and maintenance
The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
positive regulation of CD4 biosynthetic process
up regulation of CD4 biosynthetic process
up-regulation of CD4 biosynthetic process
upregulation of CD4 biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
down regulation of CD4 biosynthetic process
down-regulation of CD4 biosynthetic process
downregulation of CD4 biosynthetic process
negative regulation of CD4 biosynthetic process
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell.
external encapsulating structure organisation
external encapsulating structure organization and biogenesis
external encapsulating structure organization
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
negative regulation of cell differentiation
Any process that activates or increases the frequency, rate or extent of cell differentiation.
positive regulation of cell differentiation
Any process that modulates the frequency, rate or extent of adipocyte differentiation.
regulation of adipocyte cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
down regulation of fat cell differentiation
down-regulation of fat cell differentiation
downregulation of fat cell differentiation
negative regulation of adipocyte cell differentiation
negative regulation of adipocyte differentiation
negative regulation of fat cell differentiation
Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
positive regulation of adipocyte cell differentiation
positive regulation of adipocyte differentiation
up regulation of fat cell differentiation
up-regulation of fat cell differentiation
upregulation of fat cell differentiation
positive regulation of fat cell differentiation
Any process that modulates the frequency, rate or extent of endothelial cell differentiation.
regulation of endothelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation.
down regulation of endothelial cell differentiation
down-regulation of endothelial cell differentiation
downregulation of endothelial cell differentiation
inhibition of endothelial cell differentiation
negative regulation of endothelial cell differentiation
Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation.
up regulation of endothelial cell differentiation
up-regulation of endothelial cell differentiation
upregulation of endothelial cell differentiation
activation of endothelial cell differentiation
stimulation of endothelial cell differentiation
positive regulation of endothelial cell differentiation
Any process that modulates the frequency, rate or extent of epidermal cell differentiation.
regulation of hypodermal cell differentiation
regulation of epidermal cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation.
down regulation of epidermal cell differentiation
down-regulation of epidermal cell differentiation
downregulation of epidermal cell differentiation
inhibition of epidermal cell differentiation
negative regulation of hypodermal cell differentiation
negative regulation of epidermal cell differentiation
Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation.
up regulation of epidermal cell differentiation
up-regulation of epidermal cell differentiation
upregulation of epidermal cell differentiation
activation of epidermal cell differentiation
stimulation of epidermal cell differentiation
positive regulation of hypodermal cell differentiation
positive regulation of epidermal cell differentiation
Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
regulation of myeloid cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation.
down regulation of myeloid cell differentiation
down-regulation of myeloid cell differentiation
downregulation of myeloid cell differentiation
inhibition of myeloid cell differentiation
negative regulation of myeloid cell differentiation
Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
up regulation of myeloid cell differentiation
up-regulation of myeloid cell differentiation
upregulation of myeloid cell differentiation
activation of myeloid cell differentiation
stimulation of myeloid cell differentiation
positive regulation of myeloid cell differentiation
Any process that modulates the frequency, rate or extent of erythrocyte differentiation.
regulation of red blood cell differentiation
regulation of erythrocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
down regulation of erythrocyte differentiation
down-regulation of erythrocyte differentiation
downregulation of erythrocyte differentiation
negative regulation of RBC differentiation
negative regulation of red blood cell differentiation
inhibition of erythrocyte differentiation
negative regulation of erythrocyte differentiation
Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
positive regulation of RBC differentiation
positive regulation of red blood cell differentiation
up regulation of erythrocyte differentiation
up-regulation of erythrocyte differentiation
upregulation of erythrocyte differentiation
activation of erythrocyte differentiation
stimulation of erythrocyte differentiation
positive regulation of erythrocyte differentiation
Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.
regulation of megakaryocyte differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
down regulation of megakaryocyte differentiation
down-regulation of megakaryocyte differentiation
downregulation of megakaryocyte differentiation
inhibition of megakaryocyte differentiation
negative regulation of megakaryocyte differentiation
Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation.
up regulation of megakaryocyte differentiation
up-regulation of megakaryocyte differentiation
upregulation of megakaryocyte differentiation
activation of megakaryocyte differentiation
stimulation of megakaryocyte differentiation
positive regulation of megakaryocyte differentiation
Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
down regulation of myoblast differentiation
down-regulation of myoblast differentiation
downregulation of myoblast differentiation
negative regulation of myoblast differentiation
Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
up regulation of myoblast differentiation
up-regulation of myoblast differentiation
upregulation of myoblast differentiation
positive regulation of myoblast differentiation
Any process that modulates the frequency, rate or extent of neuron differentiation.
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
down regulation of neuron differentiation
down-regulation of neuron differentiation
downregulation of neuron differentiation
negative regulation of neuron differentiation
Any process that activates or increases the frequency, rate or extent of neuron differentiation.
positive regulation of neuron differentiation
Any process that modulates the frequency, rate or extent of epidermis development.
Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development.
down regulation of epidermis development
down-regulation of epidermis development
negative regulation of epidermal development
negative regulation of hypodermis development
negative regulation of epidermis development
Any process that activates or increases the frequency, rate or extent of epidermis development.
positive regulation of epidermal development
positive regulation of hypodermis development
positive regulation of epidermis development
Any process that modulates the frequency, rate or extent of glia cell differentiation.
regulation of glial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation.
down regulation of glial cell differentiation
down-regulation of glial cell differentiation
downregulation of glial cell differentiation
negative regulation of glia cell differentiation
negative regulation of neuroglia differentiation
inhibition of glial cell differentiation
negative regulation of glial cell differentiation
Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
positive regulation of glia cell differentiation
positive regulation of neuroglia differentiation
up regulation of glial cell differentiation
up-regulation of glial cell differentiation
upregulation of glial cell differentiation
activation of glial cell differentiation
stimulation of glial cell differentiation
positive regulation of glial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
down regulation of glycogen biosynthetic process
down-regulation of glycogen biosynthetic process
downregulation of glycogen biosynthetic process
negative regulation of glycogen anabolism
negative regulation of glycogen biosynthesis
negative regulation of glycogen formation
negative regulation of glycogen synthesis
inhibition of glycogen biosynthetic process
negative regulation of glycogen biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis.
Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
Any process that activates or increases the frequency, rate or extent of the formation of a cilium.
positive regulation of flagellum assembly
positive regulation of flagellum biogenesis
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
positive regulation of glycogen anabolism
positive regulation of glycogen biosynthesis
positive regulation of glycogen formation
positive regulation of glycogen synthesis
up regulation of glycogen biosynthetic process
up-regulation of glycogen biosynthetic process
upregulation of glycogen biosynthetic process
activation of glycogen biosynthetic process
stimulation of glycogen biosynthetic process
positive regulation of glycogen biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
positive regulation of protein anabolism
positive regulation of protein biosynthesis
positive regulation of protein biosynthetic process
positive regulation of protein formation
positive regulation of protein synthesis
up regulation of protein biosynthetic process
up-regulation of protein biosynthetic process
upregulation of protein biosynthetic process
activation of protein biosynthetic process
stimulation of protein biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
positive regulation of cellular protein breakdown
positive regulation of cellular protein catabolic process
positive regulation of cellular protein catabolism
positive regulation of cellular protein degradation
positive regulation of protein breakdown
positive regulation of protein catabolism
positive regulation of protein degradation
up regulation of cellular protein breakdown
up regulation of cellular protein catabolic process
up regulation of cellular protein catabolism
up regulation of cellular protein degradation
up regulation of protein catabolic process
up-regulation of cellular protein breakdown
up-regulation of cellular protein catabolic process
up-regulation of cellular protein catabolism
up-regulation of cellular protein degradation
up-regulation of protein catabolic process
upregulation of cellular protein breakdown
upregulation of cellular protein catabolic process
upregulation of cellular protein catabolism
upregulation of cellular protein degradation
upregulation of protein catabolic process
activation of cellular protein breakdown
activation of cellular protein catabolic process
activation of cellular protein catabolism
activation of cellular protein degradation
positive regulation of cyclin catabolic process
positive regulation of cyclin catabolism
positive regulation of cyclin degradation
positive regulation of degradation of cyclin
stimulation of protein catabolic process
positive regulation of protein catabolic process
The chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate.
down regulation of acetate catabolic process
down-regulation of acetate catabolic process
downregulation of acetate catabolic process
negative regulation of acetate breakdown
negative regulation of acetate catabolism
negative regulation of acetate degradation
negative regulation of acetate catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate.
positive regulation of acetate breakdown
positive regulation of acetate catabolism
positive regulation of acetate degradation
up regulation of acetate catabolic process
up-regulation of acetate catabolic process
upregulation of acetate catabolic process
stimulation of acetate catabolic process
positive regulation of acetate catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.
down regulation of amino acid metabolic process
down-regulation of amino acid metabolic process
downregulation of amino acid metabolic process
negative regulation of amino acid metabolism
inhibition of amino acid metabolic process
negative regulation of cellular amino acid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid.
positive regulation of amino acid metabolism
positive regulation of cellular amino acid metabolic process
up regulation of amino acid metabolic process
up-regulation of amino acid metabolic process
upregulation of amino acid metabolic process
activation of amino acid metabolic process
stimulation of amino acid metabolic process
positive regulation of amino acid metabolic process
Any process that modulates the frequency, rate or extent of angiogenesis.
Any process that activates or increases angiogenesis.
Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division.
down regulation of asymmetric cell division
down-regulation of asymmetric cell division
downregulation of asymmetric cell division
negative regulation of asymmetric cell division
Any process that activates or increases the frequency, rate or extent of asymmetric cell division.
up regulation of asymmetric cell division
up-regulation of asymmetric cell division
upregulation of asymmetric cell division
positive regulation of asymmetric cell division
Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
positive regulation of bone biosynthesis
Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
down regulation of progression through cell cycle
down-regulation of progression through cell cycle
downregulation of progression through cell cycle
negative regulation of cell cycle progression
negative regulation of progression through cell cycle
inhibition of progression through cell cycle
Any process that activates or increases the rate or extent of progression through the cell cycle.
positive regulation of cell cycle progression
positive regulation of progression through cell cycle
up regulation of progression through cell cycle
up-regulation of progression through cell cycle
upregulation of progression through cell cycle
activation of progression through cell cycle
stimulation of progression through cell cycle
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
down regulation of glycogen catabolic process
down-regulation of glycogen catabolic process
downregulation of glycogen catabolic process
negative regulation of glycogen breakdown
negative regulation of glycogen catabolism
negative regulation of glycogen degradation
inhibition of glycogen catabolic process
negative regulation of glycogen catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
positive regulation of glycogen breakdown
positive regulation of glycogen catabolism
positive regulation of glycogen degradation
up regulation of glycogen catabolic process
up-regulation of glycogen catabolic process
upregulation of glycogen catabolic process
activation of glycogen catabolic process
stimulation of glycogen catabolic process
positive regulation of glycogen catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
negative regulation of cardiac contraction
negative regulation of heart contraction
Any process that activates or increases the frequency, rate or extent of heart contraction.
positive regulation of cardiac contraction
positive regulation of heart contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids.
down regulation of lipid metabolic process
down-regulation of lipid metabolic process
downregulation of lipid metabolic process
negative regulation of lipid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.
up regulation of lipid metabolic process
up-regulation of lipid metabolic process
positive regulation of lipid metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.
negative regulation of meiotic nuclear division
Any process that activates or increases the frequency, rate or extent of meiosis.
positive regulation of meiotic nuclear division
Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
negative regulation of mitotic nuclear division
Any process that activates or increases the frequency, rate or extent of mitosis.
positive regulation of mitotic nuclear division
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development.
down regulation of striated muscle development
down-regulation of striated muscle development
downregulation of striated muscle development
inhibition of striated muscle development
negative regulation of striated muscle tissue development
Any process that activates or increases the frequency, rate or extent of striated muscle development.
up regulation of striated muscle development
up-regulation of striated muscle development
upregulation of striated muscle development
activation of striated muscle development
stimulation of striated muscle development
positive regulation of striated muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
down regulation of translational elongation
down-regulation of translational elongation
downregulation of translational elongation
negative regulation of translational elongation
Any process that activates or increases the frequency, rate or extent of translational elongation.
up regulation of translational elongation
up-regulation of translational elongation
upregulation of translational elongation
positive regulation of translational elongation
Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination.
down regulation of translational termination
down-regulation of translational termination
downregulation of translational termination
negative regulation of translational termination
Any process that activates or increases the frequency, rate or extent of translational termination.
up regulation of translational termination
up-regulation of translational termination
upregulation of translational termination
stimulation of translational termination
positive regulation of translational termination
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
down regulation of carbohydrate metabolic process
down-regulation of carbohydrate metabolic process
downregulation of carbohydrate metabolic process
negative regulation of carbohydrate metabolism
inhibition of carbohydrate metabolic process
negative regulation of carbohydrate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
positive regulation of carbohydrate metabolism
up regulation of carbohydrate metabolic process
up-regulation of carbohydrate metabolic process
upregulation of carbohydrate metabolic process
activation of carbohydrate metabolic process
stimulation of carbohydrate metabolic process
positive regulation of carbohydrate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine.
down regulation of catecholamine metabolic process
down-regulation of catecholamine metabolic process
downregulation of catecholamine metabolic process
negative regulation of catecholamine metabolism
inhibition of catecholamine metabolic process
negative regulation of catecholamine metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine.
positive regulation of catecholamine metabolism
up regulation of catecholamine metabolic process
up-regulation of catecholamine metabolic process
upregulation of catecholamine metabolic process
activation of catecholamine metabolic process
stimulation of catecholamine metabolic process
positive regulation of catecholamine metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.
Any process that activates or increases the frequency, rate or extent of exocytosis.
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
down regulation of progression through mitotic cell cycle
down-regulation of progression through mitotic cell cycle
downregulation of progression through mitotic cell cycle
negative regulation of mitotic cell cycle progression
negative regulation of progression through mitotic cell cycle
inhibition of progression through mitotic cell cycle
negative regulation of mitotic cell cycle
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
positive regulation of mitotic cell cycle progression
positive regulation of progression through mitotic cell cycle
up regulation of progression through mitotic cell cycle
up-regulation of progression through mitotic cell cycle
upregulation of progression through mitotic cell cycle
activation of progression through mitotic cell cycle
stimulation of progression through mitotic cell cycle
positive regulation of mitotic cell cycle
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction.
negative regulation of muscle contraction
Any process that activates or increases the frequency, rate or extent of muscle contraction.
positive regulation of muscle contraction
Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase-containing compound metabolic process
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase-containing compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
down regulation of phosphate metabolic process
down-regulation of phosphate metabolic process
downregulation of phosphate metabolic process
negative regulation of phosphate metabolism
inhibition of phosphate metabolic process
negative regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
positive regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids.
down regulation of steroid metabolic process
down-regulation of steroid metabolic process
downregulation of steroid metabolic process
negative regulation of steroid metabolism
negative regulation of steroid metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids.
positive regulation of steroid metabolism
up regulation of steroid metabolic process
up-regulation of steroid metabolic process
upregulation of steroid metabolic process
stimulation of steroid metabolic process
positive regulation of steroid metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
down regulation of translational initiation
down-regulation of translational initiation
downregulation of translational initiation
negative regulation of translational initiation
Any process that activates or increases the frequency, rate or extent of translational initiation.
up regulation of translational initiation
up-regulation of translational initiation
upregulation of translational initiation
positive regulation of translational initiation
Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction.
down regulation of smooth muscle contraction
down-regulation of smooth muscle contraction
downregulation of smooth muscle contraction
negative regulation of smooth muscle contraction
Any process that activates or increases the frequency, rate or extent of smooth muscle contraction.
up regulation of smooth muscle contraction
up-regulation of smooth muscle contraction
upregulation of smooth muscle contraction
stimulation of smooth muscle contraction
positive regulation of smooth muscle contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction.
down regulation of striated muscle contraction
down-regulation of striated muscle contraction
downregulation of striated muscle contraction
inhibition of striated muscle contraction
negative regulation of striated muscle contraction
Any process that activates or increases the frequency, rate or extent of striated muscle contraction.
up regulation of striated muscle contraction
up-regulation of striated muscle contraction
upregulation of striated muscle contraction
activation of striated muscle contraction
stimulation of striated muscle contraction
positive regulation of striated muscle contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development.
down regulation of embryonic development
down-regulation of embryonic development
negative regulation of embryonic development
Any process that modulates the frequency, rate or extent of embryonic development.
The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.
phenol-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.
The chemical reactions and pathways resulting in the formation of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.
The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.
The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster.
Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
regulation of photoreceptor differentiation
regulation of photoreceptor cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
down regulation of photoreceptor cell differentiation
down regulation of photoreceptor differentiation
down-regulation of photoreceptor cell differentiation
down-regulation of photoreceptor differentiation
downregulation of photoreceptor cell differentiation
downregulation of photoreceptor differentiation
negative regulation of photoreceptor differentiation
inhibition of photoreceptor cell differentiation
inhibition of photoreceptor differentiation
negative regulation of photoreceptor cell differentiation
Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
positive regulation of photoreceptor differentiation
up regulation of photoreceptor cell differentiation
up regulation of photoreceptor differentiation
up-regulation of photoreceptor cell differentiation
up-regulation of photoreceptor differentiation
upregulation of photoreceptor cell differentiation
upregulation of photoreceptor differentiation
activation of photoreceptor cell differentiation
activation of photoreceptor differentiation
stimulation of photoreceptor cell differentiation
stimulation of photoreceptor differentiation
positive regulation of photoreceptor cell differentiation
The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion.
development of primary female sexual characteristics
Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light.
Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision.
Any process that modulates the frequency, rate or extent of growth of an organ of an organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism.
Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism.
The establishment of the sex of a female organism by physical differentiation.
Programmed cell death that occurs in the developing retina.
Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium.
compound eye retinal cell programmed cell death
Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina.
regulation of retinal programmed cell death
regulation of retinal cell programmed cell death
Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
regulation of compound eye retinal cell programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the retina.
positive regulation of retinal programmed cell death
up regulation of retinal programmed cell death
up-regulation of retinal programmed cell death
upregulation of retinal programmed cell death
activation of retinal programmed cell death
stimulation of retinal programmed cell death
positive regulation of retinal cell programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the retina.
down regulation of retinal programmed cell death
down-regulation of retinal programmed cell death
downregulation of retinal programmed cell death
negative regulation of retinal programmed cell death
inhibition of retinal programmed cell death
negative regulation of retinal cell programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
activation of retinal cell programmed cell death
stimulation of retinal cell programmed cell death
up regulation of retinal cell programmed cell death
up-regulation of retinal cell programmed cell death
upregulation of retinal cell programmed cell death
positive regulation of compound eye retinal cell programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
down regulation of retinal cell programmed cell death
down-regulation of retinal cell programmed cell death
downregulation of retinal cell programmed cell death
inhibition of retinal cell programmed cell death
negative regulation of retina cell programmed cell death
negative regulation of compound eye retinal cell programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
negative regulation of insulin secretion
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbamate stimulus. Carbamates are a group of insecticides and parasiticides that act by inhibiting cholinesterase.
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state.
The controlled release of acid by a cell or a tissue.
The addition of tubulin heterodimers to one or both ends of a microtubule.
Enables the transfer of metal ions from one side of a membrane to the other.
heavy metal ion:hydrogen symporter activity
high affinity metal ion uptake transporter activity
low affinity metal ion uptake transporter activity
metal ion transmembrane transporter activity
The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell.
Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell.
positive regulation of hormone secretion
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell.
negative regulation of hormone secretion
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
positive regulation of lipid biosynthesis
up regulation of lipid biosynthetic process
up-regulation of lipid biosynthetic process
upregulation of lipid biosynthetic process
activation of lipid biosynthetic process
stimulation of lipid biosynthetic process
positive regulation of lipid biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
regulation of lipid biosynthetic process
The controlled release of a substance by a cell or a tissue.
The directed movement of substances within a cell.
Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell.
regulation of neurotransmitter secretion
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter.
down regulation of neurotransmitter secretion
down-regulation of neurotransmitter secretion
downregulation of neurotransmitter secretion
inhibition of neurotransmitter secretion
negative regulation of neurotransmitter secretion
The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
carboxylic acid transmembrane transporter activity
Exchange of isocitrate and 2-oxoglutarate across the peroxisomal membrane
The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination.
The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
regulation of pigmentation during development
regulation of developmental pigmentation
Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
down regulation of developmental pigmentation
down-regulation of developmental pigmentation
downregulation of developmental pigmentation
negative regulation of developmental pigmentation
Any process that increases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
up regulation of developmental pigmentation
up-regulation of developmental pigmentation
upregulation of developmental pigmentation
activation of developmental pigmentation
stimulation of developmental pigmentation
positive regulation of developmental pigmentation
The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
The self-renewing division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes.
female germ-line stem cell asymmetric division
The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population.
Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
up regulation of fibroblast proliferation
up-regulation of fibroblast proliferation
upregulation of fibroblast proliferation
positive regulation of fibroblast proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
down regulation of fibroblast proliferation
down-regulation of fibroblast proliferation
downregulation of fibroblast proliferation
negative regulation of fibroblast proliferation
The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation.
vesicle targeting, to, from or within dictyosome
vesicle targeting, to, from or within Golgi
Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus.
regulation of vesicle targeting, to, from or within Golgi
The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system.
Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.
The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
The creation of a single organelle from two or more organelles.
The creation of two or more organelles by division of one organelle.
The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei.
nuclear membrane fusion during karyogamy
nuclear membrane fusion involved in karyogamy
The partitioning of organelles between daughter cells at cell division.
The partitioning of Golgi apparatus between daughter cells at cell division.
The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The process in which the anatomical structures of the axial mesoderm are generated and organized.
The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process in which the anatomical structures of the mesoderm are generated and organized.
The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube.
The process in which the anatomical structures of the paraxial mesoderm are generated and organized.
The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure.
The process in which the anatomical structures of the lateral mesoderm are generated and organized.
The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The process whose specific outcome is the progression of the intermediate mesoderm over time, from its formation to the mature structure. The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
The process in which the anatomical structures of the intermediate mesoderm are generated and organized.
The process that gives rise to the intermediate mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.
The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state.
The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands.
The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development.
regulation of timing of cell differentiation
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
positive regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
negative regulation of biological process
Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation.
haematopoietic or lymphoid organ development
haemopoietic or lymphoid organ development
hemopoietic or lymphoid organ development
hematopoietic or lymphoid organ development
The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed.
Morphogenesis, during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
regulation of post-embryonic development
Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
down regulation of post-embryonic development
down-regulation of post-embryonic development
downregulation of post-embryonic development
inhibition of post-embryonic development
negative regulation of post-embryonic development
Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
up regulation of post-embryonic development
up-regulation of post-embryonic development
upregulation of post-embryonic development
activation of post-embryonic development
stimulation of post-embryonic development
positive regulation of post-embryonic development
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
positive regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another.
developmental growth of a unicellular organism
The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
The process in which the anatomical structures of the eye are generated and organized.
The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
The process in which the anatomical structures of the eye are generated and organized during embryonic development.
The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
embryonic anatomical structure morphogenesis
The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte.
oocyte morphogenesis during differentiation
The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures.
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
reproductive process in a multicellular organism
multicellular organismal reproductive process
The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
A developmental process, independent of morphogenetic (shape) change, that is required for a myoblast to attain its fully functional state. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size.
Any process that modulates the frequency, rate or extent of skeletal muscle growth.
regulation of skeletal muscle tissue growth
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle growth.
down regulation of skeletal muscle growth
down-regulation of skeletal muscle growth
downregulation of skeletal muscle growth
negative regulation of skeletal muscle tissue growth
Any process that activates, maintains or increases the rate of skeletal muscle growth.
positive regulation of skeletal muscle tissue growth
Any process that modulates the frequency, rate or extent of muscle development.
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development.
negative regulation of muscle organ development
Any process that activates, maintains or increases the rate of muscle development.
positive regulation of muscle organ development
Any process that modulates the frequency, rate or extent of developmental growth.
Any process that activates, maintains or increases the rate of developmental growth.
positive regulation of developmental growth
Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth.
negative regulation of developmental growth
Any process that modulates the frequency, rate or extent of skeletal muscle tissue development.
regulation of skeletal muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development.
down regulation of skeletal muscle development
down-regulation of skeletal muscle development
downregulation of skeletal muscle development
inhibition of skeletal muscle development
negative regulation of skeletal muscle tissue development
Any process that activates, maintains or increases the rate of skeletal muscle tissue development.
up regulation of skeletal muscle development
up-regulation of skeletal muscle development
upregulation of skeletal muscle development
activation of skeletal muscle development
stimulation of skeletal muscle development
positive regulation of skeletal muscle tissue development
The process in which the anatomical structures of muscle are generated and organized.
The process pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ.
initiation of an animal organ primordium
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
formation of an anatomical structure involved in morphogenesis
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population.
Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation.
regulation of smooth muscle cell proliferation
Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
positive regulation of SMC proliferation
up regulation of smooth muscle cell proliferation
up-regulation of smooth muscle cell proliferation
upregulation of smooth muscle cell proliferation
activation of smooth muscle cell proliferation
stimulation of smooth muscle cell proliferation
positive regulation of smooth muscle cell proliferation
Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
down regulation of smooth muscle cell proliferation
down-regulation of smooth muscle cell proliferation
downregulation of smooth muscle cell proliferation
negative regulation of SMC proliferation
inhibition of smooth muscle cell proliferation
negative regulation of smooth muscle cell proliferation
The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron.
neuron morphogenesis involved in differentiation
cell morphogenesis involved in neuron differentiation
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.
The process in which the anatomical structures of the skeleton are generated and organized.
The process in which the anatomical structures of a tissue are generated and organized.
The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion.
The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch.
The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
regulation of skeletal muscle fibre development
regulation of skeletal myofiber development
regulation of skeletal myofibre development
regulation of skeletal muscle fiber development
Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
positive regulation of skeletal muscle fibre development
positive regulation of skeletal myofiber development
positive regulation of skeletal myofibre development
up regulation of skeletal muscle fiber development
up-regulation of skeletal muscle fiber development
upregulation of skeletal muscle fiber development
activation of skeletal muscle fiber development
stimulation of skeletal muscle fiber development
positive regulation of skeletal muscle fiber development
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
down regulation of skeletal muscle fiber development
down-regulation of skeletal muscle fiber development
downregulation of skeletal muscle fiber development
negative regulation of skeletal muscle fibre development
negative regulation of skeletal myofiber development
negative regulation of skeletal myofibre development
inhibition of skeletal muscle fiber development
negative regulation of skeletal muscle fiber development
The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule.
pigment granule organization and biogenesis
The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
branching morphogenesis of an epithelial tube
The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron).
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes.
A developmental process, independent of morphogenetic (shape) change, that is required for an animal organ to attain its fully functional state. An organ is a tissue or set of tissues that work together to perform a specific function or functions.
The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure.
The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process aimed at the progression of a nucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart.
The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma.
The process in which the anatomical structures of a cell projection are generated and organized.
The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
Any process involved in the maintenance of an internal steady state at the level of the multicellular organism.
multicellular organismal-level homeostasis
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the peripheral nervous system.
peripheral nervous system neuron differentiation
The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
peripheral nervous system neuron development
Any process in which a chromosome is transported to, or maintained in, a specific location.
establishment and maintenance of chromosome localization
establishment and maintenance of chromosome position
The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
Any process that modulates the frequency, rate or extent of the regulated release of catecholamines.
The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.
Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
regulation of epithelial cell proliferation
Any process that activates or increases the rate or extent of epithelial cell proliferation.
up regulation of epithelial cell proliferation
up-regulation of epithelial cell proliferation
upregulation of epithelial cell proliferation
activation of epithelial cell proliferation
stimulation of epithelial cell proliferation
positive regulation of epithelial cell proliferation
Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
down regulation of epithelial cell proliferation
down-regulation of epithelial cell proliferation
downregulation of epithelial cell proliferation
inhibition of epithelial cell proliferation
negative regulation of epithelial cell proliferation
Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell.
negative regulation of protein secretion
Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
positive regulation of protein secretion
Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system.
Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system.
Any process that activates or increases the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system.
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the activity of an enzyme.
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
Any process that modulates the frequency, rate or extent of the regulated release of insulin.
Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
regulation of synapse structure or activity
Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
regulation of chemical synaptic transmission
modulation of chemical synaptic transmission
Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
down regulation of synaptic transmission
down-regulation of synaptic transmission
negative regulation of synaptic transmission
Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
positive regulation of synaptic transmission
Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
regulation of synapse organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
regulation of steroid biosynthetic process
A organ system process carried out by any of the organs or tissues of neurological system.
Any process that modulates the levels of body fluids.
Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system.
The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Any process pertaining to the functions of the nervous and muscular systems of an organism.
The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
sensory perception, sensory transduction of stimulus
detection of stimulus involved in sensory perception
The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception.
sensory detection of chemical stimulus during sensory perception
sensory perception, sensory detection of chemical stimulus
sensory perception, sensory transduction of chemical stimulus
sensory transduction of chemical stimulus
sensory transduction of chemical stimulus during sensory perception
detection of chemical stimulus involved in sensory perception
The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.
sensory detection of light during visual perception
sensory detection of light stimulus during visual perception
sensory transduction of light during visual perception
sensory transduction of light stimulus during visual perception
visual perception, detection of light stimulus
visual perception, sensory transduction during perception of light
visual perception, sensory transduction of light stimulus
detection of light stimulus involved in visual perception
The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte.
Note that the chromatophore mentioned here is distinct from the pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria. It is also different from the plant chromoplast, which is also sometimes called a chromatophore.
Any process that modulates the frequency, rate or extent of pigmented cell differentiation.
regulation of pigment cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of pigment cell differentiation.
down regulation of pigment cell differentiation
down-regulation of pigment cell differentiation
downregulation of pigment cell differentiation
inhibition of pigment cell differentiation
negative regulation of pigment cell differentiation
Any process that activates or increases the frequency, rate or extent of pigment cell differentiation.
up regulation of pigment cell differentiation
up-regulation of pigment cell differentiation
upregulation of pigment cell differentiation
activation of pigment cell differentiation
stimulation of pigment cell differentiation
positive regulation of pigment cell differentiation
The series of events required for an organism to receive a sensory electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
sensory perception of electrical stimulus
The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
sensory perception of mechanical stimulus
The series of events required for an organism to receive an electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. Many fish possess an electroception sense; for example, the electric eel uses low voltage pulses of electricity for navigation and prey location.
The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light.
sensory detection of light stimulus during sensory perception
sensory perception, sensory detection of light stimulus
sensory perception, sensory transduction of light stimulus
sensory transduction of light stimulus during sensory perception
detection of light stimulus involved in sensory perception
The series of events in which an electrical stimulus is received by a cell and converted into a molecular signal as part of sensory perception.
sensory detection of electrical stimulus
sensory detection of electrical stimulus during sensory perception
sensory perception, sensory detection of electrical stimulus
sensory perception, sensory transduction of electrical stimulus
sensory transduction of electrical stimulus
sensory transduction of electrical stimulus during sensory perception
detection of electrical stimulus involved in sensory perception
The series of events that contribute to electroception in which an electrical stimulus is received and converted into a molecular signal.
electroception, detection of electrical stimulus
electroception, sensory detection of electrical stimulus
electroception, sensory transduction of electrical stimulus
detection of electrical stimulus during electroreception
sensory detection of electrical stimulus during electroception
sensory transduction of electrical stimulus during electroception
detection of electrical stimulus involved in electroception
The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal.
perception of pain, detection of electrical stimulus
perception of pain, sensory detection of electrical stimulus
perception of pain, sensory transduction of electrical stimulus
detection of electrical stimulus during sensory perception of pain
sensory detection of electrical stimulus during perception of pain
sensory transduction of electrical stimulus during perception of pain
detection of electrical stimulus involved in sensory perception of pain
The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal.
perception of pain, detection of chemical stimulus
perception of pain, sensory detection of chemical stimulus
perception of pain, sensory transduction of chemical stimulus
sensory detection of chemical stimulus during perception of pain
sensory transduction of chemical stimulus during perception of pain
detection of chemical stimulus involved in sensory perception of pain
The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).
The series of events by which an electrical stimulus is received and converted into a molecular signal.
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
down regulation of lipid catabolic process
down-regulation of lipid catabolic process
downregulation of lipid catabolic process
negative regulation of lipid degradation
negative regulation of lipid catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
positive regulation of lipid degradation
up regulation of lipid catabolic process
up-regulation of lipid catabolic process
positive regulation of lipid catabolic process
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information.
nucleic acid transmembrane transporter activity
Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other.
Exportin complex translocates pre-miRNA to cytosol
Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other.
Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA.
down regulation of DNA metabolic process
down-regulation of DNA metabolic process
negative regulation of DNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA.
positive regulation of DNA metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
down regulation of lipid biosynthetic process
down-regulation of lipid biosynthetic process
downregulation of lipid biosynthetic process
negative regulation of lipid biosynthesis
inhibition of lipid biosynthetic process
negative regulation of lipid biosynthetic process
The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs.
The controlled breakdown of the nuclear membranes, for example during cellular division.
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
down regulation of developmental process
down-regulation of developmental process
negative regulation of developmental process
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
positive regulation of developmental process
Enables the transfer of a sugar from one side of a membrane to the other. A sugar is any member of a class of sweet, water-soluble, crystallizable carbohydrates, which are the monosaccharides and smaller oligosaccharides.
sugar transmembrane transporter activity
GLUT7 and GLUT11 transport glucose and fructose
SLC45A3 transports Glc from extracellular region to cytosol
SLC50A1 transports Glc from cytosol to extracellular region
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
regulation of cellular component organisation
regulation of cellular component organization and biogenesis
regulation of cellular component organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
negative regulation of cell organisation
negative regulation of cellular component organization and biogenesis
negative regulation of cellular component organization
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
positive regulation of cell organisation
positive regulation of cellular component organization and biogenesis
positive regulation of cellular component organization
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary.
The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle.
Any process that modulates the frequency, rate or extent of muscle cell differentiation.
regulation of muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation.
down regulation of muscle cell differentiation
down-regulation of muscle cell differentiation
downregulation of muscle cell differentiation
inhibition of muscle cell differentiation
negative regulation of muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
up regulation of muscle cell differentiation
up-regulation of muscle cell differentiation
upregulation of muscle cell differentiation
activation of muscle cell differentiation
stimulation of muscle cell differentiation
positive regulation of muscle cell differentiation
Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation.
regulation of smooth muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation.
down regulation of smooth muscle cell differentiation
down-regulation of smooth muscle cell differentiation
downregulation of smooth muscle cell differentiation
inhibition of smooth muscle cell differentiation
negative regulation of smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of smooth muscle cell differentiation.
up regulation of smooth muscle cell differentiation
up-regulation of smooth muscle cell differentiation
upregulation of smooth muscle cell differentiation
activation of smooth muscle cell differentiation
stimulation of smooth muscle cell differentiation
positive regulation of smooth muscle cell differentiation
Any process that modulates the frequency, rate or extent of striated muscle cell differentiation.
regulation of striated muscle cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation.
down regulation of striated muscle cell differentiation
down-regulation of striated muscle cell differentiation
downregulation of striated muscle cell differentiation
inhibition of striated muscle cell differentiation
negative regulation of striated muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation.
up regulation of striated muscle cell differentiation
up-regulation of striated muscle cell differentiation
upregulation of striated muscle cell differentiation
activation of striated muscle cell differentiation
stimulation of striated muscle cell differentiation
positive regulation of striated muscle cell differentiation
The directed movement of substances into, out of, or within the nucleus.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
regulation of nitrogen compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
down regulation of nitrogen metabolic process
down-regulation of nitrogen metabolic process
downregulation of nitrogen metabolic process
negative regulation of nitrogen metabolic process
negative regulation of nitrogen metabolism
inhibition of nitrogen metabolic process
negative regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
activation of nitrogen metabolic process
stimulation of nitrogen metabolic process
positive regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.
down regulation of sulfur metabolic process
down-regulation of sulfur metabolic process
downregulation of sulfur metabolic process
negative regulation of sulfur metabolism
negative regulation of sulphur metabolic process
negative regulation of sulphur metabolism
negative regulation of sulfur metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.
positive regulation of sulfur metabolism
positive regulation of sulphur metabolic process
positive regulation of sulphur metabolism
up regulation of sulfur metabolic process
up-regulation of sulfur metabolic process
upregulation of sulfur metabolic process
positive regulation of sulfur metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of protein transport
Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of protein transport
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
The directed movement of RNA to a specific location.
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
positive regulation of multicellular organismal process
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
negative regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
regulation of cellular protein metabolic process
regulation of cellular protein metabolism
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein.
positive regulation of cellular protein metabolic process
positive regulation of cellular protein metabolism
positive regulation of protein metabolism
up regulation of cellular protein metabolic process
up regulation of protein metabolic process
up-regulation of cellular protein metabolic process
up-regulation of protein metabolic process
upregulation of cellular protein metabolic process
upregulation of protein metabolic process
activation of cellular protein metabolic process
stimulation of cellular protein metabolic process
stimulation of protein metabolic process
positive regulation of protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein.
down regulation of cellular protein metabolic process
down regulation of protein metabolic process
down-regulation of cellular protein metabolic process
down-regulation of protein metabolic process
downregulation of cellular protein metabolic process
downregulation of protein metabolic process
negative regulation of cellular protein metabolic process
negative regulation of cellular protein metabolism
negative regulation of protein metabolism
inhibition of cellular protein metabolic process
negative regulation of protein metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA.
down regulation of RNA metabolic process
down-regulation of RNA metabolic process
negative regulation of RNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA.
positive regulation of RNA metabolic process
The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein.
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.
The directed movement of a chromosome to a specific location.
establishment of chromosome localisation
establishment of chromosome localization
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
positive regulation of hydrolase activity
Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds.
negative regulation of hydrolase activity
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
positive regulation of transferase activity
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
negative regulation of transferase activity
Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
neuron programmed cell death by apoptosis
neuronal cell programmed cell death by apoptosis
programmed cell death of neuronal cells by apoptosis
programmed cell death of neurons by apoptosis
Any process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances.
Any process that modulates the rate or extent of progression through the meiotic cell cycle.
modulation of meiotic cell cycle progression
regulation of meiotic cell cycle progression
regulation of progression through meiotic cell cycle
Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle.
positive regulation of meiotic cell cycle progression
positive regulation of progression through meiotic cell cycle
up regulation of progression through meiotic cell cycle
up-regulation of progression through meiotic cell cycle
upregulation of progression through meiotic cell cycle
activation of progression through meiotic cell cycle
stimulation of progression through meiotic cell cycle
positive regulation of meiotic cell cycle
Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle.
down regulation of progression through meiotic cell cycle
down-regulation of progression through meiotic cell cycle
downregulation of progression through meiotic cell cycle
negative regulation of meiotic cell cycle progression
negative regulation of progression through meiotic cell cycle
inhibition of progression through meiotic cell cycle
negative regulation of meiotic cell cycle
The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole.
heterotypic vacuole fusion (non-autophagic)
heterotypic vacuole fusion, non-autophagic
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
regulation of cytoskeleton organization and biogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
down regulation of cytoskeleton organization
down-regulation of cytoskeleton organization
downregulation of cytoskeleton organization
negative regulation of cytoskeleton organisation
negative regulation of cytoskeleton organization and biogenesis
negative regulation of cytoskeleton organization
Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
positive regulation of cytoskeleton organisation
up regulation of cytoskeleton organization
up-regulation of cytoskeleton organization
upregulation of cytoskeleton organization
stimulation of cytoskeleton organization
positive regulation of cytoskeleton organization and biogenesis
positive regulation of cytoskeleton organization
Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of neurotransmitter transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of neurotransmitter transport
down-regulation of neurotransmitter transport
downregulation of neurotransmitter transport
inhibition of neurotransmitter transport
negative regulation of neurotransmitter transport
Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
up regulation of neurotransmitter transport
up-regulation of neurotransmitter transport
upregulation of neurotransmitter transport
activation of neurotransmitter transport
stimulation of neurotransmitter transport
positive regulation of neurotransmitter transport
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus.
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
The directed movement of norepinephrine into a cell, typically presynaptic neurons or glial cells. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine.
Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter norepinephrine into a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of norepinephrine into a cell.
down regulation of norepinephrine uptake
down-regulation of norepinephrine uptake
negative regulation of levarterenol uptake
negative regulation of noradrenaline uptake
negative regulation of norepinephrine import
negative regulation of norepinephrine uptake
Any process that activates or increases the frequency, rate or extent of the directed movement of norepinephrine into a cell.
positive regulation of levarterenol uptake
positive regulation of noradrenaline uptake
positive regulation of norepinephrine import
positive regulation of norepinephrine uptake
The directed movement of acetylcholine into a cell, typically presynaptic neurons or glial cells. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter acetylcholine into a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of acetylcholine into a cell.
negative regulation of acetylcholine import
negative regulation of acetylcholine uptake
Any process that activates or increases the frequency, rate or extent of the directed movement of acetylcholine into a cell.
positive regulation of acetylcholine import
positive regulation of acetylcholine uptake
Any process in which an organelle is transported to, and/or maintained in, a specific location.
establishment and maintenance of organelle localization
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell.
establishment and maintenance of Golgi localization
Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell.
establishment and maintenance of nucleus localization
Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.
establishment and maintenance of vesicle localization
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of intracellular localization
establishment of localization within cell
The directed movement of a vesicle to a specific location.
The directed movement of an organelle to a specific location.
Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane.
establishment and maintenance of localization in membrane
establishment and maintenance of position in membrane
Any process in which a cell is transported to, and/or maintained in, a specific location.
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
The directed movement of the Golgi to a specific location.
establishment of Golgi apparatus localization
establishment of Golgi body localization
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
Any process that modulates the rate or extent of progression through the cell cycle.
regulation of progression through cell cycle
arrest of mitotic cell cycle progression
negative regulation of cell cycle arrest
positive regulation of cell cycle arrest
Any process that activates or increases the frequency, rate or extent of cell division.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information.
Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell.
Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
regulation of cardioblast differentiation
Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
up regulation of cardioblast differentiation
up-regulation of cardioblast differentiation
upregulation of cardioblast differentiation
activation of cardioblast differentiation
stimulation of cardioblast differentiation
positive regulation of cardioblast differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
down regulation of cardioblast differentiation
down-regulation of cardioblast differentiation
downregulation of cardioblast differentiation
inhibition of cardioblast differentiation
negative regulation of cardioblast differentiation
The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of a pigment granule to a specific location.
establishment of pigment granule localisation
establishment of pigment granule localization
Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal.
regulation of sensory perception of pain
Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal.
The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of amino acid transmembrane transport
negative regulation of amino acid transport
Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of amino acid transmembrane transport
positive regulation of amino acid transport
Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
regulation of nervous system development
Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
down regulation of nervous system development
down-regulation of nervous system development
downregulation of nervous system development
inhibition of nervous system development
negative regulation of nervous system development
Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
up regulation of nervous system development
up-regulation of nervous system development
upregulation of nervous system development
activation of nervous system development
stimulation of nervous system development
positive regulation of nervous system development
Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
negative regulation of synapse biogenesis
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
positive regulation of synapse biogenesis
Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
regulation of conduction of nerve impulse
regulation of transmission of nerve impulse
Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
down regulation of transmission of nerve impulse
down-regulation of transmission of nerve impulse
downregulation of transmission of nerve impulse
negative regulation of conduction of nerve impulse
inhibition of transmission of nerve impulse
negative regulation of transmission of nerve impulse
Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
positive regulation of conduction of nerve impulse
up regulation of transmission of nerve impulse
up-regulation of transmission of nerve impulse
upregulation of transmission of nerve impulse
activation of transmission of nerve impulse
stimulation of transmission of nerve impulse
positive regulation of transmission of nerve impulse
Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
positive regulation of chromosome segregation
Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
down regulation of chromosome segregation
down-regulation of chromosome segregation
downregulation of chromosome segregation
negative regulation of chromosome segregation
The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.
The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle.
The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells.
The process whose specific outcome is the progression of a cardiac cell over time, from its formation to the mature state. A cardiac cell is a cell that will form part of the cardiac organ of an individual.
The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
The process in which the anatomical structures of cardiac muscle tissue are generated and organized.
The process in which the anatomical structure of cardiac atrium muscle is generated and organized.
atrial cardiac muscle tissue morphogenesis
The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
ventricular cardiac muscle tissue morphogenesis
The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state.
The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
Any process that modulates the frequency, rate or extent of cardiac muscle fiber development.
regulation of cardiac muscle fibre development
regulation of heart muscle fiber development
regulation of cardiac muscle fiber development
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development.
down regulation of cardiac muscle fiber development
down-regulation of cardiac muscle fiber development
downregulation of cardiac muscle fiber development
negative regulation of cardiac muscle fibre development
inhibition of cardiac muscle fiber development
negative regulation of heart muscle fiber development
negative regulation of cardiac muscle fiber development
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development.
positive regulation of cardiac muscle fibre development
positive regulation of heart muscle fiber development
up regulation of cardiac muscle fiber development
up-regulation of cardiac muscle fiber development
upregulation of cardiac muscle fiber development
activation of cardiac muscle fiber development
stimulation of cardiac muscle fiber development
positive regulation of cardiac muscle fiber development
Any process that modulates the frequency, rate or extent of cardiac muscle growth.
regulation of cardiac muscle tissue growth
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth.
down regulation of cardiac muscle growth
down-regulation of cardiac muscle growth
negative regulation of heart muscle growth
negative regulation of cardiac muscle tissue growth
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle growth.
positive regulation of heart muscle growth
positive regulation of cardiac muscle tissue growth
Any process that modulates the frequency, rate or extent of cardiac muscle tissue development.
regulation of cardiac muscle tissue development
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development.
positive regulation of heart muscle development
up regulation of cardiac muscle development
up-regulation of cardiac muscle development
upregulation of cardiac muscle development
activation of cardiac muscle development
stimulation of cardiac muscle development
positive regulation of cardiac muscle tissue development
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle tissue development.
down regulation of cardiac muscle development
down-regulation of cardiac muscle development
downregulation of cardiac muscle development
negative regulation of heart muscle development
inhibition of cardiac muscle development
negative regulation of cardiac muscle tissue development
The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron.
The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
ATP hydrolysis coupled transmembrane transport
Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
nucleobase-containing small molecule metabolic process
The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex.
The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis.
Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
regulation of cardiac muscle contraction
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
negative regulation of cardiac muscle contraction
The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities.
The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear.
The expansion of a cardiac muscle cell population by cell division.
The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The process in which the anatomical structure of the retina is generated and organized.
retina morphogenesis in camera-style eye
Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation.
regulation of heart muscle cell proliferation
regulation of cardiomyocyte proliferation
regulation of cardiac muscle cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation.
negative regulation of heart muscle cell proliferation
negative regulation of cardiac muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation.
positive regulation of heart muscle cell proliferation
positive regulation of cardiac muscle cell proliferation
The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body.
Muscle contraction of cardiac muscle tissue.
The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter.
Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
regulation of syncytium formation by plasma membrane fusion
Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
positive regulation of syncytium formation by plasma membrane fusion
The portion of the plasma membrane surrounding a cilium.
The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
haematopoietic stem cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye.
camera-type eye photoreceptor cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell.
A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell.
epithelial cell differentiation from mesenchymal cell
Any process that modulates the frequency, rate or extent of glial cell proliferation.
Any process that activates or increases the rate or extent of glial cell proliferation.
positive regulation of glial cell proliferation
Any process that stops or decreases the rate or extent of glial cell proliferation.
negative regulation of glial cell proliferation
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule metabolic process
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Any process that modulates the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
positive regulation of oocyte development
Any process that decreases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
negative regulation of oocyte development
Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Any process that modulates the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
Any process that increases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
positive regulation of sarcomere organisation
positive regulation of sarcomere organization
Any process that decreases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
negative regulation of sarcomere organisation
negative regulation of sarcomere organization
The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body.
The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
The process of creating a trabecula in the liver. A trabecula is a tissue element in the form of a small beam, strut or rod.
The process of creating a trabecula in the spleen. A trabecula is a tissue element in the form of a small beam, strut or rod.
The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod.
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
The process in which bones are generated and organized.
The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone.
The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.
cartilage development involved in endochondral bone morphogenesis
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus.
The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.
myocardial precursor cell differentiation
cardiac muscle cell myoblast differentiation
The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules.
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
regulation of acetylcholine metabolic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
positive regulation of acetylcholine metabolic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues.
negative regulation of acetylcholine metabolic process
The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart.
The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another.
The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another.
The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
aorta smooth muscle tissue morphogenesis
The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function.
The increase in size or mass of the heart.
Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
The process in which the anatomical structures of the lung are generated and organized.
The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs.
The biological process whose specific outcome is the progression of lung connective tissue from an initial condition to its mature state. This process begins with the formation of lung connective tissue and ends with the mature structure. The lung connective tissue is a material made up of fibers forming a framework and support structure for the lungs.
The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung.
The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds.
The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches.
The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
epithelial tube branching involved in lung morphogenesis
Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine.
positive regulation of hindgut contraction
Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine.
negative regulation of hindgut contraction
Any process that increases the frequency, rate or extent of cardiac muscle contraction.
positive regulation of cardiac muscle contraction
Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
positive regulation of gastric acid secretion
Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.
negative regulation of gastric acid secretion
Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
positive regulation of digestive system process
Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
negative regulation of digestive system process
The biological process whose specific outcome is the progression of a right lung from an initial condition to its mature state. This process begins with the formation of the right lung and ends with the mature structure. The right lung is the lung which is on the right side of the anterior posterior axis looking from a dorsal to ventral aspect.
The biological process whose specific outcome is the progression of a left lung from an initial condition to its mature state. This process begins with the formation of the left lung and ends with the mature structure. The left lung is the lung which is on the left side of the anterior posterior axis looking from a dorsal to ventral aspect.
The process in which anatomical structures of the left lung are generated and organized.
The process in which anatomical structures of the right lung are generated and organized.
The biological process whose specific outcome is the progression of a lung lobe from an initial condition to its mature state. This process begins with the formation of a lung lobe by branching morphogenesis and ends with the mature structure. A lung lobe is one of the rounded projections that compose the lung.
The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung.
The developmental process pertaining to the initial formation of a lung lobe from unspecified parts. This process begins with the specific processes that contribute to the appearance of the lobe and ends when the structural rudiment is recognizable. A lung lobe is a projection that extends from the lung.
The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth.
Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate.
The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells.
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung.
pulmonary epithelial cell differentiation
Any process that modulates the rate, frequency, or extent of cell projection assembly.
Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure.
cell-cell signalling involved in lung development
cell-cell signaling involved in lung development
Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell and contributes to the development of the lung.
mesenchymal-epithelial cell signalling involved in lung development
mesenchymal-epithelial cell signaling involved in lung development
Any process that mediates the transfer of information between a mesenchymal cell and an endodermal cell.
Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape.
positive regulation of epithelial cell proliferation involved in lung morphogenesis
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung.
epithelial cell proliferation involved in lung morphogenesis
The process in which the anatomical structures of cartilage are generated and organized.
The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers.
The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue.
The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.
The process in which the anatomical structures of the diaphragm are generated and organized.
The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange.
The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.
developmental growth involved in morphogenesis
Any apoptotic process that contributes to the shaping of an anatomical structure.
apoptotic process involved in morphogenesis
The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The process in which epiblast cells acquire specialized features of neuroepithelial cells.
The morphogenetic process in which an epithelial sheet bends along a linear axis.
The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding.
The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus.
The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine.
intestinal epithelial cell differentiation
The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.
The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart.
pulmonary venous blood vessel morphogenesis
The process in which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart.
The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells within a field of cells that will exhibit a certain pattern of differentiation. Positional information is established through protein signals that emanate from a localized source within a developmental field resulting in specification of a cell type. Those signals are then interpreted in a cell-autonomous manner resulting in the determination of the cell type.
cell fate commitment involved in pattern specification
The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.
chondrocyte progenitor cell differentiation
The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.
regulation of vesicle-mediated transport
Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins.
regulation of microtubule-based movement
Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted.
Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted.
Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized.
regulation of morphogenesis of a branching structure
The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation.
cell fate commitment involved in formation of primary germ layer
The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels.
blood vessel endothelial cell differentiation
The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed.
The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed.
The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries.
arterial endothelial cell differentiation
The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins.
The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate.
The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment.
The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape.
The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
mesenchymal cell differentiation involved in lung development
The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
mesenchymal cell proliferation involved in lung development
The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.
The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node.
The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node.
atrioventricular node cell differentiation
The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.
The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state.
The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles.
His-Purkinje system cell differentiation
The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules.
The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules.
The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart.
The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels.
cardiac blood vessel endothelial cell differentiation
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart.
The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell.
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers.
The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart.
The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state.
The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ.
cell migration involved in heart development
The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells.
cell migration involved in heart formation
The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood.
Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels.
angiogenesis involved in cardiac vascular morphogenesis
angiogenesis involved in heart vascular morphogenesis
angiogenesis involved in coronary vascular morphogenesis
The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes.
vasculogenesis involved in coronary blood vessel morphogenesis
vasculogenesis involved in coronary vascular morphogenesis
The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart.
cell migration involved in coronary vasculogenesis
The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels.
cell migration involved in coronary angiogenesis
The regulated release of a hormone into the circulatory system.
An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins.
The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins.
The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine.
The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile.
The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct.
The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes.
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
The membrane organization process that joins two lipid bilayers to form a single membrane.
The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium.
Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
positive regulation of cartilage development
Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
negative regulation of cartilage development
The process in which a female gonad is generated and organized.
Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
regulation of branching involved in lung morphogenesis
Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
positive regulation of branching involved in lung morphogenesis
Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
negative regulation of branching involved in lung morphogenesis
The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
cell growth involved in cardiac muscle cell development
Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
regulation of cell growth involved in cardiac muscle cell development
Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
positive regulation of cell growth involved in cardiac muscle cell development
Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
negative regulation of cell growth involved in cardiac muscle cell development
The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle.
The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms.
Any process that modulates the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
regulation of nematode larval development
Any process that increases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
positive regulation of nematode larval development
Any process that decreases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
negative regulation of nematode larval development
The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina.
The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes.
Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
positive regulation of neural retina development
Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
negative regulation of neural retina development
The progression of the right horn of the sinus venosus from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium.
lung neuroendocrine cell differentiation
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance.
The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium.
gastric neuroendocrine cell differentiation
stomach neuroendocrine cell differentiation
Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.
regulation of stomach neuroendocrine cell differentiation
Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.
negative regulation of stomach neuroendocrine cell differentiation
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells.
Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell and contributes to the progression of the lung over time from its initial formation to the mature organ.
epithelial-mesenchymal cell signalling involved in lung development
epithelial-mesenchymal cell signaling involved in lung development
Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized.
The process in which the branches of the pancreas are generated and organized.
branching involved in pancreas morphogenesis
Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
The morphogenetic process in which the foregut region specified to become the pancreas forms a bud.
The process in which the anatomical structures of a branched epithelium are generated and organized.
The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part.
The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells.
The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
extracellular matrix organisation involved in endocardium development
extracellular matrix organization involved in endocardium development
The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery.
pulmonary artery endothelial tube morphogenesis
The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs.
Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
negative regulation of chondrocyte development
Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
positive regulation of dermatome development
Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.
negative regulation of dermatome development
Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
positive regulation of sclerotome development
Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.
The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure.
retina vasculature development in camera-type eye
The process in which the vasculature of the retina is generated and organized.
retina vasculature morphogenesis in camera-type eye
The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye.
The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches.
cardiac neural crest cell differentiation involved in heart development
The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart.
cardiac neural crest cell development involved in heart development
The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract.
cardiac neural crest cell development involved in outflow tract morphogenesis
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart.
cell proliferation involved in heart morphogenesis
The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract.
cell proliferation involved in outflow tract morphogenesis
Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.
The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell.
The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart.
fibroblast proliferation involved in heart morphogenesis
The progression of a connective tissue over time, from its formation to the mature structure.
The process in which a relatively unspecialized cell acquires specialized features of an interstitial cell of Cajal. An interstitial cell of Cajal is an intestinal neuroepithelial cell that serves as a pacemaker to trigger gut contraction.
interstitial cell of Cajal differentiation
The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction.
Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation.
regulation of type B pancreatic cell proliferation
Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells.
A process in which a protein is transported to, or maintained in, a location within a cilium.
The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure.
A cellular process that results in the breakdown of a cilium.
The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut.
The regulated release of acetylcholine by a cell.
The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter.
noradrenaline secretion, neurotransmission
norepinephrine secretion, neurotransmission
The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure.
The process in which the anatomical structures of ganglion are generated and organized.
A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state.
The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts.
The process in which the anatomical structure of a trigeminal ganglion is generated and organized.
A developmental process, independent of morphogenetic (shape) change, that is required for a trigeminal ganglion to attain its fully functional state.
A developmental process, independent of morphogenetic (shape) change, that is required for a cranial ganglion to attain its fully functional state.
The process in which the anatomical structure of a cranial ganglion is generated and organized.
The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts.
The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts.
A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle.
The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery.
Any process that reduces or removes the toxicity of inorganic compounds. These include transport of such compounds away from sensitive areas and to compartments or complexes whose purpose is sequestration of inorganic compounds.
A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
transferase complex, transferring phosphorus-containing groups
Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling.
A process in which a protein is transported to or maintained in a location within the somatodendritic compartment.
protein localization to somatodendritic compartment
The directed movement of a protein to a specific location in a plasma membrane.
establishment of protein localization to plasma membrane
The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone.
The process in which bone which forms superficially in the organism are generated and organized.
The process in which bone which forms deep in the organism are generated and organized.
Any process that modulates the rate, frequency or extent of a small molecule metabolic process.
regulation of small molecule metabolic process
Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process.
positive regulation of small molecule metabolism
positive regulation of small molecule metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process.
negative regulation of small molecule metabolism
negative regulation of small molecule metabolic process
An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells.
collagen-containing extracellular matrix
Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis.
positive regulation of mitotic sister chromatid segregation
The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ.
The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal.
detection of stimulus involved in sensory perception of pain
Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell.
The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
intracellular membrane translocation of a protein
intracellular protein membrane transport
intracellular protein transport across a membrane
intracellular protein transmembrane transport
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
cellular protein-containing complex assembly
The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex.
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell.
extracellular membrane-enclosed organelle
extracellular membrane-bounded organelle
An organelle lumen that is part of an intracellular organelle.
The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state.
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans).
Any process that modulates the frequency, rate or extent of the regulated release of glucagon.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon.
negative regulation of glucagon secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon.
positive regulation of glucagon secretion
A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix.
A process of chromosome organization that is involved in a meiotic cell cycle.
chromosome organisation involved in meiosis
chromosome organization involved in meiotic cell cycle
The directed movement of a protein to a specific location on a chromosome.
establishment of protein localisation to chromosome
establishment of protein localization to chromosome
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location.
regulation of establishment of protein localisation
regulation of establishment of protein localization
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome.
regulation of establishment of protein localisation to chromosome
regulation of establishment of protein localization to chromosome
The regulated release of somatostatin from secretory granules in the D cells of the pancreas.
The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function.
Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue.
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue.
Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue.
The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate.
The multiplication or reproduction of fat cells by cell division, resulting in the expansion of their population. A fat cell is an animal connective tissue cell specialized for the synthesis and storage of fat.
Any process that modulates the frequency, rate or extent of fat cell proliferation.
regulation of adipose cell proliferation
Any process that stops or decreases the rate or extent of fat cell proliferation.
down regulation of fat cell proliferation
down-regulation of fat cell proliferation
downregulation of fat cell proliferation
negative regulation of adipocyte proliferation
negative regulation of adipose cell proliferation
negative regulation of fat cell proliferation
Any process that activates or increases the rate or extent of fat cell proliferation.
positive regulation of adipocyte proliferation
positive regulation of adipose cell proliferation
positive regulation of fat cell proliferation
The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver.
Any process that modulates the frequency, rate or extent of hepatocyte differentiation.
regulation of liver cell differentiation
regulation of hepatocyte differentiation
Any process that stops or decreases the rate or extent of hepatocyte differentiation.
down regulation of hepatocyte differentiation
down-regulation of hepatocyte differentiation
downregulation of hepatocyte differentiation
negative regulation of liver cell differentiation
inhibition of hepatocyte differentiation
negative regulation of hepatocyte differentiation
Any process that activates or increases the rate or extent of hepatocyte differentiation.
positive regulation of liver cell differentiation
up regulation of hepatocyte differentiation
up-regulation of hepatocyte differentiation
upregulation of hepatocyte differentiation
activation of hepatocyte differentiation
stimulation of hepatocyte differentiation
positive regulation of hepatocyte differentiation
A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
exocytic constitutive secretory pathway transport vesicle
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen.
The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
regulation of microtubule cytoskeleton organisation
regulation of microtubule cytoskeleton organization
The directed movement of a substance from one side of an epithelium to the other.
The directed movement of ammonium ions from one side of an epithelium to the other.
The expansion of a leukocyte population by cell division.
Any process that modulates the frequency, rate or extent of leukocyte proliferation.
Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation.
down regulation of leukocyte proliferation
down-regulation of leukocyte proliferation
downregulation of leukocyte proliferation
negative regulation of leukocyte proliferation
Any process that activates or increases the frequency, rate or extent of leukocyte proliferation.
up regulation of leukocyte proliferation
up-regulation of leukocyte proliferation
positive regulation of leukocyte proliferation
Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue.
Note that this term has no relationship to 'membrane assembly ; GO:0071709' because the basement membrane is not a lipid bilayer.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
regulation of bile acid biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
down regulation of bile acid biosynthetic process
down-regulation of bile acid biosynthetic process
downregulation of bile acid biosynthetic process
negative regulation of bile acid anabolism
negative regulation of bile acid biosynthesis
negative regulation of bile acid formation
negative regulation of bile acid synthesis
inhibition of bile acid biosynthetic process
negative regulation of bile acid biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
positive regulation of bile acid anabolism
positive regulation of bile acid biosynthesis
positive regulation of bile acid formation
positive regulation of bile acid synthesis
up regulation of bile acid biosynthetic process
up-regulation of bile acid biosynthetic process
upregulation of bile acid biosynthetic process
activation of bile acid biosynthetic process
stimulation of bile acid biosynthetic process
positive regulation of bile acid biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
regulation of glycogen metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
negative regulation of glycogen metabolism
negative regulation of glycogen metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
positive regulation of glycogen metabolism
positive regulation of glycogen metabolic process
The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state.
Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
The directed movement of a protein to a part of a chromosome that is organized into chromatin.
establishment of protein localisation to chromatin
establishment of protein localization to chromatin
The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
The process of biting and mashing food with the teeth prior to swallowing.
Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location.
protein localisation in extracellular region
protein localization in extracellular region
protein localization to extracellular region
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state.
The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The aggregation, arrangement and bonding together of a set of components to form a membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane.
Note that this term has no relationship to 'membrane organization ; GO:0061024' because the basement membrane is not a lipid bilayer.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane.
nuclear membrane organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane.
nuclear outer membrane organization and biogenesis
The process in which a protein is transported across a membrane.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex.
DNA-protein complex subunit organization
protein-DNA complex subunit organisation
protein-DNA complex subunit organization
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
RNA-protein complex subunit organization
protein-RNA complex subunit organization
ribonucleoprotein complex subunit organisation
ribonucleoprotein complex subunit organization
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
cellular component organization or biogenesis
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monoamine stimulus. A monoamine is any of a group of molecular messengers that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system.
Note that epinephrine and norepinephrine are ligands for the same receptors, and there are multiple adrenergic receptors.
Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542).
The biosynthetic process resulting in the formation of DNA.
The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.
An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain.
The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm.
extracellular vesicular exosome assembly
The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels.
The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells.
The developmental process pertaining to the initial formation of an epithelial tube.
Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
negative regulation of mesenchymal cell proliferation
The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.
The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.
monocarboxylic acid biosynthetic process
The directed movement of compounds that contain sulfur, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis.
The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.
microtubule-based organelle localization
The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+.
A developmental process, independent of morphogenetic (shape) change, that is required for a type B pancreatic cell to attain its fully functional state. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
These processes continue to 60 DPA in Gossypium spp.
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the liver.
epithelial cell proliferation involved in liver morphogenesis
The process in which the anatomical structures of the liver are generated and organized.
Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal.
endothelial cell programmed cell death by apoptosis
programmed cell death of endothelial cells by apoptosis
programmed cell death, endothelial cells
The chemical reactions and pathways involving diatomic oxygen (O2).
The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle.
establishment of protein localisation to organelle
establishment of protein localization to organelle
A process in which a protein is transported to, or maintained in, a specific location in a membrane.
A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
A process in which a protein is transported to, or maintained at, a location in a vacuole.
The directed movement of a protein to a specific location in a vacuole.
establishment of protein localisation to vacuole
establishment of protein localization to vacuole
A process in which a protein is transported to, or maintained in, the cell cortex.
A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton.
protein localisation to microtubule cytoskeleton
protein localization to microtubule cytoskeleton
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
The aggregation, arrangement and bonding together of the extracellular matrix.
An action potential that occurs in a cardiac muscle cell.
An action potential that occurs in a sinoatrial node cardiac muscle cell.
SA node cardiac muscle cell action potential
SAN cardiac muscle cell action potential
sinoatrial node cardiac muscle cell action potential
sinus node cardiac muscle cell action potential
An action potential that occurs in an atrioventricular node cardiac muscle cell.
AV node cardiac muscle cell action potential
atrioventricular node cardiac muscle cell action potential
An action potential that occurs in a Purkinje myocyte.
Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte.
SA node cardiac muscle cell to atrial cardiac muscle cell signalling
SA node cardiomyocyte to atrial cardiomyocyte signalling
SAN cardiomyocyte to atrial cardiomyocyte signalling
sinoatrial node cardiomyocyte to atrial cardiomyocyte signalling
sinus node cardiomyocyte to atrial cardiomyocyte signalling
SA node cell to atrial cardiac muscle cell signaling
Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium.
cell-cell signalling involved in cardiac conduction
cell-cell signaling involved in cardiac conduction
Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte.
AV node cell to bundle of His cell signalling
atrioventricular node to bundle of His cell signaling
AV node cell to bundle of His cell signaling
Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell.
Purkinje myocyte to ventricular cardiac muscle cell signalling
Purkinje myocyte to ventricular cardiac muscle cell signaling
Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
cell communication involved in cardiac conduction
The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
atrioventricular node cell to bundle of His cell communication
AV node cell to bundle of His cell communication
The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Purkinje myocyte to ventricular cardiac muscle cell communication
The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
SA node cardiac muscle cell to atrial cardiac muscle cell communication
SA node cardiomyocyte to atrial cardiomyocyte communication
SAN cardiomyocyte to atrial cardiomyocyte communication
sinoatrial node cardiomyocyte to atrial cardiomyocyte communication
sinus node cardiomyocyte to atrial cardiomyocyte communication
SA node cell to atrial cardiac muscle cell communication
Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.
positive regulation of microtubule nucleation
Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
positive regulation of cell cycle process
Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
positive regulation of ribosome biogenesis
Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.
negative regulation of ribosome biogenesis
Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
positive regulation of extracellular matrix disassembly
The directed movement of a protein to a specific location in a membrane.
establishment of protein localisation in membrane
establishment of protein localization in membrane
establishment of protein localization to membrane
The specification and formation of anisotropic intracellular organization of an epithelial cell.
establishment of epithelial cell polarity
A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance.
The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance.
Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.
The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte.
The joining of two lipid bilayers to form a single organelle membrane.
Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system.
Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
positive regulation of somatostatin secretion
Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.
negative regulation of somatostatin secretion
Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
positive regulation of peptide hormone secretion
Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
negative regulation of peptide hormone secretion
Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds.
Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
positive regulation of neural crest formation
Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
negative regulation of neural crest formation
Any cellular metabolic process involving nucleic acids.
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
positive regulation of intracellular protein transport
Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells.
negative regulation of intracellular protein transport
Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
regulation of locomotion involved in locomotory behavior
Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
positive regulation of locomotion involved in locomotory behavior
Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
negative regulation of locomotion involved in locomotory behavior
The epithelial cell differentiation process in which a relatively unspecialized cell acquires specialized features of an acinar cell, a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini.
A process in which a protein is transported to, or maintained at, a location within a nuclear envelope.
protein localization in nuclear envelope
protein localization to nuclear envelope
The directed movement of catecholamine into a cell.
Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus.
Any membrane that is part of a pigment granule.
All of the contents of a cilium, excluding the plasma membrane surrounding the cilium.
Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm".
Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.
Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin.
type B pancreatic cell apoptotic process
A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.
vascular associated smooth muscle cell development
Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
The chemical reactions and pathways involving the ammonium ion.
The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
induction of apoptosis by extracellular signals
This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs.
Any apoptotic process in a hepatocyte, the main structural component of the liver.
Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.
A prolongation or process extending from a glial cell.
An arrangement of closely apposed microtubules running parallel to each other.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
extracellular fibril organization and biogenesis
Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina.
Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina.
A cardiac myofibril is a myofibril specific to cardiac muscle cells.
Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.
Any vesicle that is part of the intracellular region.
The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.
anchoring of the basal body to the plasma membrane
Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella.
ciliary basal body-plasma membrane docking
The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.
vesicle targeting, trans-Golgi to periciliary membrane compartment
The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
A neuromuscular junction in which the target muscle cell is a myotube.
In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting the myotubes of skeletal muscle (AKA skeletal muscle fibers). Neuromuscular junctions targeting other muscle cell types exist in invertebrates such as the mononucleate somatic muscles of nematodes.
The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract.
The lipid bilayer that forms the outer-most layer of an organelle.
Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes.
A membrane that is a (regional) part of the plasma membrane.
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands).
A complex of collagen trimers such as a fibril or collagen network.
A supramolecular complex that consists of collagen triple helices associated to form a network.
Any collagen timer that is part of a basement membrane.
The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.
ATP hydrolysis coupled cation transmembrane transport
monoatomic cation transmembrane transport
The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.
The process in which an inorganic ion is transported across a membrane.
The process in which an inorganic anion is transported across a membrane.
A process in which an inorganic cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
transmembrane inorganic cation transport
inorganic cation transmembrane transport
Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity.
The self-renewing division of a germline stem cell, to produce a daughter stem cell and a daughter germ cell which will divide to form one or more gametes.
The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
Not to be used for manual annotation. Please choose a more specific cell development term or if not possible, bone or bone tissue development.
Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.
The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure.
The part of a synapse that is part of the presynaptic cell.
The part of a synapse that is part of the post-synaptic cell.
Any protein complex that is part of a membrane.
Any protein complex that is part of the plasma membrane.
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system.
The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
The directed movement of a protein along a microtubule, mediated by motor proteins.
A cell projection supported by an assembly of actin filaments, and which lacks microtubules.
The increase in size or mass of an intramembranous bone that contributes to the shaping of the bone.
The increase in size or mass of a bone that contributes to the shaping of that bone.
The actin cytoskeleton that is part of a postsynapse.
The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis.
vesicle-mediated transport to the plasma membrane
A cellular process that results in the controlled breakdown of synapse. After it starts the process is continuous until the synapse has disappeared.
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term.
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of cardiac muscle cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of AV node cardiac muscle cell action potential
regulation of atrioventricular node cardiac muscle cell action potential
regulation of AV node cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of Purkinje myocyte action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
regulation of SA node cardiac muscle cell action potential
regulation of SAN cardiac muscle cell action potential
regulation of sinoatrial node cardiac muscle cell action potential
regulation of sinus node cardiac muscle cell action potential
regulation of SA node cell action potential
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Cell-cell signaling from pre to post-synapse, across the synaptic cleft.
Cell-cell signaling from post to pre-synapse, across the synaptic cleft.
Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a lipid ligand.
retrograde trans-synaptic signaling by lipid
Signal transduction in which the initial step occurs in a postsynapse.
Signal transduction in which the initial step occurs in a presynapse.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the postsynaptic actin cytoskeleton.
postsynaptic actin cytoskeleton organization
The postsynapse of a neuromuscular junction. In vertebrate muscles this includes the motor end-plate, consisting of postjunctional folds of the sarcolemma.
A synapse that uses acetylcholine as a neurotransmitter.
A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals.
Any vesicle-mediated transport that occurs in a synapse.
The lipid bilayer surrounding a neuronal dense core vesicle.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuronal dense core vesicle.
neuronal dense core vesicle organization
The aggregation, arrangement and bonding together of a set of components to form a presynapse.
The aggregation, arrangement and bonding together of a set of components to form a postsynapse.
A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber.
Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a neuropeptide.
retrograde trans-synaptic signaling by neuropeptide
Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide.
Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.
retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission
The movement of a cellular component as a result of microtubule polymerization.
microtubule polymerization based movement
A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
The transport of a protein driven by polymerization of a microtubule to which it is attached.
microtubule polymerization based protein transport
A microtubule-based process that results in the transport of proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton.
presynaptic actin cytoskeleton organization
The actin cytoskeleton that is part of a presynapse.
Cell-cell signaling in which the ligand is carried between cells by an exosome.
Transynaptic signaling in which the ligand is carried across the synapse by an exosome.
exosome mediated transynaptic signalling
Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission.
postsynaptic modulation of chemical synaptic transmission
Any process, acting in the presynapse that results in modulation of chemical synaptic transmission.
presynaptic modulation of chemical synaptic transmission
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a presynapse.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a postsynapse.
Any process that modulates the physical form of a presynapse.
regulation of presynapse organization and biogenesis
Any process that modulates the physical form of a postsynapse.
regulation of postsynapse organization and biogenesis
Any process that modulates the frequency, rate or extent of trans-synaptic signaling.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton.
Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.
The lipid bilayer surrounding an exocytic vesicle.
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits.
The transport of organelles or other particles from one location in the cell to another along actin filaments.
The directed movement of a vesicle along a cytoskeletal fiber such as a microtubule or and actin filament, mediated by motor proteins.
cytoskeletal fiber-based vesicle localization
The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission.
presynaptic process involved in chemical synaptic transmission
Cell-cell signaling to, from or within a synapse.
Cell-cell signaling in either direction across the synaptic cleft.
Cell-cell signaling to or from a synapse, mediated by a peptide.
Cell-cell signaling between presynapse and postsynapse mediated by a peptide ligand crossing the synaptic cleft.
trans-synaptic signaling by neuropeptide
Cell-cell signaling from post to pre-synapse, across the synaptic cleft, mediated by a lipid.
Any protein degradation process, occurring at a presynapse, that regulates synaptic transmission.
protein catabolic process, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating translation occurring at the synapse.
regulation of translation at synapse, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling by neuropeptide, modulating synaptic transmission
Cell-cell signaling between presynapse and postsynapse, via the release and reception of lipid molecules, that modulates the synaptic transmission properties of the synapse.
trans-synaptic signaling by lipid, modulating synaptic transmission
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
The portion of the cytoskeleton contained within the presynapse.
The portion of the cytoskeleton contained within the postsynapse.
Any process that modulates synaptic transmission by regulating protein degradation at the synapse.
regulation of protein catabolic process at synapse, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating a catabolic process occurring at a presynapse.
regulation of protein catabolic process at presynapse, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating a catabolic process occurring at a postsynapse.
regulation of protein catabolic process at postsynapse, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating translation occurring at the presynapse.
regulation of translation at presynapse, modulating synaptic transmission
Any process that modulates synaptic transmission by regulating translation occurring at the postsynapse.
regulation of translation at postsynapse, modulating synaptic transmission
A process in which protein is transported from one region of the plasma membrane to another.
protein transport within plasma membrane
The directed movement of proteins along microtubules in neuron projections.
The complete extent of cell cortex that underlies some some region of the plasma membrane.
Any action potential process that regulates skeletal muscle contraction.
regulation of skeletal muscle contraction by action potential
The multiplication or reproduction of blood vessel endothelial cells, resulting in the expansion of a cell population.
A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis.
nuclear membrane organization involved in mitotic nuclear division
This process only occurs in organisms which undergo 'closed mitosis' without nuclear breakdown.
The process in which a nuclear membrane is synthesized, aggregates, and bonds together.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite.
Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus.
regulation of vesicle fusion with Golgi apparatus
Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus.
negative regulation of vesicle fusion with Golgi apparatus
Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus.
positive regulation of vesicle fusion with Golgi apparatus
Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane.
regulation of basement membrane organization
Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin.
regulation of actomyosin structure organization
The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.
Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation.
regulation of cardiac muscle myoblast proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation.
negative regulation of cardiac muscle myoblast proliferation
Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation.
positive regulation of cardiac muscle myoblast proliferation
Any process that modulates the frequency, rate or extent of actin filament organization.
regulation of actin filament organization
Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation.
regulation of blood vessel endothelial cell differentiation
Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation.
positive regulation of blood vessel endothelial cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation.
negative regulation of blood vessel endothelial cell differentiation
A cellular transport process in which transported substances are moved in extracellular vesicles between cells; transported substances are enclosed in the vesicle lumen or located in the extracellular vesicle membrane.
vesicle-mediated intercellular transport
Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis.
positive regulation of animal organ morphogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis.
negative regulation of animal organ morphogenesis
Any process that modulates the frequency, rate, or extent of lipid transporter activity.
regulation of lipid transporter activity
Any process that increases the frequency, rate, or extent of lipid transporter activity.
positive regulation of lipid transporter activity
Any process that decreases the frequency, rate, or extent of lipid transporter activity.
negative regulation of lipid transporter activity
Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation.
regulation of compound eye photoreceptor cell differentiation
Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation.
positive regulation of compound eye photoreceptor cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation.
negative regulation of compound eye photoreceptor cell differentiation
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
plasma membrane bounded cell projection assembly
Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly.
regulation of plasma membrane bounded cell projection assembly
Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly.
negative regulation of plasma membrane bounded cell projection assembly
Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly.
positive regulation of plasma membrane bounded cell projection assembly
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections.
regulation of plasma membrane bounded cell projection organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon.
plasma membrane bounded cell projection organization
The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized.
plasma membrane bounded cell projection morphogenesis
All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection.
Any process that activates or increases the frequency, rate or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.
positive regulation of collagen breakdown
positive regulation of collagen catabolism
positive regulation of collagen degradation
up regulation of collagen catabolic process
up-regulation of collagen catabolic process
upregulation of collagen catabolic process
activation of collagen catabolic process
positive regulation of collagen catabolic process
The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin.
negative regulation of protein localisation to chromatin
negative regulation of protein localization to chromatin
Any process that activates or increases the frequency, rate or extent of protein localization to chromatin.
positive regulation of protein localisation to chromatin
positive regulation of protein localization to chromatin
Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.
Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.
positive regulation of bile acid secretion
Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.
negative regulation of bile acid secretion
Any process that modulates the frequency, rate or extent of blastocyst development.
Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism.
The developmental process pertaining to the initial formation of an endothelial tube.
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
The cellular processes that contribute to exocytosis.
The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.
organelle localization by membrane tethering
Catalytic activity that acts to modify a protein.
Catalytic activity that acts to modify DNA.
Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.
Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein.
catalytic activity, acting on a glycoprotein
The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content.
Translation that occurs at the presynapse.
Translation that occurs at the presynapse, and that modulates chemical synaptic transmission.
translation at presynapse, modulating chemical synaptic transmission
Translation that occurs at the postsynapse.
Any process that regulates translation occurring at the synapse.
Any process that regulates translation occurring at the presynapse.
Any process that regulates translation occurring at the postsynapse.
regulation of translation at postsynapse
The chemical reactions and pathways resulting in the breakdown of a protein at a synapse.
The chemical reactions and pathways resulting in the breakdown of a protein at a presynapse.
The chemical reactions and pathways resulting in the breakdown of a protein at a postsynapse.
protein catabolic process at postsynapse
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the synapse.
regulation protein catabolic process at synapse
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the presynapse.
regulation protein catabolic process at presynapse
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the postsynapse.
regulation protein catabolic process at postsynapse
A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.
Directly binding to a specific protein and delivering it to a specific cellular location.
Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation.
iRHOM2 transports ADAM17 from ER to the Golgi-network
iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane
The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis.
The directed movement of a lipid from a cell, into the extracellular region.
The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.
The division of a vacuole within a cell to form two or more separate vacuoles.
Catalytic activity that acts to modify a nucleic acid.
catalytic activity, acting on a nucleic acid
The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.
non-membrane-bounded organelle formation
non-membrane-enclosed organelle assembly
non-membrane-enclosed organelle formation
The elimination of ammonium ions from an excretory cell.
Any process carried out at the cellular level that reduces or removes the toxicity of a metal ion.
Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse.
The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways.
Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum.
Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine.
A process in which a protein is transported to, or maintained, in a location within a cell-cell junction.
protein localization to cell-cell junction
Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction.
regulation of protein localization to cell-cell junction
Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction.
positive regulation of protein localization to cell-cell junction
Any process that modulates the frequency, rate or extent of transepithelial transport.
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction.
negative regulation of protein localisation to cell-cell junction
negative regulation of protein localization to cell-cell junction
The disaggregation of a cell junction into its constituent components.
The disaggregation of a cell-cell junction into its constituent components.
The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain.
The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter.
catecholamine secretion, neurotransmission
The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure.
Any regulation of signal transduction that takes place in the extracellular region.
regulation of signaling pathway in extracellular region
regulation of signalling pathway in extracellular region
extracellular regulation of signal transduction
Any negative regulation of signal transduction that takes place in extracellular region.
down regulation of signal transduction in extracellular region
down-regulation of signal transduction in extracellular region
downregulation of signal transduction in extracellular region
negative regulation of signaling pathway in extracellular region
negative regulation of signalling pathway in extracellular region
extracellular inhibition of signaling pathway
inhibition of signal transduction in extracellular region
extracellular negative regulation of signal transduction
Any process that modulates the frequency, rate or extent of execution phase of apoptosis.
regulation of execution phase of apoptosis
Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
down regulation of execution phase of apoptosis
down-regulation of execution phase of apoptosis
downregulation of execution phase of apoptosis
inhibition of execution phase of apoptosis
negative regulation of execution phase of apoptosis
Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
up regulation of execution phase of apoptosis
up-regulation of execution phase of apoptosis
upregulation of execution phase of apoptosis
activation of execution phase of apoptosis
positive regulation of execution phase of apoptosis
Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process.
regulation of hyaluronan biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process.
down regulation of hyaluronan biosynthesis
down regulation of hyaluronan biosynthetic process
down-regulation of hyaluronan biosynthesis
down-regulation of hyaluronan biosynthetic process
downregulation of hyaluronan biosynthesis
downregulation of hyaluronan biosynthetic process
negative regulation of hyaluronan anabolism
negative regulation of hyaluronan biosynthesis
negative regulation of hyaluronan formation
negative regulation of hyaluronan synthesis
inhibition of hyaluronan biosynthetic process
negative regulation of hyaluronan biosynthetic process
Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
positive regulation of hyaluronan anabolism
positive regulation of hyaluronan biosynthesis
positive regulation of hyaluronan formation
positive regulation of hyaluronan synthesis
up regulation of hyaluronan biosynthesis
up regulation of hyaluronan biosynthetic process
up-regulation of hyaluronan biosynthesis
up-regulation of hyaluronan biosynthetic process
upregulation of hyaluronan biosynthetic process
activation of hyaluronan biosynthetic process
positive regulation of hyaluronan biosynthetic process
Any process that modulates the frequency, rate or extent of protein localization to nucleus.
regulation of protein localisation to nucleus
regulation of protein localization in cell nucleus
regulation of protein localization in nucleus
regulation of protein localization to nucleus
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus.
down regulation of protein localisation to nucleus
down regulation of protein localization in cell nucleus
down regulation of protein localization in nucleus
down regulation of protein localization to nucleus
down-regulation of protein localisation to nucleus
down-regulation of protein localization in cell nucleus
down-regulation of protein localization in nucleus
down-regulation of protein localization to nucleus
downregulation of protein localisation to nucleus
downregulation of protein localization in cell nucleus
downregulation of protein localization in nucleus
downregulation of protein localization to nucleus
negative regulation of protein localisation to nucleus
negative regulation of protein localization in cell nucleus
negative regulation of protein localization in nucleus
inhibition of protein localisation to nucleus
inhibition of protein localization in cell nucleus
inhibition of protein localization in nucleus
inhibition of protein localization to nucleus
negative regulation of protein localization to nucleus
Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
activation of protein localization in nucleus
positive regulation of protein localisation to nucleus
positive regulation of protein localization in cell nucleus
positive regulation of protein localization in nucleus
up regulation of protein localisation to nucleus
up regulation of protein localization in cell nucleus
up regulation of protein localization in nucleus
up regulation of protein localization to nucleus
up-regulation of protein localisation to nucleus
up-regulation of protein localization in cell nucleus
up-regulation of protein localization in nucleus
up-regulation of protein localization to nucleus
upregulation of protein localisation to nucleus
upregulation of protein localization in cell nucleus
upregulation of protein localization in nucleus
upregulation of protein localization to nucleus
activation of protein localisation to nucleus
activation of protein localization in cell nucleus
activation of protein localization to nucleus
positive regulation of protein localization to nucleus
Any process that modulates the frequency, rate or extent of oocyte maturation.
Any process that stops, prevents or reduces the frequency, rate or extent of oocyte maturation.
negative regulation of oocyte maturation
Any process that activates or increases the frequency, rate or extent of oocyte maturation.
positive regulation of oocyte maturation
Any process that modulates the frequency, rate or extent of secondary metabolite biosynthetic process.
regulation of secondary metabolite biosynthesis
regulation of secondary metabolite biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of secondary metabolite biosynthetic process.
down regulation of secondary metabolite biosynthesis
down regulation of secondary metabolite biosynthetic process
down-regulation of secondary metabolite biosynthesis
down-regulation of secondary metabolite biosynthetic process
downregulation of secondary metabolite biosynthesis
downregulation of secondary metabolite biosynthetic process
inhibition of secondary metabolite biosynthesis
negative regulation of secondary metabolite biosynthesis
inhibition of secondary metabolite biosynthetic process
negative regulation of secondary metabolite biosynthetic process
Any process that activates or increases the frequency, rate or extent of secondary metabolite biosynthetic process.
activation of secondary metabolite biosynthesis
positive regulation of secondary metabolite biosynthesis
up regulation of secondary metabolite biosynthesis
up regulation of secondary metabolite biosynthetic process
up-regulation of secondary metabolite biosynthesis
up-regulation of secondary metabolite biosynthetic process
upregulation of secondary metabolite biosynthesis
upregulation of secondary metabolite biosynthetic process
activation of secondary metabolite biosynthetic process
positive regulation of secondary metabolite biosynthetic process
The chemical reactions and pathways involving an acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid.
The chemical reactions and pathways resulting in the formation of an acetate esteran acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid.
The chemical reactions and pathways involving carbohydrate derivative.
carbohydrate derivative metabolic process
The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative.
carbohydrate derivative catabolic process
The chemical reactions and pathways resulting in the formation of carbohydrate derivative.
carbohydrate derivative biosynthetic process
The chemical reactions and pathways involving insulin.
The chemical reactions and pathways resulting in the breakdown of insulin.
Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form.
expression of extracellular matrix proteins
gene expression involved in extracellular matrix organization
The chemical reactions and pathways involving primary amino compound.
primary amino compound metabolic process
The chemical reactions and pathways resulting in the breakdown of primary amino compound.
primary amino compound catabolic process
The chemical reactions and pathways resulting in the formation of primary amino compound.
primary amino compound biosynthetic process
Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.
regulation of translation initiation ternary complex assembly
regulation of formation of translation initiation ternary complex
Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.
down regulation of formation of translation initiation ternary complex
down regulation of translation initiation ternary complex assembly
down-regulation of formation of translation initiation ternary complex
down-regulation of translation initiation ternary complex assembly
downregulation of formation of translation initiation ternary complex
downregulation of translation initiation ternary complex assembly
inhibition of translation initiation ternary complex assembly
negative regulation of translation initiation ternary complex assembly
inhibition of formation of translation initiation ternary complex
negative regulation of formation of translation initiation ternary complex
Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.
activation of translation initiation ternary complex assembly
positive regulation of translation initiation ternary complex assembly
up regulation of formation of translation initiation ternary complex
up regulation of translation initiation ternary complex assembly
up-regulation of formation of translation initiation ternary complex
up-regulation of translation initiation ternary complex assembly
upregulation of formation of translation initiation ternary complex
upregulation of translation initiation ternary complex assembly
activation of formation of translation initiation ternary complex
positive regulation of formation of translation initiation ternary complex
Any process that modulates the frequency, rate or extent of extracellular matrix assembly.
regulation of extracellular matrix assembly
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly.
down regulation of extracellular matrix assembly
down-regulation of extracellular matrix assembly
downregulation of extracellular matrix assembly
inhibition of extracellular matrix assembly
negative regulation of extracellular matrix assembly
Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly.
up regulation of extracellular matrix assembly
up-regulation of extracellular matrix assembly
upregulation of extracellular matrix assembly
activation of extracellular matrix assembly
positive regulation of extracellular matrix assembly
Any process that modulates the frequency, rate or extent of cardiac chamber formation.
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation.
down regulation of cardiac chamber formation
down regulation of heart chamber formation
down-regulation of cardiac chamber formation
down-regulation of heart chamber formation
downregulation of cardiac chamber formation
downregulation of heart chamber formation
negative regulation of heart chamber formation
negative regulation of cardiac chamber formation
Any process that activates or increases the frequency, rate or extent of cardiac chamber formation.
positive regulation of heart chamber formation
up regulation of cardiac chamber formation
up regulation of heart chamber formation
up-regulation of cardiac chamber formation
up-regulation of heart chamber formation
upregulation of cardiac chamber formation
positive regulation of cardiac chamber formation
Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis.
regulation of heart chamber morphogenesis
regulation of cardiac chamber morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis.
down regulation of cardiac chamber morphogenesis
down regulation of heart chamber morphogenesis
down-regulation of cardiac chamber morphogenesis
down-regulation of heart chamber morphogenesis
downregulation of cardiac chamber morphogenesis
downregulation of heart chamber morphogenesis
negative regulation of heart chamber morphogenesis
inhibition of cardiac chamber morphogenesis
inhibition of heart chamber morphogenesis
negative regulation of cardiac chamber morphogenesis
Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis.
positive regulation of heart chamber morphogenesis
up regulation of cardiac chamber morphogenesis
up regulation of heart chamber morphogenesis
up-regulation of cardiac chamber morphogenesis
up-regulation of heart chamber morphogenesis
upregulation of cardiac chamber morphogenesis
upregulation of heart chamber morphogenesis
activation of cardiac chamber morphogenesis
activation of heart chamber morphogenesis
positive regulation of cardiac chamber morphogenesis
Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation.
regulation of lung ciliated cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation.
down regulation of lung ciliated cell differentiation
down-regulation of lung ciliated cell differentiation
downregulation of lung ciliated cell differentiation
inhibition of lung ciliated cell differentiation
negative regulation of lung ciliated cell differentiation
Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation.
up regulation of lung ciliated cell differentiation
up-regulation of lung ciliated cell differentiation
upregulation of lung ciliated cell differentiation
activation of lung ciliated cell differentiation
positive regulation of lung ciliated cell differentiation
The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of vasculature development.
regulation of vascular system development
Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development.
down regulation of vasculature development
down-regulation of vasculature development
downregulation of vasculature development
down regulation of vascular system development
down-regulation of vascular system development
downregulation of vascular system development
inhibition of vascular system development
negative regulation of vascular system development
negative regulation of vasculature development
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound biosynthetic process
The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an acetate ester from one side of a membrane to the other.
acetate ester transmembrane transporter activity
Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process.
regulation of tetrapyrrole metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process.
down regulation of tetrapyrrole metabolic process
down regulation of tetrapyrrole metabolism
down-regulation of tetrapyrrole metabolic process
down-regulation of tetrapyrrole metabolism
downregulation of tetrapyrrole metabolic process
downregulation of tetrapyrrole metabolism
negative regulation of tetrapyrrole metabolism
inhibition of tetrapyrrole metabolic process
negative regulation of tetrapyrrole metabolic process
Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process.
positive regulation of tetrapyrrole metabolism
up regulation of tetrapyrrole metabolic process
up regulation of tetrapyrrole metabolism
up-regulation of tetrapyrrole metabolic process
up-regulation of tetrapyrrole metabolism
upregulation of tetrapyrrole metabolic process
activation of tetrapyrrole metabolic process
positive regulation of tetrapyrrole metabolic process
Any process that modulates the frequency, rate or extent of tetrapyrrole catabolic process.
regulation of tetrapyrrole catabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole catabolic process.
down regulation of tetrapyrrole breakdown
down regulation of tetrapyrrole catabolic process
down regulation of tetrapyrrole catabolism
down regulation of tetrapyrrole degradation
down-regulation of tetrapyrrole breakdown
down-regulation of tetrapyrrole catabolic process
down-regulation of tetrapyrrole catabolism
down-regulation of tetrapyrrole degradation
downregulation of tetrapyrrole breakdown
downregulation of tetrapyrrole catabolic process
downregulation of tetrapyrrole catabolism
downregulation of tetrapyrrole degradation
negative regulation of tetrapyrrole breakdown
negative regulation of tetrapyrrole catabolism
negative regulation of tetrapyrrole degradation
inhibition of tetrapyrrole catabolic process
negative regulation of tetrapyrrole catabolic process
Any process that activates or increases the frequency, rate or extent of tetrapyrrole catabolic process.
positive regulation of tetrapyrrole breakdown
positive regulation of tetrapyrrole catabolism
positive regulation of tetrapyrrole degradation
up regulation of tetrapyrrole catabolic process
up regulation of tetrapyrrole catabolism
up regulation of tetrapyrrole degradation
up-regulation of tetrapyrrole catabolic process
up-regulation of tetrapyrrole catabolism
up-regulation of tetrapyrrole degradation
upregulation of tetrapyrrole catabolic process
upregulation of tetrapyrrole degradation
activation of tetrapyrrole catabolic process
positive regulation of tetrapyrrole catabolic process
Any process that modulates the frequency, rate or extent of response to acetate.
Any process that stops, prevents or reduces the frequency, rate or extent of response to acetate.
negative regulation of response to acetate
Any process that activates or increases the frequency, rate or extent of response to acetate.
positive regulation of response to acetate
Any process that modulates the frequency, rate or extent of tetrapyrrole biosynthetic process.
regulation of tetrapyrrole biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole biosynthetic process.
down regulation of tetrapyrrole anabolism
down regulation of tetrapyrrole biosynthesis
down regulation of tetrapyrrole biosynthetic process
down regulation of tetrapyrrole formation
down regulation of tetrapyrrole synthesis
down-regulation of tetrapyrrole anabolism
down-regulation of tetrapyrrole biosynthesis
down-regulation of tetrapyrrole biosynthetic process
down-regulation of tetrapyrrole formation
down-regulation of tetrapyrrole synthesis
downregulation of tetrapyrrole anabolism
downregulation of tetrapyrrole biosynthesis
downregulation of tetrapyrrole biosynthetic process
downregulation of tetrapyrrole formation
downregulation of tetrapyrrole synthesis
negative regulation of tetrapyrrole anabolism
negative regulation of tetrapyrrole biosynthesis
negative regulation of tetrapyrrole formation
negative regulation of tetrapyrrole synthesis
inhibition of tetrapyrrole biosynthetic process
negative regulation of tetrapyrrole biosynthetic process
Any process that activates or increases the frequency, rate or extent of tetrapyrrole biosynthetic process.
positive regulation of tetrapyrrole anabolism
positive regulation of tetrapyrrole biosynthesis
positive regulation of tetrapyrrole formation
positive regulation of tetrapyrrole synthesis
up regulation of tetrapyrrole biosynthesis
up regulation of tetrapyrrole biosynthetic process
up-regulation of tetrapyrrole biosynthesis
up-regulation of tetrapyrrole biosynthetic process
upregulation of tetrapyrrole biosynthesis
upregulation of tetrapyrrole biosynthetic process
activation of tetrapyrrole biosynthetic process
positive regulation of tetrapyrrole biosynthetic process
Enables the transfer of carbohydrate derivative from one side of a membrane to the other.
carbohydrate derivative transporter activity
carbohydrate derivative transmembrane transporter activity
Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.
regulation of endothelial tube morphogenesis
Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation.
regulation of haematopoietic progenitor cell differentiation
regulation of haemopoietic progenitor cell differentiation
regulation of hemopoietic progenitor cell differentiation
regulation of hematopoietic progenitor cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation.
down regulation of haematopoietic progenitor cell differentiation
down regulation of haemopoietic progenitor cell differentiation
down regulation of hemopoietic progenitor cell differentiation
down-regulation of haematopoietic progenitor cell differentiation
down-regulation of haemopoietic progenitor cell differentiation
down-regulation of hemopoietic progenitor cell differentiation
downregulation of haematopoietic progenitor cell differentiation
downregulation of haemopoietic progenitor cell differentiation
downregulation of hemopoietic progenitor cell differentiation
inhibition of haematopoietic progenitor cell differentiation
inhibition of haemopoietic progenitor cell differentiation
negative regulation of haematopoietic progenitor cell differentiation
negative regulation of haemopoietic progenitor cell differentiation
negative regulation of hemopoietic progenitor cell differentiation
inhibition of hemopoietic progenitor cell differentiation
down regulation of hematopoietic progenitor cell differentiation
down-regulation of hematopoietic progenitor cell differentiation
downregulation of hematopoietic progenitor cell differentiation
inhibition of hematopoietic progenitor cell differentiation
negative regulation of hematopoietic progenitor cell differentiation
Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation.
activation of haematopoietic progenitor cell differentiation
activation of haemopoietic progenitor cell differentiation
positive regulation of haematopoietic progenitor cell differentiation
positive regulation of haemopoietic progenitor cell differentiation
positive regulation of hemopoietic progenitor cell differentiation
up regulation of haematopoietic progenitor cell differentiation
up regulation of haemopoietic progenitor cell differentiation
up regulation of hemopoietic progenitor cell differentiation
up-regulation of haematopoietic progenitor cell differentiation
up-regulation of haemopoietic progenitor cell differentiation
up-regulation of hemopoietic progenitor cell differentiation
upregulation of haematopoietic progenitor cell differentiation
upregulation of haemopoietic progenitor cell differentiation
upregulation of hemopoietic progenitor cell differentiation
activation of hemopoietic progenitor cell differentiation
activation of hematopoietic progenitor cell differentiation
up regulation of hematopoietic progenitor cell differentiation
up-regulation of hematopoietic progenitor cell differentiation
upregulation of hematopoietic progenitor cell differentiation
positive regulation of hematopoietic progenitor cell differentiation
Any process that modulates the frequency, rate or extent of endothelial cell development.
regulation of endothelial cell development
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development.
down regulation of endothelial cell development
down-regulation of endothelial cell development
downregulation of endothelial cell development
inhibition of endothelial cell development
negative regulation of endothelial cell development
Any process that activates or increases the frequency, rate or extent of endothelial cell development.
up regulation of endothelial cell development
up-regulation of endothelial cell development
upregulation of endothelial cell development
activation of endothelial cell development
positive regulation of endothelial cell development
The chemical reactions and pathways involving organonitrogen compound.
organonitrogen compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.
organonitrogen compound catabolic process
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
organonitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
The chemical reactions and pathways involving an alpha-amino acid.
The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid.
The chemical reactions and pathways resulting in the formation of an alpha-amino acid.
Any process that modulates the frequency, rate or extent of vesicle transport along microtubule.
regulation of microtubule-based vesicle localization
regulation of vesicle transport along microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule.
down regulation of microtubule-based vesicle localization
down regulation of vesicle transport along microtubule
down-regulation of microtubule-based vesicle localization
down-regulation of vesicle transport along microtubule
downregulation of microtubule-based vesicle localization
downregulation of vesicle transport along microtubule
inhibition of microtubule-based vesicle localization
negative regulation of microtubule-based vesicle localization
inhibition of vesicle transport along microtubule
negative regulation of vesicle transport along microtubule
Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule.
activation of microtubule-based vesicle localization
positive regulation of microtubule-based vesicle localization
up regulation of microtubule-based vesicle localization
up regulation of vesicle transport along microtubule
up-regulation of microtubule-based vesicle localization
up-regulation of vesicle transport along microtubule
upregulation of microtubule-based vesicle localization
upregulation of vesicle transport along microtubule
activation of vesicle transport along microtubule
positive regulation of vesicle transport along microtubule
The chemical reactions and pathways involving organic hydroxy compound.
organic hydroxy compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organic hydroxy compound.
organic hydroxy compound catabolic process
The chemical reactions and pathways resulting in the formation of organic hydroxy compound.
organic hydroxy compound biosynthetic process
Enables the transfer of organic hydroxy compound from one side of a membrane to the other.
organic hydroxy compound transmembrane transporter activity
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.
A response that results in a state of tolerance to ketone.
process resulting in tolerance to ketone
Enables the transfer of a sulfur compound from one side of a membrane to the other.
sulfur molecular entity transmembrane transporter activity
sulfur compound transmembrane transporter activity
Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process.
regulation of compound eye retinal cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process.
down regulation of compound eye retinal cell apoptotic process
down-regulation of compound eye retinal cell apoptotic process
downregulation of compound eye retinal cell apoptotic process
inhibition of compound eye retinal cell apoptotic process
negative regulation of compound eye retinal cell apoptotic process
Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process.
up regulation of compound eye retinal cell apoptotic process
up-regulation of compound eye retinal cell apoptotic process
upregulation of compound eye retinal cell apoptotic process
activation of compound eye retinal cell apoptotic process
induction of compound eye retinal cell programmed cell death
positive regulation of compound eye retinal cell apoptotic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.
Enables the transfer of salt from one side of a membrane to the other.
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state.
mesenchymal cell differentiation involved in bone development
Any process that modulates the frequency, rate or extent of muscle tissue development.
Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development.
down regulation of muscle tissue development
down-regulation of muscle tissue development
downregulation of muscle tissue development
negative regulation of muscle tissue development
Any process that activates or increases the frequency, rate or extent of muscle tissue development.
up regulation of muscle tissue development
up-regulation of muscle tissue development
upregulation of muscle tissue development
positive regulation of muscle tissue development
Any process that modulates the frequency, rate or extent of protein depolymerization.
regulation of protein polymer catabolic process
regulation of protein polymer catabolism
regulation of protein polymer degradation
Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization.
down regulation of protein depolymerization
down regulation of protein polymer breakdown
down regulation of protein polymer catabolic process
down regulation of protein polymer catabolism
down regulation of protein polymer degradation
down-regulation of protein depolymerization
down-regulation of protein polymer breakdown
down-regulation of protein polymer catabolic process
down-regulation of protein polymer catabolism
down-regulation of protein polymer degradation
downregulation of protein depolymerization
downregulation of protein polymer breakdown
downregulation of protein polymer catabolic process
downregulation of protein polymer catabolism
downregulation of protein polymer degradation
inhibition of protein polymer catabolic process
inhibition of protein polymer catabolism
inhibition of protein polymer degradation
negative regulation of protein polymer breakdown
negative regulation of protein polymer catabolic process
negative regulation of protein polymer catabolism
negative regulation of protein polymer degradation
negative regulation of protein depolymerization
Any process that activates or increases the frequency, rate or extent of protein depolymerization.
activation of protein polymer catabolic process
activation of protein polymer catabolism
activation of protein polymer degradation
positive regulation of protein polymer breakdown
positive regulation of protein polymer catabolic process
positive regulation of protein polymer catabolism
positive regulation of protein polymer degradation
up regulation of protein depolymerization
up regulation of protein polymer breakdown
up regulation of protein polymer catabolic process
up regulation of protein polymer catabolism
up regulation of protein polymer degradation
up-regulation of protein depolymerization
up-regulation of protein polymer breakdown
up-regulation of protein polymer catabolic process
up-regulation of protein polymer catabolism
up-regulation of protein polymer degradation
upregulation of protein depolymerization
upregulation of protein polymer breakdown
upregulation of protein polymer catabolic process
upregulation of protein polymer catabolism
upregulation of protein polymer degradation
positive regulation of protein depolymerization
Any process that modulates the frequency, rate or extent of cell junction assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly.
down regulation of cell junction assembly
down-regulation of cell junction assembly
downregulation of cell junction assembly
negative regulation of cell junction assembly
Any process that activates or increases the frequency, rate or extent of cell junction assembly.
positive regulation of cell junction assembly
Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.
regulation of cell proliferation involved in outflow tract morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.
up regulation of cell proliferation involved in outflow tract morphogenesis
up-regulation of cell proliferation involved in outflow tract morphogenesis
upregulation of cell proliferation involved in outflow tract morphogenesis
activation of cell proliferation involved in outflow tract morphogenesis
positive regulation of cell proliferation involved in outflow tract morphogenesis
Any process that modulates the frequency, rate or extent of cilium assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly.
negative regulation of cilium biogenesis
Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation.
regulation of hemopoietic stem cell proliferation
regulation of hematopoietic stem cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation.
down regulation of hematopoietic stem cell proliferation
down regulation of hemopoietic stem cell proliferation
down-regulation of hematopoietic stem cell proliferation
down-regulation of hemopoietic stem cell proliferation
downregulation of hematopoietic stem cell proliferation
downregulation of hemopoietic stem cell proliferation
negative regulation of hemopoietic stem cell proliferation
inhibition of hematopoietic stem cell proliferation
inhibition of hemopoietic stem cell proliferation
negative regulation of hematopoietic stem cell proliferation
Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation.
positive regulation of hemopoietic stem cell proliferation
up regulation of hematopoietic stem cell proliferation
up regulation of hemopoietic stem cell proliferation
up-regulation of hematopoietic stem cell proliferation
up-regulation of hemopoietic stem cell proliferation
upregulation of hematopoietic stem cell proliferation
upregulation of hemopoietic stem cell proliferation
activation of hematopoietic stem cell proliferation
activation of hemopoietic stem cell proliferation
positive regulation of hematopoietic stem cell proliferation
Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.
regulation of haematopoietic stem cell differentiation
regulation of haemopoietic stem cell differentiation
regulation of hemopoietic stem cell differentiation
regulation of hematopoietic stem cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation.
down regulation of haematopoietic stem cell differentiation
down regulation of haemopoietic stem cell differentiation
down regulation of hematopoietic stem cell differentiation
down regulation of hemopoietic stem cell differentiation
down-regulation of haematopoietic stem cell differentiation
down-regulation of haemopoietic stem cell differentiation
down-regulation of hematopoietic stem cell differentiation
down-regulation of hemopoietic stem cell differentiation
downregulation of haematopoietic stem cell differentiation
downregulation of haemopoietic stem cell differentiation
downregulation of hematopoietic stem cell differentiation
downregulation of hemopoietic stem cell differentiation
negative regulation of haematopoietic stem cell differentiation
negative regulation of haemopoietic stem cell differentiation
negative regulation of hemopoietic stem cell differentiation
inhibition of haematopoietic stem cell differentiation
inhibition of haemopoietic stem cell differentiation
inhibition of hematopoietic stem cell differentiation
inhibition of hemopoietic stem cell differentiation
negative regulation of hematopoietic stem cell differentiation
Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation.
positive regulation of haematopoietic stem cell differentiation
positive regulation of haemopoietic stem cell differentiation
positive regulation of hemopoietic stem cell differentiation
up regulation of haematopoietic stem cell differentiation
up regulation of haemopoietic stem cell differentiation
up regulation of hematopoietic stem cell differentiation
up regulation of hemopoietic stem cell differentiation
up-regulation of haematopoietic stem cell differentiation
up-regulation of haemopoietic stem cell differentiation
up-regulation of hematopoietic stem cell differentiation
up-regulation of hemopoietic stem cell differentiation
upregulation of haematopoietic stem cell differentiation
upregulation of haemopoietic stem cell differentiation
upregulation of hematopoietic stem cell differentiation
upregulation of hemopoietic stem cell differentiation
activation of haematopoietic stem cell differentiation
activation of haemopoietic stem cell differentiation
activation of hematopoietic stem cell differentiation
activation of hemopoietic stem cell differentiation
positive regulation of hematopoietic stem cell differentiation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salt stimulus.
Any process that modulates the frequency, rate or extent of leukocyte differentiation.
regulation of immune cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation.
down regulation of immune cell differentiation
down regulation of leucocyte differentiation
down regulation of leukocyte differentiation
down-regulation of immune cell differentiation
down-regulation of leucocyte differentiation
down-regulation of leukocyte differentiation
downregulation of immune cell differentiation
downregulation of leucocyte differentiation
downregulation of leukocyte differentiation
negative regulation of immune cell differentiation
negative regulation of leucocyte differentiation
inhibition of immune cell differentiation
negative regulation of leukocyte differentiation
Any process that activates or increases the frequency, rate or extent of leukocyte differentiation.
positive regulation of immune cell differentiation
positive regulation of leucocyte differentiation
up regulation of immune cell differentiation
up regulation of leucocyte differentiation
up regulation of leukocyte differentiation
up-regulation of immune cell differentiation
up-regulation of leucocyte differentiation
up-regulation of leukocyte differentiation
upregulation of immune cell differentiation
upregulation of leucocyte differentiation
upregulation of leukocyte differentiation
activation of immune cell differentiation
positive regulation of leukocyte differentiation
Any process that modulates the frequency, rate or extent of organelle assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly.
negative regulation of organelle assembly
Any process that activates or increases the frequency, rate or extent of organelle assembly.
positive regulation of organelle assembly
Any apoptotic process in an erythrocyte.
Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process.
regulation of red blood cell apoptotic process
regulation of erythrocyte apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process.
down regulation of RBC apoptotic process
down regulation of erythrocyte apoptotic process
down regulation of red blood cell apoptotic process
down-regulation of RBC apoptotic process
down-regulation of erythrocyte apoptotic process
down-regulation of red blood cell apoptotic process
downregulation of erythrocyte apoptotic process
downregulation of red blood cell apoptotic process
negative regulation of RBC apoptotic process
negative regulation of red blood cell apoptotic process
down regulation of erythrocyte apoptosis
down regulation of red blood cell apoptosis
down-regulation of erythrocyte apoptosis
down-regulation of red blood cell apoptosis
downregulation of red blood cell apoptosis
inhibition of erythrocyte apoptotic process
inhibition of red blood cell apoptotic process
negative regulation of erythrocyte apoptosis
negative regulation of red blood cell apoptosis
negative regulation of erythrocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process.
positive regulation of RBC apoptotic process
positive regulation of red blood cell apoptotic process
up regulation of erythrocyte apoptotic process
up regulation of red blood cell apoptotic process
up-regulation of erythrocyte apoptotic process
up-regulation of red blood cell apoptotic process
upregulation of erythrocyte apoptotic process
upregulation of red blood cell apoptotic process
activation of erythrocyte apoptotic process
activation of red blood cell apoptotic process
positive regulation of erythrocyte apoptosis
positive regulation of red blood cell apoptosis
up regulation of red blood cell apoptosis
up-regulation of red blood cell apoptosis
upregulation of red blood cell apoptosis
positive regulation of erythrocyte apoptotic process
Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
regulation of apoptosis involved in outflow tract morphogenesis
regulation of apoptotic process involved in outflow tract morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
down regulation of apoptotic process involved in outflow tract morphogenesis
down-regulation of apoptotic process involved in outflow tract morphogenesis
downregulation of apoptotic process involved in outflow tract morphogenesis
down regulation of apoptosis involved in outflow tract morphogenesis
down-regulation of apoptosis involved in outflow tract morphogenesis
downregulation of apoptosis involved in outflow tract morphogenesis
inhibition of apoptosis involved in outflow tract morphogenesis
inhibition of apoptotic process involved in outflow tract morphogenesis
negative regulation of apoptosis involved in outflow tract morphogenesis
negative regulation of apoptotic process involved in outflow tract morphogenesis
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
up regulation of apoptotic process involved in outflow tract morphogenesis
up-regulation of apoptotic process involved in outflow tract morphogenesis
upregulation of apoptotic process involved in outflow tract morphogenesis
activation of apoptosis involved in outflow tract morphogenesis
activation of apoptotic process involved in outflow tract morphogenesis
positive regulation of apoptosis involved in outflow tract morphogenesis
up regulation of apoptosis involved in outflow tract morphogenesis
up-regulation of apoptosis involved in outflow tract morphogenesis
upregulation of apoptosis involved in outflow tract morphogenesis
positive regulation of apoptotic process involved in outflow tract morphogenesis
Any apoptotic process that is involved in blood vessel morphogenesis.
apoptotic cell death involved in patterning of blood vessels
apoptotic programmed cell death involved in patterning of blood vessels
programmed cell death by apoptosis involved in patterning of blood vessels
apoptosis involved in patterning of blood vessels
apoptotic program involved in patterning of blood vessels
type I programmed cell death involved in patterning of blood vessels
signaling (initiator) caspase activity involved in patterning of blood vessels
apoptotic process involved in blood vessel morphogenesis
Any process that modulates the frequency, rate or extent of chromatin organization.
regulation of establishment or maintenance of chromatin architecture
regulation of chromatin assembly or disassembly
regulation of chromatin assembly/disassembly
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport.
regulation of sodium ion membrane transport
regulation of sodium ion transmembrane transport
Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transport.
down regulation of sodium ion membrane transport
down regulation of sodium ion transmembrane transport
down-regulation of sodium ion membrane transport
down-regulation of sodium ion transmembrane transport
downregulation of sodium ion membrane transport
downregulation of sodium ion transmembrane transport
negative regulation of sodium ion membrane transport
inhibition of sodium ion membrane transport
inhibition of sodium ion transmembrane transport
negative regulation of sodium ion transmembrane transport
Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport.
positive regulation of sodium ion membrane transport
up regulation of sodium ion membrane transport
up regulation of sodium ion transmembrane transport
up-regulation of sodium ion membrane transport
up-regulation of sodium ion transmembrane transport
upregulation of sodium ion membrane transport
upregulation of sodium ion transmembrane transport
activation of sodium ion membrane transport
activation of sodium ion transmembrane transport
positive regulation of sodium ion transmembrane transport
Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis.
regulation of apoptosis involved in morphogenesis
regulation of apoptosis involved in development
regulation of apoptotic process involved in morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis.
down regulation of apoptotic process involved in morphogenesis
down-regulation of apoptotic process involved in morphogenesis
downregulation of apoptotic process involved in morphogenesis
down regulation of apoptosis involved in morphogenesis
down-regulation of apoptosis involved in morphogenesis
downregulation of apoptosis involved in morphogenesis
inhibition of apoptosis involved in morphogenesis
inhibition of apoptotic process involved in morphogenesis
negative regulation of apoptosis involved in morphogenesis
down regulation of apoptosis involved in development
down regulation of morphogenetic apoptosis
down-regulation of apoptosis involved in development
down-regulation of morphogenetic apoptosis
downregulation of apoptosis involved in development
downregulation of morphogenetic apoptosis
inhibition of apoptosis involved in development
negative regulation of apoptosis involved in development
negative regulation of morphogenetic apoptosis
negative regulation of apoptotic process involved in morphogenesis
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis.
up regulation of apoptotic process involved in morphogenesis
up-regulation of apoptotic process involved in morphogenesis
upregulation of apoptotic process involved in morphogenesis
activation of apoptosis involved in morphogenesis
activation of apoptotic process involved in morphogenesis
positive regulation of apoptosis involved in morphogenesis
up regulation of apoptosis involved in morphogenesis
up-regulation of apoptosis involved in morphogenesis
upregulation of apoptosis involved in morphogenesis
activation of apoptosis involved in development
positive regulation of apoptosis involved in development
positive regulation of morphogenetic apoptosis
up regulation of apoptosis involved in development
up regulation of morphogenetic apoptosis
up-regulation of apoptosis involved in development
up-regulation of morphogenetic apoptosis
upregulation of apoptosis involved in development
positive regulation of apoptotic process involved in morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation.
down regulation of chromosome condensation
down regulation of eukaryotic chromosome condensation
down regulation of nuclear chromosome condensation
down-regulation of chromosome condensation
down-regulation of eukaryotic chromosome condensation
down-regulation of nuclear chromosome condensation
downregulation of chromosome condensation
downregulation of eukaryotic chromosome condensation
downregulation of nuclear chromosome condensation
negative regulation of eukaryotic chromosome condensation
negative regulation of nuclear chromosome condensation
inhibition of eukaryotic chromosome condensation
inhibition of nuclear chromosome condensation
negative regulation of chromosome condensation
The directed movement of sulfate across a membrane.
Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process.
down regulation of RNA catabolic process
down-regulation of RNA catabolic process
negative regulation of RNA catabolic process
A process in which a protein is transported to, or maintained in, a location within a cell junction.
A process in which a protein is transported to, or maintained in, a location within a cell leading edge.
protein localisation in cell leading edge
protein localisation to cell leading edge
protein localization in cell leading edge
protein localization to cell leading edge
Any process that modulates the frequency, rate or extent of protein localization to synapse.
regulation of protein localisation to synapse
regulation of protein localization to synapse
Any process that activates or increases the frequency, rate or extent of protein localization to synapse.
positive regulation of protein localisation to synapse
up regulation of protein localisation to synapse
up regulation of protein localization to synapse
up-regulation of protein localisation to synapse
up-regulation of protein localization to synapse
upregulation of protein localisation to synapse
upregulation of protein localization to synapse
activation of protein localisation to synapse
activation of protein localization to synapse
positive regulation of protein localization to synapse
Any apoptotic process in a cholangiocyte.
epithelial cell of bile duct apoptotic process
A protein complex which is capable of catalytic activity.
A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other.
Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.
regulation of DNA catabolic process during apoptosis
regulation of DNA catabolism during apoptosis
regulation of DNA fragmentation involved in apoptotic nuclear change
regulation of endonucleolytic DNA catabolic process involved in apoptosis
DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases (see GO:0006309 'apoptotic DNA fragmentation'). Gene products involved in compartmentalization of such nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
regulation of apoptotic DNA fragmentation
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation.
down regulation of DNA catabolic process during apoptosis
down regulation of DNA catabolism during apoptosis
down regulation of DNA fragmentation involved in apoptotic nuclear change
down regulation of apoptotic DNA fragmentation
down regulation of endonucleolytic DNA catabolic process involved in apoptosis
down-regulation of DNA catabolic process during apoptosis
down-regulation of DNA catabolism during apoptosis
down-regulation of DNA fragmentation involved in apoptotic nuclear change
down-regulation of apoptotic DNA fragmentation
down-regulation of endonucleolytic DNA catabolic process involved in apoptosis
downregulation of DNA catabolic process during apoptosis
downregulation of DNA catabolism during apoptosis
downregulation of DNA fragmentation involved in apoptotic nuclear change
downregulation of apoptotic DNA fragmentation
downregulation of endonucleolytic DNA catabolic process involved in apoptosis
negative regulation of DNA catabolic process during apoptosis
negative regulation of DNA catabolism during apoptosis
negative regulation of DNA fragmentation involved in apoptotic nuclear change
negative regulation of endonucleolytic DNA catabolic process involved in apoptosis
inhibition of DNA catabolic process during apoptosis
inhibition of DNA catabolism during apoptosis
inhibition of DNA fragmentation involved in apoptotic nuclear change
inhibition of apoptotic DNA fragmentation
inhibition of endonucleolytic DNA catabolic process involved in apoptosis
negative regulation of apoptotic DNA fragmentation
Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation.
positive regulation of DNA catabolic process during apoptosis
positive regulation of DNA catabolism during apoptosis
positive regulation of DNA fragmentation involved in apoptotic nuclear change
positive regulation of endonucleolytic DNA catabolic process involved in apoptosis
up regulation of DNA catabolic process during apoptosis
up regulation of DNA catabolism during apoptosis
up regulation of DNA fragmentation involved in apoptotic nuclear change
up regulation of apoptotic DNA fragmentation
up regulation of endonucleolytic DNA catabolic process involved in apoptosis
up-regulation of DNA catabolic process during apoptosis
up-regulation of DNA catabolism during apoptosis
up-regulation of DNA fragmentation involved in apoptotic nuclear change
up-regulation of apoptotic DNA fragmentation
up-regulation of endonucleolytic DNA catabolic process involved in apoptosis
upregulation of DNA catabolic process during apoptosis
upregulation of DNA catabolism during apoptosis
upregulation of DNA fragmentation involved in apoptotic nuclear change
upregulation of apoptotic DNA fragmentation
upregulation of endonucleolytic DNA catabolic process involved in apoptosis
activation of DNA catabolic process during apoptosis
activation of DNA catabolism during apoptosis
activation of DNA fragmentation involved in apoptotic nuclear change
activation of apoptotic DNA fragmentation
activation of endonucleolytic DNA catabolic process involved in apoptosis
positive regulation of apoptotic DNA fragmentation
Any process that modulates the frequency, rate or extent of organelle transport along microtubule.
regulation of microtubule-based organelle localization
regulation of organelle transport along microtubule
Any process that modulates the frequency, rate or extent of intracellular signal transduction.
regulation of intracellular signaling cascade
regulation of intracellular signaling chain
regulation of intracellular protein kinase cascade
regulation of intracellular signal transduction pathway
regulation of signal transmission via intracellular cascade
regulation of intracellular signaling pathway
regulation of signal transduction via intracellular signaling cascade
regulation of intracellular signal transduction
Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.
down regulation of intracellular signal transduction
down regulation of intracellular signaling chain
down-regulation of intracellular signal transduction
down-regulation of intracellular signaling chain
downregulation of intracellular signal transduction
downregulation of intracellular signaling chain
negative regulation of intracellular protein kinase cascade
negative regulation of intracellular signaling cascade
negative regulation of intracellular signaling chain
down regulation of intracellular signal transduction pathway
down regulation of intracellular signaling cascade
down regulation of signal transmission via intracellular cascade
down-regulation of intracellular signal transduction pathway
downregulation of intracellular signal transduction pathway
downregulation of intracellular signaling cascade
downregulation of signal transmission via intracellular cascade
inhibition of intracellular signal transduction
inhibition of intracellular signal transduction pathway
inhibition of intracellular signaling cascade
inhibition of intracellular signaling chain
inhibition of signal transmission via intracellular cascade
negative regulation of intracellular signal transduction pathway
negative regulation of signal transmission via intracellular cascade
down regulation of intracellular signaling pathway
down regulation of signal transduction via intracellular signaling cascade
down-regulation of intracellular signaling cascade
down-regulation of intracellular signaling pathway
down-regulation of signal transduction via intracellular signaling cascade
down-regulation of signal transmission via intracellular cascade
downregulation of intracellular signaling pathway
downregulation of signal transduction via intracellular signaling cascade
inhibition of intracellular signaling pathway
inhibition of signal transduction via intracellular signaling cascade
negative regulation of intracellular signaling pathway
negative regulation of signal transduction via intracellular signaling cascade
negative regulation of intracellular signal transduction
Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
positive regulation of intracellular signaling chain
up regulation of intracellular signal transduction
up regulation of intracellular signaling chain
up-regulation of intracellular signal transduction
up-regulation of intracellular signaling chain
upregulation of intracellular signal transduction
upregulation of intracellular signaling chain
activation of intracellular signal transduction
activation of intracellular signal transduction pathway
activation of intracellular signaling cascade
activation of intracellular signaling chain
activation of signal transmission via intracellular cascade
positive regulation of intracellular protein kinase cascade
positive regulation of intracellular signal transduction pathway
positive regulation of signal transmission via intracellular cascade
up regulation of intracellular signal transduction pathway
up regulation of signal transmission via intracellular cascade
up-regulation of intracellular signal transduction pathway
up-regulation of signal transmission via intracellular cascade
upregulation of intracellular signal transduction pathway
upregulation of signal transmission via intracellular cascade
activation of intracellular signaling pathway
activation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signaling cascade
positive regulation of intracellular signaling pathway
positive regulation of signal transduction via intracellular signaling cascade
up regulation of intracellular signaling cascade
up regulation of intracellular signaling pathway
up regulation of signal transduction via intracellular signaling cascade
up-regulation of intracellular signaling cascade
up-regulation of intracellular signaling pathway
up-regulation of signal transduction via intracellular signaling cascade
upregulation of intracellular signaling cascade
upregulation of intracellular signaling pathway
upregulation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signal transduction
A process in which a protein is transported to, or maintained in, a location within a nucleolus.
Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
down regulation of RNA biosynthetic process
down-regulation of RNA biosynthetic process
downregulation of RNA biosynthetic process
negative regulation of RNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
up regulation of RNA biosynthetic process
up-regulation of RNA biosynthetic process
upregulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
Any process that modulates the frequency, rate or extent of neuroblast proliferation.
Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.
regulation of chondrocyte differentiation involved in endochondral bone morphogenesis
Any apoptotic process that is involved in anatomical structure development.
apoptotic cell death involved in anatomical structure development
apoptotic cell death involved in development of an anatomical structure
apoptotic process involved in anatomical structure development
apoptotic process involved in development of an anatomical structure
apoptotic programmed cell death involved in anatomical structure development
apoptotic programmed cell death involved in development of an anatomical structure
programmed cell death by apoptosis involved in anatomical structure development
programmed cell death by apoptosis involved in development of an anatomical structure
activation of apoptosis involved in anatomical structure development
activation of apoptosis involved in development of an anatomical structure
apoptosis involved in anatomical structure development
apoptosis involved in development of an anatomical structure
apoptosis signaling involved in anatomical structure development
apoptosis signaling involved in development of an anatomical structure
apoptotic program involved in anatomical structure development
apoptotic program involved in development of an anatomical structure
type I programmed cell death involved in anatomical structure development
type I programmed cell death involved in development of an anatomical structure
apoptosis activator activity involved in anatomical structure development
apoptosis activator activity involved in development of an anatomical structure
commitment to apoptosis involved in anatomical structure development
commitment to apoptosis involved in development of an anatomical structure
induction of apoptosis by p53 involved in anatomical structure development
induction of apoptosis by p53 involved in development of an anatomical structure
induction of apoptosis involved in anatomical structure development
induction of apoptosis involved in development of an anatomical structure
signaling (initiator) caspase activity involved in anatomical structure development
signaling (initiator) caspase activity involved in development of an anatomical structure
apoptotic process involved in development
Any process that activates or increases the frequency, rate or extent of chondrocyte development.
up regulation of chondrocyte development
up-regulation of chondrocyte development
positive regulation of chondrocyte development
Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation.
regulation of skeletal muscle fiber differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation.
down regulation of skeletal muscle fiber differentiation
down-regulation of skeletal muscle fiber differentiation
downregulation of skeletal muscle fiber differentiation
inhibition of skeletal muscle fiber differentiation
negative regulation of skeletal muscle fiber differentiation
Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation.
up regulation of skeletal muscle fiber differentiation
up-regulation of skeletal muscle fiber differentiation
upregulation of skeletal muscle fiber differentiation
activation of skeletal muscle fiber differentiation
positive regulation of skeletal muscle fiber differentiation
Any process that modulates the frequency, rate or extent of protein localization to microtubule.
regulation of protein localisation to microtubule
regulation of protein localization to microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule.
down regulation of protein localisation to microtubule
down regulation of protein localization to microtubule
down-regulation of protein localisation to microtubule
down-regulation of protein localization to microtubule
downregulation of protein localisation to microtubule
downregulation of protein localization to microtubule
negative regulation of protein localisation to microtubule
inhibition of protein localisation to microtubule
inhibition of protein localization to microtubule
negative regulation of protein localization to microtubule
Any process that modulates the frequency, rate or extent of nuclear migration along microtubule.
regulation of nuclear movement, microtubule-mediated
regulation of microtubule cytoskeleton-dependent nuclear positioning
regulation of microtubule cytoskeleton-dependent nucleus positioning
regulation of microtubule-dependent nuclear positioning
regulation of microtubule-dependent nucleus positioning
regulation of microtubule-mediated nuclear migration
regulation of nuclear migration, microtubule-mediated
regulation of transport of nucleus by microtubules
regulation of transport of nucleus, microtubule-mediated
regulation of nuclear migration along microtubule
Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule.
down regulation of microtubule cytoskeleton-dependent nuclear positioning
down regulation of microtubule cytoskeleton-dependent nucleus positioning
down regulation of microtubule-dependent nuclear positioning
down regulation of microtubule-dependent nucleus positioning
down regulation of microtubule-mediated nuclear migration
down regulation of nuclear migration along microtubule
down regulation of nuclear migration, microtubule-mediated
down regulation of transport of nucleus by microtubules
down regulation of transport of nucleus, microtubule-mediated
down-regulation of microtubule cytoskeleton-dependent nuclear positioning
down-regulation of microtubule cytoskeleton-dependent nucleus positioning
down-regulation of microtubule-dependent nuclear positioning
down-regulation of microtubule-dependent nucleus positioning
down-regulation of microtubule-mediated nuclear migration
down-regulation of nuclear migration along microtubule
down-regulation of nuclear migration, microtubule-mediated
down-regulation of transport of nucleus by microtubules
down-regulation of transport of nucleus, microtubule-mediated
downregulation of microtubule cytoskeleton-dependent nuclear positioning
downregulation of microtubule cytoskeleton-dependent nucleus positioning
downregulation of microtubule-dependent nuclear positioning
downregulation of microtubule-dependent nucleus positioning
downregulation of microtubule-mediated nuclear migration
downregulation of nuclear migration along microtubule
downregulation of nuclear migration, microtubule-mediated
downregulation of transport of nucleus by microtubules
downregulation of transport of nucleus, microtubule-mediated
negative regulation of microtubule cytoskeleton-dependent nuclear positioning
negative regulation of microtubule cytoskeleton-dependent nucleus positioning
negative regulation of microtubule-dependent nuclear positioning
negative regulation of microtubule-dependent nucleus positioning
negative regulation of microtubule-mediated nuclear migration
negative regulation of nuclear migration, microtubule-mediated
negative regulation of transport of nucleus by microtubules
negative regulation of transport of nucleus, microtubule-mediated
inhibition of microtubule cytoskeleton-dependent nuclear positioning
inhibition of microtubule cytoskeleton-dependent nucleus positioning
inhibition of microtubule-dependent nuclear positioning
inhibition of microtubule-dependent nucleus positioning
inhibition of microtubule-mediated nuclear migration
inhibition of nuclear migration along microtubule
inhibition of nuclear migration, microtubule-mediated
inhibition of transport of nucleus by microtubules
inhibition of transport of nucleus, microtubule-mediated
negative regulation of nuclear migration along microtubule
Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule.
positive regulation of microtubule cytoskeleton-dependent nuclear positioning
positive regulation of microtubule cytoskeleton-dependent nucleus positioning
positive regulation of microtubule-dependent nuclear positioning
positive regulation of microtubule-dependent nucleus positioning
positive regulation of microtubule-mediated nuclear migration
positive regulation of nuclear migration, microtubule-mediated
positive regulation of transport of nucleus by microtubules
positive regulation of transport of nucleus, microtubule-mediated
up regulation of microtubule cytoskeleton-dependent nuclear positioning
up regulation of microtubule cytoskeleton-dependent nucleus positioning
up regulation of microtubule-dependent nuclear positioning
up regulation of microtubule-dependent nucleus positioning
up regulation of microtubule-mediated nuclear migration
up regulation of nuclear migration along microtubule
up regulation of nuclear migration, microtubule-mediated
up regulation of transport of nucleus by microtubules
up regulation of transport of nucleus, microtubule-mediated
up-regulation of microtubule cytoskeleton-dependent nuclear positioning
up-regulation of microtubule cytoskeleton-dependent nucleus positioning
up-regulation of microtubule-dependent nuclear positioning
up-regulation of microtubule-dependent nucleus positioning
up-regulation of microtubule-mediated nuclear migration
up-regulation of nuclear migration along microtubule
up-regulation of nuclear migration, microtubule-mediated
up-regulation of transport of nucleus by microtubules
up-regulation of transport of nucleus, microtubule-mediated
upregulation of microtubule cytoskeleton-dependent nuclear positioning
upregulation of microtubule cytoskeleton-dependent nucleus positioning
upregulation of microtubule-dependent nuclear positioning
upregulation of microtubule-dependent nucleus positioning
upregulation of microtubule-mediated nuclear migration
upregulation of nuclear migration along microtubule
upregulation of nuclear migration, microtubule-mediated
upregulation of transport of nucleus by microtubules
upregulation of transport of nucleus, microtubule-mediated
activation of microtubule cytoskeleton-dependent nuclear positioning
activation of microtubule cytoskeleton-dependent nucleus positioning
activation of microtubule-dependent nuclear positioning
activation of microtubule-dependent nucleus positioning
activation of microtubule-mediated nuclear migration
activation of nuclear migration along microtubule
activation of nuclear migration, microtubule-mediated
activation of transport of nucleus by microtubules
activation of transport of nucleus, microtubule-mediated
positive regulation of nuclear migration along microtubule
Any microtubule cytoskeleton organization that is involved in mitosis.
microtubule cytoskeleton organisation involved in mitosis
microtubule dynamics involved in mitosis
microtubule cytoskeleton organization and biogenesis involved in mitosis
microtubule cytoskeleton organization involved in mitosis
Any process that modulates the frequency, rate or extent of embryonic camera-type eye development.
regulation of embryonic camera-type eye development
Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development.
down regulation of embryonic camera-type eye development
down regulation of embryonic eye development
down-regulation of embryonic camera-type eye development
down-regulation of embryonic eye development
downregulation of embryonic camera-type eye development
downregulation of embryonic eye development
negative regulation of embryonic eye development
inhibition of embryonic camera-type eye development
negative regulation of embryonic camera-type eye development
Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development.
positive regulation of embryonic eye development
up regulation of embryonic camera-type eye development
up regulation of embryonic eye development
up-regulation of embryonic camera-type eye development
up-regulation of embryonic eye development
upregulation of embryonic camera-type eye development
upregulation of embryonic eye development
activation of embryonic camera-type eye development
positive regulation of embryonic camera-type eye development
Any process that modulates the frequency, rate or extent of retina development in camera-type eye.
regulation of retina development in camera-style eye
regulation of retina development in camera-type eye
Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye.
down regulation of retina development in camera-style eye
down regulation of retina development in camera-type eye
down-regulation of retina development in camera-style eye
down-regulation of retina development in camera-type eye
downregulation of retina development in camera-style eye
downregulation of retina development in camera-type eye
negative regulation of retina development in camera-style eye
inhibition of retina development in camera-style eye
inhibition of retina development in camera-type eye
negative regulation of retinal development
negative regulation of retina development in camera-type eye
Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye.
positive regulation of retina development in camera-style eye
up regulation of retina development in camera-style eye
up regulation of retina development in camera-type eye
up-regulation of retina development in camera-style eye
up-regulation of retina development in camera-type eye
upregulation of retina development in camera-style eye
upregulation of retina development in camera-type eye
activation of retina development in camera-style eye
activation of retina development in camera-type eye
positive regulation of retinal development
positive regulation of retina development in camera-type eye
Any process that modulates the frequency, rate or extent of supramolecular fiber organization.
HSPA8, human, P11142 in PMID:23921388 inferred from direct assay to negatively regulate fibrillation of alpha-Syn in vitro
regulation of supramolecular fiber organization
Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization.
negative regulation of fibril organisation
negative regulation of supramolecular fiber organization
Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization.
positive regulation of fibril organisation
positive regulation of supramolecular fiber organization
Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation.
up regulation of neuroepithelial cell differentiation
up-regulation of neuroepithelial cell differentiation
upregulation of neuroepithelial cell differentiation
activation of neuroepithelial cell differentiation
positive regulation of neuroepithelial cell differentiation
The disaggregation of an organelle into its constituent components.
Any process that modulates the frequency, rate or extent of bone development.
Any process that stops, prevents or reduces the frequency, rate or extent of bone development.
Any process that activates or increases the frequency, rate or extent of bone development.
Any process that modulates the frequency, rate or extent of glycoprotein metabolic process.
human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein
regulation of glycoprotein metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process.
down regulation of glycoprotein metabolic process
down regulation of glycoprotein metabolism
down-regulation of glycoprotein metabolic process
down-regulation of glycoprotein metabolism
downregulation of glycoprotein metabolic process
downregulation of glycoprotein metabolism
negative regulation of glycoprotein metabolism
inhibition of glycoprotein metabolic process
negative regulation of glycoprotein metabolic process
Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process.
positive regulation of glycoprotein metabolism
up regulation of glycoprotein metabolic process
up regulation of glycoprotein metabolism
up-regulation of glycoprotein metabolic process
up-regulation of glycoprotein metabolism
upregulation of glycoprotein metabolic process
activation of glycoprotein metabolic process
positive regulation of glycoprotein metabolic process
A process that is part of the meiotic cell cycle.
A process that is part of the mitotic cell cycle.
Any process that modulates the frequency, rate or extent of extracellular matrix organization.
regulation of extracellular matrix organisation
regulation of extracellular matrix organization and biogenesis
regulation of extracellular matrix organization
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization.
down regulation of extracellular matrix organisation
down regulation of extracellular matrix organization
down-regulation of extracellular matrix organisation
down-regulation of extracellular matrix organization
downregulation of extracellular matrix organisation
downregulation of extracellular matrix organization
negative regulation of extracellular matrix organisation
inhibition of extracellular matrix organisation
inhibition of extracellular matrix organization
down regulation of extracellular matrix organization and biogenesis
down-regulation of extracellular matrix organization and biogenesis
downregulation of extracellular matrix organization and biogenesis
inhibition of extracellular matrix organization and biogenesis
negative regulation of extracellular matrix organization and biogenesis
negative regulation of extracellular matrix organization
Any process that activates or increases the frequency, rate or extent of extracellular matrix organization.
positive regulation of extracellular matrix organisation
up regulation of extracellular matrix organisation
up regulation of extracellular matrix organization
up-regulation of extracellular matrix organisation
up-regulation of extracellular matrix organization
upregulation of extracellular matrix organisation
upregulation of extracellular matrix organization
activation of extracellular matrix organisation
activation of extracellular matrix organization
activation of extracellular matrix organization and biogenesis
positive regulation of extracellular matrix organization and biogenesis
up regulation of extracellular matrix organization and biogenesis
up-regulation of extracellular matrix organization and biogenesis
upregulation of extracellular matrix organization and biogenesis
positive regulation of extracellular matrix organization
Any process that modulates the frequency, rate or extent of protein localization to plasma membrane.
regulation of protein localization in plasma membrane
regulation of establishment of protein localisation in plasma membrane
regulation of establishment of protein localization in plasma membrane
regulation of establishment of protein localization to plasma membrane
regulation of protein localisation in plasma membrane
regulation of protein targeting to plasma membrane
regulation of protein-plasma membrane targeting
regulation of protein localization to plasma membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
down regulation of protein localisation in plasma membrane
down regulation of protein localization in plasma membrane
down regulation of protein localization to plasma membrane
down-regulation of protein localisation in plasma membrane
down-regulation of protein localization in plasma membrane
down-regulation of protein localization to plasma membrane
downregulation of protein localisation in plasma membrane
downregulation of protein localization in plasma membrane
downregulation of protein localization to plasma membrane
negative regulation of protein localization in plasma membrane
inhibition of protein localisation in plasma membrane
inhibition of protein localization in plasma membrane
inhibition of protein localization to plasma membrane
inhibition of protein targeting to plasma membrane
inhibition of protein-plasma membrane targeting
down regulation of protein targeting to plasma membrane
down regulation of protein-plasma membrane targeting
down-regulation of protein targeting to plasma membrane
down-regulation of protein-plasma membrane targeting
downregulation of protein targeting to plasma membrane
downregulation of protein-plasma membrane targeting
negative regulation of establishment of protein localisation in plasma membrane
negative regulation of establishment of protein localization in plasma membrane
negative regulation of establishment of protein localization to plasma membrane
negative regulation of protein localisation in plasma membrane
negative regulation of protein targeting to plasma membrane
negative regulation of protein-plasma membrane targeting
negative regulation of protein localization to plasma membrane
Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane.
positive regulation of protein localisation in plasma membrane
positive regulation of protein localization in plasma membrane
up regulation of protein localisation in plasma membrane
up regulation of protein localization in plasma membrane
up regulation of protein localization to plasma membrane
up-regulation of protein localisation in plasma membrane
up-regulation of protein localization in plasma membrane
up-regulation of protein localization to plasma membrane
upregulation of protein localisation in plasma membrane
upregulation of protein localization in plasma membrane
upregulation of protein localization to plasma membrane
activation of protein localisation in plasma membrane
activation of protein localization in plasma membrane
activation of protein localization to plasma membrane
activation of protein targeting to plasma membrane
activation of protein-plasma membrane targeting
positive regulation of establishment of protein localisation in plasma membrane
positive regulation of establishment of protein localization to plasma membrane
positive regulation of protein targeting to plasma membrane
positive regulation of protein-plasma membrane targeting
up regulation of protein targeting to plasma membrane
up regulation of protein-plasma membrane targeting
up-regulation of protein targeting to plasma membrane
up-regulation of protein-plasma membrane targeting
upregulation of protein targeting to plasma membrane
upregulation of protein-plasma membrane targeting
positive regulation of protein localization to plasma membrane
Any process that modulates the frequency, rate or extent of actin filament-based movement.
regulation of actin filament-based movement
Any process that activates or increases the frequency, rate or extent of actin filament-based movement.
up regulation of actin filament-based movement
up-regulation of actin filament-based movement
upregulation of actin filament-based movement
activation of actin filament-based movement
positive regulation of actin filament-based movement
A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton.
protein localisation in actin cytoskeleton
protein localisation to actin cytoskeleton
protein localization in actin cytoskeleton
protein localization to actin cytoskeleton
A process in which a protein is transported to, or maintained in, the location of an actin filament bundle.
protein localisation in actin filament bundle
protein localisation to actin filament bundle
protein localization in actin filament bundle
protein localization to actin filament bundle
The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell.
Any process that modulates the frequency, rate or extent of endodermal cell differentiation.
regulation of endoderm cell differentiation
regulation of endodermal cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation.
down regulation of endoderm cell differentiation
down regulation of endodermal cell differentiation
down-regulation of endoderm cell differentiation
down-regulation of endodermal cell differentiation
downregulation of endoderm cell differentiation
downregulation of endodermal cell differentiation
negative regulation of endoderm cell differentiation
inhibition of endoderm cell differentiation
inhibition of endodermal cell differentiation
negative regulation of endodermal cell differentiation
Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation.
positive regulation of endoderm cell differentiation
up regulation of endoderm cell differentiation
up regulation of endodermal cell differentiation
up-regulation of endoderm cell differentiation
up-regulation of endodermal cell differentiation
upregulation of endoderm cell differentiation
upregulation of endodermal cell differentiation
activation of endoderm cell differentiation
activation of endodermal cell differentiation
positive regulation of endodermal cell differentiation
A process in which a protein is transported to, or maintained in, a location within a Golgi membrane.
Any process that modulates the frequency, rate or extent of vacuolar transport.
Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport.
negative regulation of vacuolar transport
Any process that activates or increases the frequency, rate or extent of vacuolar transport.
positive regulation of vacuolar transport
Any process that modulates the frequency, rate or extent of nucleus organization.
regulation of nuclear organization and biogenesis
regulation of nucleus organization and biogenesis
Any process that modulates the frequency, rate or extent of Golgi organization.
regulation of Golgi organization and biogenesis
Any process that modulates the frequency, rate or extent of mitotic chromosome condensation.
regulation of mitotic chromosome condensation
Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation.
up regulation of mitotic chromosome condensation
up-regulation of mitotic chromosome condensation
upregulation of mitotic chromosome condensation
activation of mitotic chromosome condensation
positive regulation of mitotic chromosome condensation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus.
Any process that modulates the frequency, rate or extent of cell maturation.
regulation of functional differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation.
down regulation of functional differentiation
down-regulation of functional differentiation
downregulation of functional differentiation
inhibition of functional differentiation
negative regulation of functional differentiation
Any process that activates or increases the frequency, rate or extent of cell maturation.
activation of functional differentiation
positive regulation of functional differentiation
up regulation of functional differentiation
up-regulation of functional differentiation
upregulation of functional differentiation
A process in which a protein is transported to, or maintained in, a location within a ciliary membrane.
protein localisation in ciliary membrane
protein localisation to ciliary membrane
protein localization in ciliary membrane
protein localization to ciliary membrane
The chemical reactions and pathways involving mucopolysaccharide.
Any process that modulates the frequency, rate or extent of blood circulation.
Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation.
down regulation of hemolymph circulation
down-regulation of hemolymph circulation
negative regulation of hemolymph circulation
negative regulation of blood circulation
Any process that activates or increases the frequency, rate or extent of blood circulation.
positive regulation of hemolymph circulation
positive regulation of blood circulation
Any process that modulates the frequency, rate or extent of secretion by cell.
Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell.
negative regulation of cellular secretion
negative regulation of secretion by cell
Any process that activates or increases the frequency, rate or extent of secretion by cell.
positive regulation of cellular secretion
positive regulation of secretion by cell
Any meiotic cell cycle process that is involved in oocyte maturation.
meiotic cell cycle process involved in oocyte maturation
Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.
regulation of meiosis involved in oocyte maturation
regulation of meiotic cell cycle process involved in oocyte maturation
Any process that modulates the frequency, rate or extent of exosomal secretion.
regulation of exosomal secretory pathway
regulation of extracellular vesicular exosome secretion
regulation of exosomal protein secretion
Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion.
down regulation of exosomal secretory pathway
down regulation of extracellular vesicular exosome secretion
down-regulation of exosomal secretory pathway
down-regulation of extracellular vesicular exosome secretion
downregulation of exosomal secretory pathway
downregulation of extracellular vesicular exosome secretion
negative regulation of exosomal secretory pathway
negative regulation of extracellular vesicular exosome secretion
negative regulation of secretion of exosome
down regulation of exosomal protein secretion
down-regulation of exosomal protein secretion
downregulation of exosomal protein secretion
inhibition of exosomal protein secretion
inhibition of exosomal secretory pathway
inhibition of extracellular vesicular exosome secretion
negative regulation of exosomal protein secretion
negative regulation of exosomal secretion
Any process that activates or increases the frequency, rate or extent of exosomal secretion.
positive regulation of exosomal secretory pathway
positive regulation of extracellular vesicular exosome secretion
positive regulation of secretion of exosome
up regulation of exosomal secretory pathway
up regulation of extracellular vesicular exosome secretion
up-regulation of exosomal secretory pathway
up-regulation of extracellular vesicular exosome secretion
upregulation of exosomal secretory pathway
upregulation of extracellular vesicular exosome secretion
activation of exosomal protein secretion
activation of exosomal secretory pathway
activation of extracellular vesicular exosome secretion
positive regulation of exosomal protein secretion
up regulation of exosomal protein secretion
up-regulation of exosomal protein secretion
upregulation of exosomal protein secretion
positive regulation of exosomal secretion
Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.
regulation of extracellular vesicular exosome assembly
regulation of extracellular exosome assembly
Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly.
down regulation of extracellular vesicular exosome assembly
down-regulation of extracellular vesicular exosome assembly
downregulation of extracellular vesicular exosome assembly
negative regulation of extracellular vesicular exosome assembly
inhibition of extracellular vesicular exosome assembly
negative regulation of extracellular exosome assembly
Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.
up regulation of extracellular vesicular exosome assembly
up-regulation of extracellular vesicular exosome assembly
upregulation of extracellular vesicular exosome assembly
activation of extracellular vesicular exosome assembly
positive regulation of extracellular vesicular exosome assembly
positive regulation of extracellular exosome assembly
Any vesicle that is part of the extracellular region.
Any process that modulates the frequency, rate or extent of protein localization to cilium.
regulation of protein localization to cilium
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium.
down regulation of protein localization to cilium
down-regulation of protein localization to cilium
downregulation of protein localization to cilium
inhibition of protein localization to cilium
negative regulation of protein localization to cilium
Any process that activates or increases the frequency, rate or extent of protein localization to cilium.
up regulation of protein localization to cilium
up-regulation of protein localization to cilium
upregulation of protein localization to cilium
activation of protein localization to cilium
positive regulation of protein localization to cilium
Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane.
regulation of protein localisation in ciliary membrane
regulation of protein localisation to ciliary membrane
regulation of protein localization in ciliary membrane
regulation of protein localization to ciliary membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane.
down regulation of protein localisation in ciliary membrane
down regulation of protein localisation to ciliary membrane
down regulation of protein localization in ciliary membrane
down regulation of protein localization to ciliary membrane
down-regulation of protein localisation in ciliary membrane
down-regulation of protein localisation to ciliary membrane
down-regulation of protein localization in ciliary membrane
down-regulation of protein localization to ciliary membrane
downregulation of protein localisation in ciliary membrane
downregulation of protein localisation to ciliary membrane
downregulation of protein localization in ciliary membrane
downregulation of protein localization to ciliary membrane
negative regulation of protein localisation in ciliary membrane
negative regulation of protein localisation to ciliary membrane
negative regulation of protein localization in ciliary membrane
inhibition of protein localisation in ciliary membrane
inhibition of protein localisation to ciliary membrane
inhibition of protein localization in ciliary membrane
inhibition of protein localization to ciliary membrane
negative regulation of protein localization to ciliary membrane
Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane.
positive regulation of protein localisation in ciliary membrane
positive regulation of protein localisation to ciliary membrane
positive regulation of protein localization in ciliary membrane
up regulation of protein localisation in ciliary membrane
up regulation of protein localisation to ciliary membrane
up regulation of protein localization in ciliary membrane
up regulation of protein localization to ciliary membrane
up-regulation of protein localisation in ciliary membrane
up-regulation of protein localisation to ciliary membrane
up-regulation of protein localization in ciliary membrane
up-regulation of protein localization to ciliary membrane
upregulation of protein localisation in ciliary membrane
upregulation of protein localisation to ciliary membrane
upregulation of protein localization in ciliary membrane
upregulation of protein localization to ciliary membrane
activation of protein localisation in ciliary membrane
activation of protein localisation to ciliary membrane
activation of protein localization in ciliary membrane
activation of protein localization to ciliary membrane
positive regulation of protein localization to ciliary membrane
Any process that modulates the frequency, rate or extent of DNA catabolic process.
Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process.
down regulation of DNA catabolic process
down-regulation of DNA catabolic process
negative regulation of DNA catabolic process
Any process that activates or increases the frequency, rate or extent of DNA catabolic process.
positive regulation of DNA catabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly.
down regulation of microvillus biogenesis
down-regulation of microvillus biogenesis
downregulation of microvillus biogenesis
negative regulation of microvillus biogenesis
negative regulation of microvillus assembly
Any process that activates or increases the frequency, rate or extent of microvillus assembly.
positive regulation of microvillus biogenesis
positive regulation of microvillus assembly
The process whose specific outcome is the progression of a caecum over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure.
substantia propria of cornea development
The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of hemopoiesis.
An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype.
Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis.
down regulation of blood cell biosynthesis
down-regulation of blood cell biosynthesis
downregulation of blood cell biosynthesis
negative regulation of blood cell biosynthesis
negative regulation of blood cell formation
Any process that activates or increases the frequency, rate or extent of hemopoiesis.
positive regulation of blood cell biosynthesis
positive regulation of blood cell formation
up regulation of blood cell biosynthesis
up-regulation of blood cell biosynthesis
Any process that modulates the frequency, rate or extent of plasma membrane organization.
regulation of plasma membrane organisation
regulation of plasma membrane organization and biogenesis
regulation of plasma membrane organization
A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane.
protein localisation in vacuolar membrane
protein localisation to vacuolar membrane
protein localization in vacuolar membrane
protein localization to vacuolar membrane
Any process that modulates the frequency, rate or extent of cardiac conduction.
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction.
negative regulation of cardiac conduction
Any process that activates or increases the frequency, rate or extent of cardiac conduction.
positive regulation of cardiac conduction
Any process that modulates the frequency, rate or extent of amino acid transmembrane transport.
regulation of amino acid membrane transport
regulation of amino acid transmembrane transport
Any process that modulates the frequency, rate or extent of inorganic anion transmembrane transport.
regulation of inorganic anion membrane transport
regulation of transmembrane inorganic anion transport
regulation of inorganic anion transmembrane transport
Any process that stops, prevents or reduces the frequency, rate or extent of inorganic anion transmembrane transport.
down regulation of inorganic anion membrane transport
down regulation of inorganic anion transmembrane transport
down regulation of transmembrane inorganic anion transport
down-regulation of inorganic anion membrane transport
down-regulation of inorganic anion transmembrane transport
down-regulation of transmembrane inorganic anion transport
downregulation of inorganic anion membrane transport
downregulation of inorganic anion transmembrane transport
downregulation of transmembrane inorganic anion transport
negative regulation of inorganic anion membrane transport
negative regulation of transmembrane inorganic anion transport
inhibition of inorganic anion membrane transport
inhibition of inorganic anion transmembrane transport
inhibition of transmembrane inorganic anion transport
negative regulation of inorganic anion transmembrane transport
Any process that activates or increases the frequency, rate or extent of inorganic anion transmembrane transport.
positive regulation of inorganic anion membrane transport
positive regulation of transmembrane inorganic anion transport
up regulation of inorganic anion membrane transport
up regulation of inorganic anion transmembrane transport
up regulation of transmembrane inorganic anion transport
up-regulation of inorganic anion membrane transport
up-regulation of inorganic anion transmembrane transport
up-regulation of transmembrane inorganic anion transport
upregulation of inorganic anion membrane transport
upregulation of inorganic anion transmembrane transport
upregulation of transmembrane inorganic anion transport
activation of inorganic anion membrane transport
activation of inorganic anion transmembrane transport
activation of transmembrane inorganic anion transport
positive regulation of inorganic anion transmembrane transport
The process in which an organic acid is transported across a membrane.
Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization.
down regulation of cellular protein localisation
down regulation of cellular protein localization
down-regulation of cellular protein localisation
down-regulation of cellular protein localization
downregulation of cellular protein localisation
downregulation of cellular protein localization
negative regulation of cellular protein localisation
negative regulation of cellular protein localization
inhibition of cellular protein localisation
inhibition of cellular protein localization
negative regulation of protein localization
Any process that activates or increases the frequency, rate or extent of a protein localization.
positive regulation of cellular protein localisation
positive regulation of cellular protein localization
up regulation of cellular protein localisation
up regulation of cellular protein localization
up-regulation of cellular protein localisation
up-regulation of cellular protein localization
upregulation of cellular protein localisation
upregulation of cellular protein localization
positive regulation of protein localization
Any process that modulates the frequency, rate or extent of aorta morphogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis.
negative regulation of aorta morphogenesis
Any process that activates or increases the frequency, rate or extent of aorta morphogenesis.
positive regulation of aorta morphogenesis
The process whose specific outcome is the progression of an extraembryonic membrane over time, from its formation to the mature structure.
Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange.
down regulation of respiratory gaseous exchange
down-regulation of respiratory gaseous exchange
downregulation of respiratory gaseous exchange
inhibition of respiratory gaseous exchange
negative regulation of respiratory gaseous exchange
Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange.
up regulation of respiratory gaseous exchange
up-regulation of respiratory gaseous exchange
upregulation of respiratory gaseous exchange
activation of respiratory gaseous exchange
positive regulation of respiratory gaseous exchange
Any process that modulates the frequency, rate or extent of hepatocyte apoptotic process.
regulation of hepatocyte apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte apoptotic process.
down regulation of hepatocyte apoptotic process
down-regulation of hepatocyte apoptotic process
downregulation of hepatocyte apoptotic process
inhibition of hepatocyte apoptotic process
negative regulation of hepatocyte apoptosis
negative regulation of hepatocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of hepatocyte apoptotic process.
up regulation of hepatocyte apoptotic process
up-regulation of hepatocyte apoptotic process
upregulation of hepatocyte apoptotic process
activation of hepatocyte apoptotic process
positive regulation of hepatocyte apoptosis
positive regulation of hepatocyte apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential.
down regulation of AV node cardiac muscle cell action potential
down regulation of AV node cell action potential
down regulation of atrioventricular node cardiac muscle cell action potential
down-regulation of AV node cardiac muscle cell action potential
down-regulation of AV node cell action potential
down-regulation of atrioventricular node cardiac muscle cell action potential
downregulation of AV node cardiac muscle cell action potential
downregulation of AV node cell action potential
downregulation of atrioventricular node cardiac muscle cell action potential
negative regulation of AV node cardiac muscle cell action potential
negative regulation of atrioventricular node cardiac muscle cell action potential
inhibition of AV node cardiac muscle cell action potential
inhibition of AV node cell action potential
inhibition of atrioventricular node cardiac muscle cell action potential
negative regulation of AV node cell action potential
Any process that activates or increases the frequency, rate or extent of AV node cell action potential.
positive regulation of AV node cardiac muscle cell action potential
positive regulation of atrioventricular node cardiac muscle cell action potential
up regulation of AV node cardiac muscle cell action potential
up regulation of AV node cell action potential
up regulation of atrioventricular node cardiac muscle cell action potential
up-regulation of AV node cardiac muscle cell action potential
up-regulation of AV node cell action potential
up-regulation of atrioventricular node cardiac muscle cell action potential
upregulation of AV node cardiac muscle cell action potential
upregulation of AV node cell action potential
upregulation of atrioventricular node cardiac muscle cell action potential
activation of AV node cardiac muscle cell action potential
activation of AV node cell action potential
activation of atrioventricular node cardiac muscle cell action potential
positive regulation of AV node cell action potential
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus.
Any process that activates or increases the frequency, rate or extent of vasculature development.
up regulation of vasculature development
up-regulation of vasculature development
activation of vascular system development
positive regulation of vascular system development
up regulation of vascular system development
up-regulation of vascular system development
upregulation of vascular system development
positive regulation of vasculature development
Any apoptotic process in an epithelial cell.
Any process that modulates the frequency, rate or extent of collagen fibril organization.
regulation of collagen fibril organisation
regulation of fibrillar collagen organization
regulation of collagen fibril organization
Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization.
down regulation of collagen fibril organisation
down regulation of collagen fibril organization
down regulation of fibrillar collagen organization
down-regulation of collagen fibril organisation
down-regulation of collagen fibril organization
down-regulation of fibrillar collagen organization
downregulation of collagen fibril organisation
downregulation of collagen fibril organization
downregulation of fibrillar collagen organization
negative regulation of collagen fibril organisation
negative regulation of fibrillar collagen organization
inhibition of collagen fibril organisation
inhibition of collagen fibril organization
inhibition of fibrillar collagen organization
negative regulation of collagen fibril organization
Any process that activates or increases the frequency, rate or extent of collagen fibril organization.
positive regulation of collagen fibril organisation
positive regulation of fibrillar collagen organization
up regulation of collagen fibril organisation
up regulation of collagen fibril organization
up regulation of fibrillar collagen organization
up-regulation of collagen fibril organisation
up-regulation of collagen fibril organization
up-regulation of fibrillar collagen organization
upregulation of collagen fibril organisation
upregulation of collagen fibril organization
upregulation of fibrillar collagen organization
activation of collagen fibril organisation
activation of collagen fibril organization
activation of fibrillar collagen organization
positive regulation of collagen fibril organization
Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process.
regulation of epitheliocyte apoptotic process
regulation of epithelial cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process.
down regulation of epithelial cell apoptotic process
down regulation of epitheliocyte apoptotic process
down-regulation of epithelial cell apoptotic process
down-regulation of epitheliocyte apoptotic process
downregulation of epithelial cell apoptotic process
downregulation of epitheliocyte apoptotic process
negative regulation of epitheliocyte apoptotic process
down regulation of epithelial cell apoptosis
down regulation of epitheliocyte apoptosis
down-regulation of epithelial cell apoptosis
down-regulation of epitheliocyte apoptosis
downregulation of epithelial cell apoptosis
downregulation of epitheliocyte apoptosis
inhibition of epithelial cell apoptotic process
inhibition of epitheliocyte apoptotic process
negative regulation of epithelial cell apoptosis
negative regulation of epitheliocyte apoptosis
negative regulation of epithelial cell apoptotic process
Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process.
positive regulation of epitheliocyte apoptotic process
up regulation of epithelial cell apoptotic process
up regulation of epitheliocyte apoptotic process
up-regulation of epithelial cell apoptotic process
up-regulation of epitheliocyte apoptotic process
upregulation of epithelial cell apoptotic process
upregulation of epitheliocyte apoptotic process
activation of epithelial cell apoptotic process
activation of epitheliocyte apoptotic process
positive regulation of epithelial cell apoptosis
positive regulation of epitheliocyte apoptosis
up regulation of epithelial cell apoptosis
up regulation of epitheliocyte apoptosis
up-regulation of epithelial cell apoptosis
up-regulation of epitheliocyte apoptosis
upregulation of epithelial cell apoptosis
positive regulation of epithelial cell apoptotic process
Any process that modulates the frequency, rate or extent of cholangiocyte proliferation.
regulation of cholangiocyte proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte proliferation.
down regulation of cholangiocyte proliferation
down regulation of hepatoblast proliferation
down-regulation of cholangiocyte proliferation
down-regulation of hepatoblast proliferation
downregulation of cholangiocyte proliferation
downregulation of hepatoblast proliferation
negative regulation of hepatoblast proliferation
inhibition of cholangiocyte proliferation
negative regulation of cholangiocyte proliferation
Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation.
positive regulation of hepatoblast proliferation
up regulation of cholangiocyte proliferation
up regulation of hepatoblast proliferation
up-regulation of cholangiocyte proliferation
up-regulation of hepatoblast proliferation
upregulation of cholangiocyte proliferation
upregulation of hepatoblast proliferation
activation of cholangiocyte proliferation
positive regulation of cholangiocyte proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain.
down regulation of sensory perception of pain
down-regulation of sensory perception of pain
downregulation of sensory perception of pain
down regulation of perception of physiological pain
down-regulation of perception of physiological pain
downregulation of perception of physiological pain
inhibition of perception of physiological pain
inhibition of sensory perception of pain
negative regulation of perception of physiological pain
negative regulation of sensory perception of pain
Any process that activates or increases the frequency, rate or extent of sensory perception of pain.
up regulation of sensory perception of pain
up-regulation of sensory perception of pain
upregulation of sensory perception of pain
activation of perception of physiological pain
activation of sensory perception of pain
positive regulation of perception of physiological pain
up regulation of perception of physiological pain
up-regulation of perception of physiological pain
upregulation of perception of physiological pain
positive regulation of sensory perception of pain
Any process that modulates the frequency, rate or extent of cation transmembrane transport.
regulation of cation transmembrane transport
regulation of monoatomic cation transmembrane transport
Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport.
down regulation of cation transmembrane transport
down-regulation of cation transmembrane transport
downregulation of cation transmembrane transport
inhibition of cation transmembrane transport
negative regulation of cation transmembrane transport
Any process that activates or increases the frequency, rate or extent of cation transmembrane transport.
up regulation of cation transmembrane transport
up-regulation of cation transmembrane transport
upregulation of cation transmembrane transport
activation of cation transmembrane transport
positive regulation of cation transmembrane transport
Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation.
regulation of trophectoderm cell proliferation
regulation of trophectodermal cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of trophectodermal cell proliferation.
down regulation of trophectoderm cell proliferation
down regulation of trophectodermal cell proliferation
down-regulation of trophectoderm cell proliferation
down-regulation of trophectodermal cell proliferation
downregulation of trophectoderm cell proliferation
downregulation of trophectodermal cell proliferation
negative regulation of trophectoderm cell proliferation
inhibition of trophectoderm cell proliferation
inhibition of trophectodermal cell proliferation
negative regulation of trophectodermal cell proliferation
Any process that activates or increases the frequency, rate or extent of trophectodermal cell proliferation.
positive regulation of trophectoderm cell proliferation
up regulation of trophectoderm cell proliferation
up regulation of trophectodermal cell proliferation
up-regulation of trophectoderm cell proliferation
up-regulation of trophectodermal cell proliferation
upregulation of trophectoderm cell proliferation
upregulation of trophectodermal cell proliferation
activation of trophectoderm cell proliferation
activation of trophectodermal cell proliferation
positive regulation of trophectodermal cell proliferation
A process in which a protein is transported to, or maintained in, a location within a microvillus.
Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.
down regulation of meiotic cell cycle process involved in oocyte maturation
down-regulation of meiotic cell cycle process involved in oocyte maturation
downregulation of meiotic cell cycle process involved in oocyte maturation
inhibition of meiotic cell cycle process involved in oocyte maturation
negative regulation of meiotic cell cycle process involved in oocyte maturation
Any process that activates or increases the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.
up regulation of meiotic cell cycle process involved in oocyte maturation
up-regulation of meiotic cell cycle process involved in oocyte maturation
upregulation of meiotic cell cycle process involved in oocyte maturation
activation of meiotic cell cycle process involved in oocyte maturation
positive regulation of meiotic cell cycle process involved in oocyte maturation
Any process that modulates the frequency, rate or extent of bleb assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly.
Any process that activates or increases the frequency, rate or extent of bleb assembly.
Any process that modulates the frequency, rate or extent of adipose tissue development.
regulation of adipose tissue development
Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development.
down regulation of adipose tissue development
down-regulation of adipose tissue development
downregulation of adipose tissue development
inhibition of adipose tissue development
negative regulation of adipose tissue development
Any process that activates or increases the frequency, rate or extent of adipose tissue development.
up regulation of adipose tissue development
up-regulation of adipose tissue development
upregulation of adipose tissue development
activation of adipose tissue development
positive regulation of adipose tissue development
Any process that modulates the frequency, rate or extent of cholangiocyte apoptotic process.
regulation of epithelial cell of bile duct apoptotic process
regulation of epithelial cell of bile duct apoptosis
regulation of cholangiocyte apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte apoptotic process.
down regulation of cholangiocyte apoptotic process
down regulation of epithelial cell of bile duct apoptotic process
down-regulation of cholangiocyte apoptotic process
down-regulation of epithelial cell of bile duct apoptotic process
downregulation of cholangiocyte apoptotic process
downregulation of epithelial cell of bile duct apoptotic process
negative regulation of epithelial cell of bile duct apoptotic process
down regulation of cholangiocyte apoptosis
down regulation of epithelial cell of bile duct apoptosis
down-regulation of cholangiocyte apoptosis
down-regulation of epithelial cell of bile duct apoptosis
downregulation of cholangiocyte apoptosis
downregulation of epithelial cell of bile duct apoptosis
inhibition of cholangiocyte apoptotic process
inhibition of epithelial cell of bile duct apoptosis
inhibition of epithelial cell of bile duct apoptotic process
negative regulation of cholangiocyte apoptosis
negative regulation of epithelial cell of bile duct apoptosis
negative regulation of cholangiocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of cholangiocyte apoptotic process.
positive regulation of epithelial cell of bile duct apoptotic process
up regulation of cholangiocyte apoptotic process
up regulation of epithelial cell of bile duct apoptotic process
up-regulation of cholangiocyte apoptotic process
up-regulation of epithelial cell of bile duct apoptotic process
upregulation of cholangiocyte apoptotic process
upregulation of epithelial cell of bile duct apoptotic process
activation of cholangiocyte apoptotic process
activation of epithelial cell of bile duct apoptosis
activation of epithelial cell of bile duct apoptotic process
positive regulation of cholangiocyte apoptosis
positive regulation of epithelial cell of bile duct apoptosis
up regulation of cholangiocyte apoptosis
up regulation of epithelial cell of bile duct apoptosis
up-regulation of cholangiocyte apoptosis
up-regulation of epithelial cell of bile duct apoptosis
upregulation of epithelial cell of bile duct apoptosis
positive regulation of cholangiocyte apoptotic process
Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy.
regulation of skeletal muscle hypertrophy
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy.
down regulation of skeletal muscle hypertrophy
down-regulation of skeletal muscle hypertrophy
downregulation of skeletal muscle hypertrophy
inhibition of skeletal muscle hypertrophy
negative regulation of skeletal muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy.
up regulation of skeletal muscle hypertrophy
up-regulation of skeletal muscle hypertrophy
upregulation of skeletal muscle hypertrophy
activation of skeletal muscle hypertrophy
positive regulation of skeletal muscle hypertrophy
Any process that modulates the frequency, rate or extent of bile acid metabolic process.
regulation of bile acid metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process.
down regulation of bile acid metabolic process
down-regulation of bile acid metabolic process
downregulation of bile acid metabolic process
negative regulation of bile acid metabolism
inhibition of bile acid metabolic process
negative regulation of bile acid metabolic process
Any process that activates or increases the frequency, rate or extent of bile acid metabolic process.
positive regulation of bile acid metabolism
up regulation of bile acid metabolic process
up-regulation of bile acid metabolic process
upregulation of bile acid metabolic process
activation of bile acid metabolic process
positive regulation of bile acid metabolic process
The cell cortex of the leading edge of a cell.
peripheral cytoplasm of cell leading edge
peripheral cytoplasm of leading edge of cell
Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.
regulation of gastro-intestinal system smooth muscle contraction
Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.
down regulation of gastro-intestinal system smooth muscle contraction
down-regulation of gastro-intestinal system smooth muscle contraction
downregulation of gastro-intestinal system smooth muscle contraction
inhibition of gastro-intestinal system smooth muscle contraction
negative regulation of gastro-intestinal system smooth muscle contraction
Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.
up regulation of gastro-intestinal system smooth muscle contraction
up-regulation of gastro-intestinal system smooth muscle contraction
upregulation of gastro-intestinal system smooth muscle contraction
activation of gastro-intestinal system smooth muscle contraction
positive regulation of gastro-intestinal system smooth muscle contraction
Any process that modulates the frequency, rate or extent of colon smooth muscle contraction.
regulation of colon smooth muscle contraction
Any process that stops, prevents or reduces the frequency, rate or extent of colon smooth muscle contraction.
down regulation of colon smooth muscle contraction
down-regulation of colon smooth muscle contraction
downregulation of colon smooth muscle contraction
inhibition of colon smooth muscle contraction
negative regulation of colon smooth muscle contraction
Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction.
up regulation of colon smooth muscle contraction
up-regulation of colon smooth muscle contraction
upregulation of colon smooth muscle contraction
activation of colon smooth muscle contraction
positive regulation of colon smooth muscle contraction
Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation.
regulation of stomach mucosal blood circulation
regulation of gastric mucosal blood circulation
Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation.
down regulation of gastric mucosal blood circulation
down regulation of stomach mucosal blood circulation
down-regulation of gastric mucosal blood circulation
down-regulation of stomach mucosal blood circulation
downregulation of gastric mucosal blood circulation
downregulation of stomach mucosal blood circulation
negative regulation of stomach mucosal blood circulation
inhibition of gastric mucosal blood circulation
inhibition of stomach mucosal blood circulation
negative regulation of gastric mucosal blood circulation
Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation.
positive regulation of stomach mucosal blood circulation
up regulation of gastric mucosal blood circulation
up regulation of stomach mucosal blood circulation
up-regulation of gastric mucosal blood circulation
up-regulation of stomach mucosal blood circulation
upregulation of gastric mucosal blood circulation
upregulation of stomach mucosal blood circulation
activation of gastric mucosal blood circulation
activation of stomach mucosal blood circulation
positive regulation of gastric mucosal blood circulation
Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction.
regulation of small intestine smooth muscle contraction
Any process that stops, prevents or reduces the frequency, rate or extent of small intestine smooth muscle contraction.
down regulation of small intestine smooth muscle contraction
down-regulation of small intestine smooth muscle contraction
downregulation of small intestine smooth muscle contraction
inhibition of small intestine smooth muscle contraction
negative regulation of small intestine smooth muscle contraction
Any process that activates or increases the frequency, rate or extent of small intestine smooth muscle contraction.
up regulation of small intestine smooth muscle contraction
up-regulation of small intestine smooth muscle contraction
upregulation of small intestine smooth muscle contraction
activation of small intestine smooth muscle contraction
positive regulation of small intestine smooth muscle contraction
Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole.
regulation of vacuolar protein breakdown
regulation of vacuolar protein catabolic process
regulation of vacuolar protein catabolism
regulation of vacuolar protein degradation
regulation of protein catabolic process in the vacuole
Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole.
down regulation of protein catabolic process in the vacuole
down-regulation of protein catabolic process in the vacuole
downregulation of protein catabolic process in the vacuole
inhibition of protein catabolic process in the vacuole
down regulation of vacuolar protein breakdown
down regulation of vacuolar protein catabolic process
down regulation of vacuolar protein catabolism
down regulation of vacuolar protein degradation
down-regulation of vacuolar protein breakdown
down-regulation of vacuolar protein catabolic process
down-regulation of vacuolar protein catabolism
down-regulation of vacuolar protein degradation
downregulation of vacuolar protein breakdown
downregulation of vacuolar protein catabolic process
downregulation of vacuolar protein catabolism
downregulation of vacuolar protein degradation
inhibition of vacuolar protein breakdown
inhibition of vacuolar protein catabolic process
inhibition of vacuolar protein catabolism
inhibition of vacuolar protein degradation
negative regulation of vacuolar protein breakdown
negative regulation of vacuolar protein catabolic process
negative regulation of vacuolar protein catabolism
negative regulation of vacuolar protein degradation
negative regulation of protein catabolic process in the vacuole
Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole.
up regulation of protein catabolic process in the vacuole
up-regulation of protein catabolic process in the vacuole
upregulation of protein catabolic process in the vacuole
activation of protein catabolic process in the vacuole
activation of vacuolar protein breakdown
activation of vacuolar protein catabolic process
activation of vacuolar protein catabolism
activation of vacuolar protein degradation
positive regulation of vacuolar protein breakdown
positive regulation of vacuolar protein catabolic process
positive regulation of vacuolar protein catabolism
positive regulation of vacuolar protein degradation
up regulation of vacuolar protein breakdown
up regulation of vacuolar protein catabolic process
up regulation of vacuolar protein catabolism
up regulation of vacuolar protein degradation
up-regulation of vacuolar protein breakdown
up-regulation of vacuolar protein catabolic process
up-regulation of vacuolar protein catabolism
up-regulation of vacuolar protein degradation
upregulation of vacuolar protein breakdown
upregulation of vacuolar protein catabolic process
upregulation of vacuolar protein catabolism
upregulation of vacuolar protein degradation
positive regulation of protein catabolic process in the vacuole
Any process that modulates the frequency, rate or extent of protein localization to cell periphery.
regulation of protein localization to cell periphery
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery.
down regulation of protein localization to cell periphery
down-regulation of protein localization to cell periphery
downregulation of protein localization to cell periphery
inhibition of protein localization to cell periphery
negative regulation of protein localization to cell periphery
Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery.
up regulation of protein localization to cell periphery
up-regulation of protein localization to cell periphery
upregulation of protein localization to cell periphery
activation of protein localization to cell periphery
positive regulation of protein localization to cell periphery
Any process that modulates the frequency, rate or extent of neuromuscular junction development.
regulation of neuromuscular junction organization
regulation of neuromuscular junction stability
regulation of neuromuscular junction development
Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development.
down regulation of neuromuscular junction development
down regulation of neuromuscular junction organization
down-regulation of neuromuscular junction development
down-regulation of neuromuscular junction organization
downregulation of neuromuscular junction development
downregulation of neuromuscular junction organization
negative regulation of neuromuscular junction organization
inhibition of neuromuscular junction development
inhibition of neuromuscular junction organization
down regulation of neuromuscular junction stability
down-regulation of neuromuscular junction stability
downregulation of neuromuscular junction stability
inhibition of neuromuscular junction stability
negative regulation of neuromuscular junction stability
negative regulation of neuromuscular junction development
Any process that activates or increases the frequency, rate or extent of neuromuscular junction development.
positive regulation of neuromuscular junction organization
up regulation of neuromuscular junction development
up regulation of neuromuscular junction organization
up-regulation of neuromuscular junction development
up-regulation of neuromuscular junction organization
upregulation of neuromuscular junction development
upregulation of neuromuscular junction organization
activation of neuromuscular junction development
activation of neuromuscular junction organization
activation of neuromuscular junction stability
positive regulation of neuromuscular junction stability
up regulation of neuromuscular junction stability
up-regulation of neuromuscular junction stability
upregulation of neuromuscular junction stability
positive regulation of neuromuscular junction development
Any process that modulates the frequency, rate or extent of secretory granule organization.
regulation of secretory granule organisation
regulation of secretory granule organization and biogenesis
regulation of secretory granule organization
Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization.
down regulation of secretory granule organisation
down regulation of secretory granule organization
down-regulation of secretory granule organisation
down-regulation of secretory granule organization
downregulation of secretory granule organisation
downregulation of secretory granule organization
negative regulation of secretory granule organisation
inhibition of secretory granule organisation
inhibition of secretory granule organization
down regulation of secretory granule organization and biogenesis
down-regulation of secretory granule organization and biogenesis
downregulation of secretory granule organization and biogenesis
inhibition of secretory granule organization and biogenesis
negative regulation of secretory granule organization and biogenesis
negative regulation of secretory granule organization
Any process that activates or increases the frequency, rate or extent of secretory granule organization.
positive regulation of secretory granule organisation
up regulation of secretory granule organisation
up regulation of secretory granule organization
up-regulation of secretory granule organisation
up-regulation of secretory granule organization
upregulation of secretory granule organisation
upregulation of secretory granule organization
activation of secretory granule organisation
activation of secretory granule organization
activation of secretory granule organization and biogenesis
positive regulation of secretory granule organization and biogenesis
up regulation of secretory granule organization and biogenesis
up-regulation of secretory granule organization and biogenesis
upregulation of secretory granule organization and biogenesis
positive regulation of secretory granule organization
Any process that modulates the frequency, rate or extent of cardiac ventricle development.
regulation of cardiac ventricle development
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development.
down regulation of cardiac ventricle development
down-regulation of cardiac ventricle development
downregulation of cardiac ventricle development
inhibition of cardiac ventricle development
negative regulation of cardiac ventricle development
Any process that activates or increases the frequency, rate or extent of cardiac ventricle development.
up regulation of cardiac ventricle development
up-regulation of cardiac ventricle development
upregulation of cardiac ventricle development
activation of cardiac ventricle development
positive regulation of cardiac ventricle development
Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential.
down regulation of neuronal action potential
down-regulation of neuronal action potential
downregulation of neuronal action potential
down regulation of generation of action potential
down-regulation of generation of action potential
downregulation of generation of action potential
inhibition of generation of action potential
negative regulation of generation of action potential
negative regulation of neuronal action potential
Any process that activates or increases the frequency, rate or extent of neuronal action potential.
up regulation of neuronal action potential
up-regulation of neuronal action potential
upregulation of neuronal action potential
activation of generation of action potential
positive regulation of generation of action potential
up regulation of generation of action potential
up-regulation of generation of action potential
upregulation of generation of action potential
positive regulation of neuronal action potential
The process whose specific outcome is the progression of a cloacal gland over time, from its formation to the mature structure.
A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone.
protein localisation in ciliary transition zone
protein localisation to ciliary transition zone
protein localization in ciliary transition zone
protein localization to ciliary transition zone
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus.
Any process that modulates the frequency, rate or extent of fat cell apoptotic process.
regulation of adipocyte apoptotic process
regulation of adipose cell apoptotic process
regulation of fat cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process.
down regulation of adipocyte apoptotic process
down regulation of adipose cell apoptotic process
down regulation of fat cell apoptotic process
down-regulation of adipocyte apoptotic process
down-regulation of adipose cell apoptotic process
down-regulation of fat cell apoptotic process
downregulation of adipocyte apoptotic process
downregulation of adipose cell apoptotic process
downregulation of fat cell apoptotic process
negative regulation of adipocyte apoptotic process
negative regulation of adipose cell apoptotic process
down regulation of adipose cell apoptosis
down-regulation of adipose cell apoptosis
downregulation of adipose cell apoptosis
inhibition of adipocyte apoptotic process
inhibition of adipose cell apoptotic process
inhibition of fat cell apoptotic process
negative regulation of adipocyte apoptosis
negative regulation of adipose cell apoptosis
negative regulation of fat cell apoptosis
negative regulation of fat cell apoptotic process
Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process.
positive regulation of adipocyte apoptotic process
positive regulation of adipose cell apoptotic process
up regulation of adipocyte apoptotic process
up regulation of adipose cell apoptotic process
up regulation of fat cell apoptotic process
up-regulation of adipocyte apoptotic process
up-regulation of adipose cell apoptotic process
up-regulation of fat cell apoptotic process
upregulation of adipocyte apoptotic process
upregulation of adipose cell apoptotic process
upregulation of fat cell apoptotic process
activation of adipocyte apoptotic process
activation of adipose cell apoptotic process
activation of fat cell apoptotic process
positive regulation of adipocyte apoptosis
positive regulation of adipose cell apoptosis
positive regulation of fat cell apoptosis
positive regulation of fat cell apoptotic process
The process in which glucose is transported across a membrane.
Any process that modulates the frequency, rate or extent of somatic stem cell division.
regulation of somatic stem cell division
Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division.
down regulation of somatic stem cell division
down regulation of somatic stem cell renewal
down-regulation of somatic stem cell division
down-regulation of somatic stem cell renewal
downregulation of somatic stem cell division
downregulation of somatic stem cell renewal
negative regulation of somatic stem cell renewal
inhibition of somatic stem cell division
negative regulation of somatic stem cell division
Any process that activates or increases the frequency, rate or extent of somatic stem cell division.
positive regulation of somatic stem cell renewal
up regulation of somatic stem cell division
up regulation of somatic stem cell renewal
up-regulation of somatic stem cell division
up-regulation of somatic stem cell renewal
upregulation of somatic stem cell division
upregulation of somatic stem cell renewal
activation of somatic stem cell division
positive regulation of somatic stem cell division
Enables the transfer of a peptide from one side of a membrane to the other.
peptide transmembrane transporter activity
Glutathione is taken up by the bacterium
Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation.
down regulation of pancreatic B cell proliferation
down regulation of pancreatic beta cell proliferation
down regulation of type B pancreatic cell proliferation
down-regulation of pancreatic B cell proliferation
down-regulation of pancreatic beta cell proliferation
down-regulation of type B pancreatic cell proliferation
downregulation of pancreatic B cell proliferation
downregulation of pancreatic beta cell proliferation
downregulation of type B pancreatic cell proliferation
negative regulation of pancreatic B cell proliferation
negative regulation of pancreatic beta cell proliferation
inhibition of pancreatic B cell proliferation
inhibition of pancreatic beta cell proliferation
inhibition of type B pancreatic cell proliferation
negative regulation of type B pancreatic cell proliferation
Any process that activates or increases the frequency, rate or extent of type B pancreatic cell proliferation.
positive regulation of pancreatic B cell proliferation
positive regulation of pancreatic beta cell proliferation
up regulation of pancreatic B cell proliferation
up regulation of pancreatic beta cell proliferation
up regulation of type B pancreatic cell proliferation
up-regulation of pancreatic B cell proliferation
up-regulation of pancreatic beta cell proliferation
up-regulation of type B pancreatic cell proliferation
upregulation of pancreatic B cell proliferation
upregulation of pancreatic beta cell proliferation
upregulation of type B pancreatic cell proliferation
activation of pancreatic B cell proliferation
activation of pancreatic beta cell proliferation
activation of type B pancreatic cell proliferation
positive regulation of type B pancreatic cell proliferation
The developmental process by which a midbrain is generated and organized.
Any process that modulates the frequency, rate or extent of acinar cell proliferation.
regulation of acinous cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of acinar cell proliferation.
down regulation of acinar cell proliferation
down regulation of acinic cell proliferation
down regulation of acinous cell proliferation
down-regulation of acinar cell proliferation
down-regulation of acinic cell proliferation
down-regulation of acinous cell proliferation
downregulation of acinar cell proliferation
downregulation of acinic cell proliferation
downregulation of acinous cell proliferation
negative regulation of acinic cell proliferation
negative regulation of acinous cell proliferation
inhibition of acinous cell proliferation
negative regulation of acinar cell proliferation
Any process that activates or increases the frequency, rate or extent of acinar cell proliferation.
positive regulation of acinic cell proliferation
positive regulation of acinous cell proliferation
up regulation of acinar cell proliferation
up regulation of acinic cell proliferation
up regulation of acinous cell proliferation
up-regulation of acinar cell proliferation
up-regulation of acinic cell proliferation
up-regulation of acinous cell proliferation
upregulation of acinar cell proliferation
upregulation of acinic cell proliferation
upregulation of acinous cell proliferation
activation of acinous cell proliferation
positive regulation of acinar cell proliferation
Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation.
regulation of vascular smooth muscle cell proliferation
regulation of vascular associated smooth muscle cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation.
down regulation of vascular smooth muscle cell proliferation
down-regulation of vascular smooth muscle cell proliferation
downregulation of vascular smooth muscle cell proliferation
negative regulation of VSMC proliferation
negative regulation of vascular smooth muscle cell proliferation
inhibition of vascular smooth muscle cell proliferation
negative regulation of vascular associated smooth muscle cell proliferation
Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation.
positive regulation of VSMC proliferation
positive regulation of vascular smooth muscle cell proliferation
up regulation of vascular smooth muscle cell proliferation
up-regulation of vascular smooth muscle cell proliferation
upregulation of vascular smooth muscle cell proliferation
activation of vascular smooth muscle cell proliferation
positive regulation of vascular associated smooth muscle cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.
down regulation of apoptotic cell death involved in anatomical structure development
down regulation of apoptotic cell death involved in development of an anatomical structure
down regulation of apoptotic process involved in anatomical structure development
down regulation of apoptotic process involved in development
down regulation of apoptotic process involved in development of an anatomical structure
down regulation of apoptotic programmed cell death involved in anatomical structure development
down regulation of apoptotic programmed cell death involved in development of an anatomical structure
down regulation of programmed cell death by apoptosis involved in anatomical structure development
down regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down-regulation of apoptotic cell death involved in anatomical structure development
down-regulation of apoptotic cell death involved in development of an anatomical structure
down-regulation of apoptotic process involved in anatomical structure development
down-regulation of apoptotic process involved in development
down-regulation of apoptotic process involved in development of an anatomical structure
down-regulation of apoptotic programmed cell death involved in anatomical structure development
down-regulation of apoptotic programmed cell death involved in development of an anatomical structure
down-regulation of programmed cell death by apoptosis involved in anatomical structure development
down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
downregulation of apoptotic cell death involved in anatomical structure development
downregulation of apoptotic cell death involved in development of an anatomical structure
downregulation of apoptotic process involved in anatomical structure development
downregulation of apoptotic process involved in development
downregulation of apoptotic process involved in development of an anatomical structure
downregulation of apoptotic programmed cell death involved in anatomical structure development
downregulation of apoptotic programmed cell death involved in development of an anatomical structure
downregulation of programmed cell death by apoptosis involved in anatomical structure development
downregulation of programmed cell death by apoptosis involved in development of an anatomical structure
negative regulation of apoptotic cell death involved in anatomical structure development
negative regulation of apoptotic cell death involved in development of an anatomical structure
negative regulation of apoptotic process involved in anatomical structure development
negative regulation of apoptotic process involved in development of an anatomical structure
negative regulation of apoptotic programmed cell death involved in anatomical structure development
negative regulation of apoptotic programmed cell death involved in development of an anatomical structure
negative regulation of programmed cell death by apoptosis involved in anatomical structure development
negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down regulation of activation of apoptosis involved in anatomical structure development
down regulation of activation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis involved in anatomical structure development
down regulation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis signaling involved in anatomical structure development
down regulation of apoptosis signaling involved in development of an anatomical structure
down regulation of apoptotic program involved in anatomical structure development
down regulation of apoptotic program involved in development of an anatomical structure
down regulation of type I programmed cell death involved in anatomical structure development
down regulation of type I programmed cell death involved in development of an anatomical structure
down-regulation of activation of apoptosis involved in anatomical structure development
down-regulation of activation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis involved in anatomical structure development
down-regulation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis signaling involved in anatomical structure development
down-regulation of apoptosis signaling involved in development of an anatomical structure
down-regulation of apoptotic program involved in anatomical structure development
down-regulation of apoptotic program involved in development of an anatomical structure
down-regulation of type I programmed cell death involved in anatomical structure development
down-regulation of type I programmed cell death involved in development of an anatomical structure
downregulation of activation of apoptosis involved in anatomical structure development
downregulation of activation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis involved in anatomical structure development
downregulation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis signaling involved in anatomical structure development
downregulation of apoptosis signaling involved in development of an anatomical structure
downregulation of apoptotic program involved in anatomical structure development
downregulation of apoptotic program involved in development of an anatomical structure
downregulation of type I programmed cell death involved in anatomical structure development
downregulation of type I programmed cell death involved in development of an anatomical structure
inhibition of activation of apoptosis involved in anatomical structure development
inhibition of activation of apoptosis involved in development of an anatomical structure
inhibition of apoptosis involved in anatomical structure development
inhibition of apoptosis involved in development of an anatomical structure
inhibition of apoptosis signaling involved in anatomical structure development
inhibition of apoptosis signaling involved in development of an anatomical structure
inhibition of apoptotic cell death involved in anatomical structure development
inhibition of apoptotic cell death involved in development of an anatomical structure
inhibition of apoptotic process involved in anatomical structure development
inhibition of apoptotic process involved in development
inhibition of apoptotic process involved in development of an anatomical structure
inhibition of apoptotic program involved in anatomical structure development
inhibition of apoptotic program involved in development of an anatomical structure
inhibition of apoptotic programmed cell death involved in anatomical structure development
inhibition of apoptotic programmed cell death involved in development of an anatomical structure
inhibition of programmed cell death by apoptosis involved in anatomical structure development
inhibition of programmed cell death by apoptosis involved in development of an anatomical structure
inhibition of type I programmed cell death involved in anatomical structure development
inhibition of type I programmed cell death involved in development of an anatomical structure
negative regulation of activation of apoptosis involved in anatomical structure development
negative regulation of activation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis involved in anatomical structure development
negative regulation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis signaling involved in anatomical structure development
negative regulation of apoptosis signaling involved in development of an anatomical structure
negative regulation of apoptotic program involved in anatomical structure development
negative regulation of apoptotic program involved in development of an anatomical structure
negative regulation of type I programmed cell death involved in anatomical structure development
negative regulation of type I programmed cell death involved in development of an anatomical structure
down regulation of apoptosis activator activity involved in anatomical structure development
down regulation of apoptosis activator activity involved in development of an anatomical structure
down regulation of commitment to apoptosis involved in anatomical structure development
down regulation of commitment to apoptosis involved in development of an anatomical structure
down regulation of induction of apoptosis by p53 involved in anatomical structure development
down regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down regulation of induction of apoptosis involved in anatomical structure development
down regulation of induction of apoptosis involved in development of an anatomical structure
down regulation of signaling (initiator) caspase activity involved in anatomical structure development
down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
down-regulation of apoptosis activator activity involved in anatomical structure development
down-regulation of apoptosis activator activity involved in development of an anatomical structure
down-regulation of commitment to apoptosis involved in anatomical structure development
down-regulation of commitment to apoptosis involved in development of an anatomical structure
down-regulation of induction of apoptosis by p53 involved in anatomical structure development
down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down-regulation of induction of apoptosis involved in anatomical structure development
down-regulation of induction of apoptosis involved in development of an anatomical structure
down-regulation of signaling (initiator) caspase activity involved in anatomical structure development
down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
downregulation of apoptosis activator activity involved in anatomical structure development
downregulation of apoptosis activator activity involved in development of an anatomical structure
downregulation of commitment to apoptosis involved in anatomical structure development
downregulation of commitment to apoptosis involved in development of an anatomical structure
downregulation of induction of apoptosis by p53 involved in anatomical structure development
downregulation of induction of apoptosis by p53 involved in development of an anatomical structure
downregulation of induction of apoptosis involved in anatomical structure development
downregulation of induction of apoptosis involved in development of an anatomical structure
downregulation of signaling (initiator) caspase activity involved in anatomical structure development
downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
inhibition of apoptosis activator activity involved in anatomical structure development
inhibition of apoptosis activator activity involved in development of an anatomical structure
inhibition of commitment to apoptosis involved in anatomical structure development
inhibition of commitment to apoptosis involved in development of an anatomical structure
inhibition of induction of apoptosis by p53 involved in anatomical structure development
inhibition of induction of apoptosis by p53 involved in development of an anatomical structure
inhibition of induction of apoptosis involved in anatomical structure development
inhibition of induction of apoptosis involved in development of an anatomical structure
inhibition of signaling (initiator) caspase activity involved in anatomical structure development
inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure
negative regulation of apoptosis activator activity involved in anatomical structure development
negative regulation of apoptosis activator activity involved in development of an anatomical structure
negative regulation of commitment to apoptosis involved in anatomical structure development
negative regulation of commitment to apoptosis involved in development of an anatomical structure
negative regulation of induction of apoptosis by p53 involved in anatomical structure development
negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure
negative regulation of induction of apoptosis involved in anatomical structure development
negative regulation of induction of apoptosis involved in development of an anatomical structure
negative regulation of signaling (initiator) caspase activity involved in anatomical structure development
negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
U4PR86 in PMID:22801495 inferred from mutant phenotype
negative regulation of apoptotic process involved in development
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development.
positive regulation of apoptotic cell death involved in anatomical structure development
positive regulation of apoptotic cell death involved in development of an anatomical structure
positive regulation of apoptotic process involved in anatomical structure development
positive regulation of apoptotic process involved in development of an anatomical structure
positive regulation of apoptotic programmed cell death involved in anatomical structure development
positive regulation of apoptotic programmed cell death involved in development of an anatomical structure
positive regulation of programmed cell death by apoptosis involved in anatomical structure development
positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up regulation of apoptotic cell death involved in anatomical structure development
up regulation of apoptotic cell death involved in development of an anatomical structure
up regulation of apoptotic process involved in anatomical structure development
up regulation of apoptotic process involved in development
up regulation of apoptotic process involved in development of an anatomical structure
up regulation of apoptotic programmed cell death involved in anatomical structure development
up regulation of apoptotic programmed cell death involved in development of an anatomical structure
up regulation of programmed cell death by apoptosis involved in anatomical structure development
up regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up-regulation of apoptotic cell death involved in anatomical structure development
up-regulation of apoptotic cell death involved in development of an anatomical structure
up-regulation of apoptotic process involved in anatomical structure development
up-regulation of apoptotic process involved in development
up-regulation of apoptotic process involved in development of an anatomical structure
up-regulation of apoptotic programmed cell death involved in anatomical structure development
up-regulation of apoptotic programmed cell death involved in development of an anatomical structure
up-regulation of programmed cell death by apoptosis involved in anatomical structure development
up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
upregulation of apoptotic cell death involved in anatomical structure development
upregulation of apoptotic cell death involved in development of an anatomical structure
upregulation of apoptotic process involved in anatomical structure development
upregulation of apoptotic process involved in development
upregulation of apoptotic process involved in development of an anatomical structure
upregulation of apoptotic programmed cell death involved in anatomical structure development
upregulation of apoptotic programmed cell death involved in development of an anatomical structure
upregulation of programmed cell death by apoptosis involved in anatomical structure development
upregulation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of activation of apoptosis involved in anatomical structure development
activation of activation of apoptosis involved in development of an anatomical structure
activation of apoptosis signaling involved in anatomical structure development
activation of apoptosis signaling involved in development of an anatomical structure
activation of apoptotic cell death involved in anatomical structure development
activation of apoptotic cell death involved in development of an anatomical structure
activation of apoptotic process involved in anatomical structure development
activation of apoptotic process involved in development
activation of apoptotic process involved in development of an anatomical structure
activation of apoptotic program involved in anatomical structure development
activation of apoptotic program involved in development of an anatomical structure
activation of apoptotic programmed cell death involved in anatomical structure development
activation of apoptotic programmed cell death involved in development of an anatomical structure
activation of programmed cell death by apoptosis involved in anatomical structure development
activation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of type I programmed cell death involved in anatomical structure development
activation of type I programmed cell death involved in development of an anatomical structure
positive regulation of activation of apoptosis involved in anatomical structure development
positive regulation of activation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis involved in anatomical structure development
positive regulation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis signaling involved in anatomical structure development
positive regulation of apoptosis signaling involved in development of an anatomical structure
positive regulation of apoptotic program involved in anatomical structure development
positive regulation of apoptotic program involved in development of an anatomical structure
positive regulation of type I programmed cell death involved in anatomical structure development
positive regulation of type I programmed cell death involved in development of an anatomical structure
up regulation of activation of apoptosis involved in anatomical structure development
up regulation of activation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis involved in anatomical structure development
up regulation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis signaling involved in anatomical structure development
up regulation of apoptosis signaling involved in development of an anatomical structure
up regulation of apoptotic program involved in anatomical structure development
up regulation of apoptotic program involved in development of an anatomical structure
up regulation of type I programmed cell death involved in anatomical structure development
up regulation of type I programmed cell death involved in development of an anatomical structure
up-regulation of activation of apoptosis involved in anatomical structure development
up-regulation of activation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis involved in anatomical structure development
up-regulation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis signaling involved in anatomical structure development
up-regulation of apoptosis signaling involved in development of an anatomical structure
up-regulation of apoptotic program involved in anatomical structure development
up-regulation of apoptotic program involved in development of an anatomical structure
up-regulation of type I programmed cell death involved in anatomical structure development
up-regulation of type I programmed cell death involved in development of an anatomical structure
upregulation of activation of apoptosis involved in anatomical structure development
upregulation of activation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis involved in anatomical structure development
upregulation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis signaling involved in anatomical structure development
upregulation of apoptosis signaling involved in development of an anatomical structure
upregulation of apoptotic program involved in anatomical structure development
upregulation of apoptotic program involved in development of an anatomical structure
upregulation of type I programmed cell death involved in anatomical structure development
upregulation of type I programmed cell death involved in development of an anatomical structure
activation of apoptosis activator activity involved in anatomical structure development
activation of apoptosis activator activity involved in development of an anatomical structure
activation of commitment to apoptosis involved in anatomical structure development
activation of commitment to apoptosis involved in development of an anatomical structure
activation of induction of apoptosis by p53 involved in anatomical structure development
activation of induction of apoptosis by p53 involved in development of an anatomical structure
activation of induction of apoptosis involved in anatomical structure development
activation of induction of apoptosis involved in development of an anatomical structure
activation of signaling (initiator) caspase activity involved in anatomical structure development
activation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptosis activator activity involved in anatomical structure development
positive regulation of apoptosis activator activity involved in development of an anatomical structure
positive regulation of commitment to apoptosis involved in anatomical structure development
positive regulation of commitment to apoptosis involved in development of an anatomical structure
positive regulation of induction of apoptosis by p53 involved in anatomical structure development
positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure
positive regulation of induction of apoptosis involved in anatomical structure development
positive regulation of induction of apoptosis involved in development of an anatomical structure
positive regulation of signaling (initiator) caspase activity involved in anatomical structure development
positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up regulation of apoptosis activator activity involved in anatomical structure development
up regulation of apoptosis activator activity involved in development of an anatomical structure
up regulation of commitment to apoptosis involved in anatomical structure development
up regulation of commitment to apoptosis involved in development of an anatomical structure
up regulation of induction of apoptosis by p53 involved in anatomical structure development
up regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up regulation of induction of apoptosis involved in anatomical structure development
up regulation of induction of apoptosis involved in development of an anatomical structure
up regulation of signaling (initiator) caspase activity involved in anatomical structure development
up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up-regulation of apoptosis activator activity involved in anatomical structure development
up-regulation of apoptosis activator activity involved in development of an anatomical structure
up-regulation of commitment to apoptosis involved in anatomical structure development
up-regulation of commitment to apoptosis involved in development of an anatomical structure
up-regulation of induction of apoptosis by p53 involved in anatomical structure development
up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up-regulation of induction of apoptosis involved in anatomical structure development
up-regulation of induction of apoptosis involved in development of an anatomical structure
up-regulation of signaling (initiator) caspase activity involved in anatomical structure development
up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
upregulation of apoptosis activator activity involved in anatomical structure development
upregulation of apoptosis activator activity involved in development of an anatomical structure
upregulation of commitment to apoptosis involved in anatomical structure development
upregulation of commitment to apoptosis involved in development of an anatomical structure
upregulation of induction of apoptosis by p53 involved in anatomical structure development
upregulation of induction of apoptosis by p53 involved in development of an anatomical structure
upregulation of induction of apoptosis involved in anatomical structure development
upregulation of induction of apoptosis involved in development of an anatomical structure
upregulation of signaling (initiator) caspase activity involved in anatomical structure development
upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of apoptotic process involved in development.
regulation of apoptotic cell death involved in anatomical structure development
regulation of apoptotic cell death involved in development of an anatomical structure
regulation of apoptotic process involved in anatomical structure development
regulation of apoptotic process involved in development of an anatomical structure
regulation of apoptotic programmed cell death involved in anatomical structure development
regulation of apoptotic programmed cell death involved in development of an anatomical structure
regulation of programmed cell death by apoptosis involved in anatomical structure development
regulation of programmed cell death by apoptosis involved in development of an anatomical structure
regulation of activation of apoptosis involved in anatomical structure development
regulation of activation of apoptosis involved in development of an anatomical structure
regulation of apoptosis involved in anatomical structure development
regulation of apoptosis involved in development of an anatomical structure
regulation of apoptosis signaling involved in anatomical structure development
regulation of apoptosis signaling involved in development of an anatomical structure
regulation of apoptotic program involved in anatomical structure development
regulation of apoptotic program involved in development of an anatomical structure
regulation of type I programmed cell death involved in anatomical structure development
regulation of type I programmed cell death involved in development of an anatomical structure
regulation of apoptosis activator activity involved in anatomical structure development
regulation of apoptosis activator activity involved in development of an anatomical structure
regulation of commitment to apoptosis involved in anatomical structure development
regulation of commitment to apoptosis involved in development of an anatomical structure
regulation of induction of apoptosis by p53 involved in anatomical structure development
regulation of induction of apoptosis by p53 involved in development of an anatomical structure
regulation of induction of apoptosis involved in anatomical structure development
regulation of induction of apoptosis involved in development of an anatomical structure
regulation of signaling (initiator) caspase activity involved in anatomical structure development
regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
Q10943 in PMID:22801495, inferred from mutant phenotype
regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of protein localization to nucleolus.
regulation of protein localisation in nucleolus
regulation of protein localisation to nucleolus
regulation of protein localization in nucleolus
regulation of protein localization to nucleolus
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus.
down regulation of protein localisation in nucleolus
down regulation of protein localisation to nucleolus
down regulation of protein localization in nucleolus
down regulation of protein localization to nucleolus
down-regulation of protein localisation in nucleolus
down-regulation of protein localisation to nucleolus
down-regulation of protein localization in nucleolus
down-regulation of protein localization to nucleolus
downregulation of protein localisation in nucleolus
downregulation of protein localisation to nucleolus
downregulation of protein localization in nucleolus
downregulation of protein localization to nucleolus
negative regulation of protein localisation in nucleolus
negative regulation of protein localisation to nucleolus
negative regulation of protein localization in nucleolus
inhibition of protein localisation in nucleolus
inhibition of protein localisation to nucleolus
inhibition of protein localization in nucleolus
inhibition of protein localization to nucleolus
negative regulation of protein localization to nucleolus
Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus.
positive regulation of protein localisation in nucleolus
positive regulation of protein localisation to nucleolus
positive regulation of protein localization in nucleolus
up regulation of protein localisation in nucleolus
up regulation of protein localisation to nucleolus
up regulation of protein localization in nucleolus
up regulation of protein localization to nucleolus
up-regulation of protein localisation in nucleolus
up-regulation of protein localisation to nucleolus
up-regulation of protein localization in nucleolus
up-regulation of protein localization to nucleolus
upregulation of protein localisation in nucleolus
upregulation of protein localisation to nucleolus
upregulation of protein localization in nucleolus
upregulation of protein localization to nucleolus
activation of protein localisation in nucleolus
activation of protein localisation to nucleolus
activation of protein localization in nucleolus
activation of protein localization to nucleolus
positive regulation of protein localization to nucleolus
The developmental process by which an intramembranous bone is generated and organized.
Any process that modulates the frequency, rate or extent of protein localization to cell cortex.
regulation of protein localisation to cell cortex
An example is cye-1 in C. elegans, UniProt ID O01501 in PMID:17115027.
regulation of protein localization to cell cortex
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex.
down regulation of protein localisation to cell cortex
down regulation of protein localization to cell cortex
down-regulation of protein localisation to cell cortex
down-regulation of protein localization to cell cortex
downregulation of protein localisation to cell cortex
downregulation of protein localization to cell cortex
negative regulation of protein localisation to cell cortex
inhibition of protein localisation to cell cortex
inhibition of protein localization to cell cortex
negative regulation of protein localization to cell cortex
Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex.
positive regulation of protein localisation to cell cortex
up regulation of protein localisation to cell cortex
up regulation of protein localization to cell cortex
up-regulation of protein localisation to cell cortex
up-regulation of protein localization to cell cortex
upregulation of protein localisation to cell cortex
upregulation of protein localization to cell cortex
activation of protein localisation to cell cortex
activation of protein localization to cell cortex
positive regulation of protein localization to cell cortex
The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure.
The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation.
regulation of aortic smooth muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation.
down regulation of aortic smooth muscle cell differentiation
down-regulation of aortic smooth muscle cell differentiation
downregulation of aortic smooth muscle cell differentiation
inhibition of aortic smooth muscle cell differentiation
negative regulation of aortic smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation.
up regulation of aortic smooth muscle cell differentiation
up-regulation of aortic smooth muscle cell differentiation
upregulation of aortic smooth muscle cell differentiation
activation of aortic smooth muscle cell differentiation
positive regulation of aortic smooth muscle cell differentiation
The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
Any process that modulates the frequency, rate or extent of cell proliferation in midbrain.
regulation of cell proliferation in mesencephalon
regulation of mesencepahalic cell proliferation
regulation of cell proliferation in midbrain
Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain.
down regulation of cell proliferation in mesencephalon
down regulation of cell proliferation in midbrain
down-regulation of cell proliferation in mesencephalon
down-regulation of cell proliferation in midbrain
downregulation of cell proliferation in mesencephalon
downregulation of cell proliferation in midbrain
negative regulation of cell proliferation in mesencephalon
inhibition of cell proliferation in mesencephalon
inhibition of cell proliferation in midbrain
down regulation of mesencepahalic cell proliferation
down-regulation of mesencepahalic cell proliferation
downregulation of mesencepahalic cell proliferation
inhibition of mesencepahalic cell proliferation
negative regulation of mesencepahalic cell proliferation
negative regulation of cell proliferation in midbrain
Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain.
positive regulation of cell proliferation in mesencephalon
up regulation of cell proliferation in mesencephalon
up regulation of cell proliferation in midbrain
up-regulation of cell proliferation in mesencephalon
up-regulation of cell proliferation in midbrain
upregulation of cell proliferation in mesencephalon
upregulation of cell proliferation in midbrain
activation of cell proliferation in mesencephalon
activation of cell proliferation in midbrain
activation of mesencepahalic cell proliferation
positive regulation of mesencepahalic cell proliferation
up regulation of mesencepahalic cell proliferation
up-regulation of mesencepahalic cell proliferation
upregulation of mesencepahalic cell proliferation
positive regulation of cell proliferation in midbrain
Any process that modulates the frequency, rate or extent of cardiac ventricle formation.
regulation of cardiac ventricle formation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation.
down regulation of cardiac ventricle formation
down-regulation of cardiac ventricle formation
downregulation of cardiac ventricle formation
inhibition of cardiac ventricle formation
negative regulation of cardiac ventricle formation
Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation.
up regulation of cardiac ventricle formation
up-regulation of cardiac ventricle formation
upregulation of cardiac ventricle formation
activation of cardiac ventricle formation
positive regulation of cardiac ventricle formation
Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization.
down regulation of establishment of protein localisation
down regulation of establishment of protein localization
down-regulation of establishment of protein localisation
down-regulation of establishment of protein localization
downregulation of establishment of protein localisation
downregulation of establishment of protein localization
negative regulation of establishment of protein localisation
negative regulation of protein positioning
negative regulation of protein recruitment
inhibition of establishment of protein localisation
inhibition of establishment of protein localization
negative regulation of establishment of protein localization
Any process that activates or increases the frequency, rate or extent of establishment of protein localization.
positive regulation of establishment of protein localisation
positive regulation of protein positioning
positive regulation of protein recruitment
up regulation of establishment of protein localisation
up regulation of establishment of protein localization
up-regulation of establishment of protein localisation
up-regulation of establishment of protein localization
upregulation of establishment of protein localisation
upregulation of establishment of protein localization
activation of establishment of protein localisation
activation of establishment of protein localization
positive regulation of establishment of protein localization
The process in which carboxylic acid is transported across a membrane.
Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation.
regulation of vascular smooth muscle cell differentiation
regulation of vascular associated smooth muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation.
down regulation of vascular associated smooth muscle cell differentiation
down regulation of vascular smooth muscle cell differentiation
down-regulation of vascular associated smooth muscle cell differentiation
down-regulation of vascular smooth muscle cell differentiation
downregulation of vascular associated smooth muscle cell differentiation
downregulation of vascular smooth muscle cell differentiation
negative regulation of VSMC differentiation
negative regulation of vascular smooth muscle cell differentiation
inhibition of vascular associated smooth muscle cell differentiation
inhibition of vascular smooth muscle cell differentiation
negative regulation of vascular associated smooth muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation.
positive regulation of VSMC differentiation
positive regulation of vascular smooth muscle cell differentiation
up regulation of vascular associated smooth muscle cell differentiation
up regulation of vascular smooth muscle cell differentiation
up-regulation of vascular associated smooth muscle cell differentiation
up-regulation of vascular smooth muscle cell differentiation
upregulation of vascular associated smooth muscle cell differentiation
upregulation of vascular smooth muscle cell differentiation
activation of vascular associated smooth muscle cell differentiation
activation of vascular smooth muscle cell differentiation
positive regulation of vascular associated smooth muscle cell differentiation
Any process that modulates the frequency, rate or extent of axo-dendritic protein transport.
regulation of axo-dendritic protein transport
Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport.
down regulation of axo-dendritic protein transport
down-regulation of axo-dendritic protein transport
downregulation of axo-dendritic protein transport
down regulation of axonal protein transport
down-regulation of axonal protein transport
downregulation of axonal protein transport
inhibition of axo-dendritic protein transport
negative regulation of axonal protein transport
negative regulation of axo-dendritic protein transport
Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport.
up regulation of axo-dendritic protein transport
up-regulation of axo-dendritic protein transport
upregulation of axo-dendritic protein transport
activation of axo-dendritic protein transport
positive regulation of axonal protein transport
up regulation of axonal protein transport
up-regulation of axonal protein transport
upregulation of axonal protein transport
positive regulation of axo-dendritic protein transport
The process that gives rise to the apical ectodermal ridge. This process pertains to the initial formation of a structure from unspecified parts.
Any process that modulates the frequency, rate or extent of apical ectodermal ridge formation.
regulation of apical epidermal ridge formation
regulation of crista ectodermalis apicalis formation
regulation of apical ectodermal ridge formation
Any process that stops, prevents or reduces the frequency, rate or extent of apical ectodermal ridge formation.
down regulation of apical ectodermal ridge formation
down regulation of apical epidermal ridge formation
down-regulation of apical ectodermal ridge formation
down-regulation of apical epidermal ridge formation
downregulation of apical ectodermal ridge formation
downregulation of apical epidermal ridge formation
negative regulation of apical epidermal ridge formation
inhibition of apical ectodermal ridge formation
inhibition of apical epidermal ridge formation
down regulation of crista ectodermalis apicalis formation
down-regulation of crista ectodermalis apicalis formation
downregulation of crista ectodermalis apicalis formation
inhibition of crista ectodermalis apicalis formation
negative regulation of crista ectodermalis apicalis formation
negative regulation of apical ectodermal ridge formation
Any process that activates or increases the frequency, rate or extent of apical ectodermal ridge formation.
positive regulation of apical epidermal ridge formation
up regulation of apical ectodermal ridge formation
up regulation of apical epidermal ridge formation
up-regulation of apical ectodermal ridge formation
up-regulation of apical epidermal ridge formation
upregulation of apical ectodermal ridge formation
upregulation of apical epidermal ridge formation
positive regulation of crista ectodermalis apicalis formation
up regulation of crista ectodermalis apicalis formation
up-regulation of crista ectodermalis apicalis formation
upregulation of crista ectodermalis apicalis formation
positive regulation of apical ectodermal ridge formation
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus.
Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy.
Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy.
down regulation of smooth muscle hypertrophy
down-regulation of smooth muscle hypertrophy
downregulation of smooth muscle hypertrophy
negative regulation of smooth muscle hypertrophy
Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy.
up regulation of smooth muscle hypertrophy
up-regulation of smooth muscle hypertrophy
upregulation of smooth muscle hypertrophy
positive regulation of smooth muscle hypertrophy
Any process that modulates the frequency, rate or extent of cardiocyte differentiation.
regulation of cardiac cell differentiation
regulation of heart cell differentiation
regulation of cardiocyte differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation.
down regulation of cardiac cell differentiation
down regulation of cardiocyte differentiation
down regulation of heart cell differentiation
down-regulation of cardiac cell differentiation
down-regulation of cardiocyte differentiation
down-regulation of heart cell differentiation
downregulation of cardiac cell differentiation
downregulation of cardiocyte differentiation
downregulation of heart cell differentiation
negative regulation of cardiac cell differentiation
negative regulation of heart cell differentiation
inhibition of cardiac cell differentiation
inhibition of cardiocyte differentiation
inhibition of heart cell differentiation
negative regulation of cardiocyte differentiation
Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation.
positive regulation of cardiac cell differentiation
positive regulation of heart cell differentiation
up regulation of cardiac cell differentiation
up regulation of cardiocyte differentiation
up regulation of heart cell differentiation
up-regulation of cardiac cell differentiation
up-regulation of cardiocyte differentiation
up-regulation of heart cell differentiation
upregulation of cardiac cell differentiation
upregulation of cardiocyte differentiation
upregulation of heart cell differentiation
activation of cardiac cell differentiation
activation of cardiocyte differentiation
activation of heart cell differentiation
positive regulation of cardiocyte differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation.
negative regulation of mitotic chromosome condensation
The developmental process by which an epicardium is generated and organized.
visceral serous pericardium of heart morphogenesis
visceral serous pericardium proper morphogenesis
pericardium visceral mesothelium morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization.
down regulation of chromatin organisation
down regulation of chromatin organization
down regulation of establishment or maintenance of chromatin architecture
down-regulation of chromatin organisation
down-regulation of chromatin organization
down-regulation of establishment or maintenance of chromatin architecture
downregulation of chromatin organisation
downregulation of chromatin organization
downregulation of establishment or maintenance of chromatin architecture
negative regulation of chromatin assembly/disassembly
negative regulation of chromatin organisation
negative regulation of establishment or maintenance of chromatin architecture
inhibition of chromatin assembly or disassembly
inhibition of establishment or maintenance of chromatin architecture
down regulation of chromatin assembly or disassembly
down-regulation of chromatin assembly or disassembly
downregulation of chromatin assembly or disassembly
negative regulation of chromatin assembly or disassembly
negative regulation of chromatin modification
negative regulation of chromatin organization
Any process that activates or increases the frequency, rate or extent of chromatin organization.
positive regulation of chromatin organisation
positive regulation of establishment or maintenance of chromatin architecture
up regulation of establishment or maintenance of chromatin architecture
up-regulation of establishment or maintenance of chromatin architecture
upregulation of chromatin assembly or disassembly
upregulation of establishment or maintenance of chromatin architecture
activation of chromatin assembly or disassembly
activation of establishment or maintenance of chromatin architecture
stimulation of chromatin assembly or disassembly
positive regulation of chromatin assembly or disassembly
positive regulation of chromatin assembly/disassembly
positive regulation of chromatin modification
up regulation of chromatin assembly or disassembly
up-regulation of chromatin assembly or disassembly
positive regulation of chromatin organization
Any process that modulates the frequency, rate or extent of epithelial tube formation.
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation.
down regulation of epithelial tube formation
down-regulation of epithelial tube formation
downregulation of epithelial tube formation
negative regulation of epithelial tube formation
Any process that activates or increases the frequency, rate or extent of epithelial tube formation.
up regulation of epithelial tube formation
up-regulation of epithelial tube formation
upregulation of epithelial tube formation
positive regulation of epithelial tube formation
Any apoptotic process in a vascular associated smooth muscle cell.
vascular smooth muscle cell apoptotic process
vascular associated smooth muscle cell apoptosis
vascular associated smooth muscle cell apoptotic process
Any process that modulates the frequency, rate or extent of neural crest cell differentiation.
regulation of neural crest cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation.
down regulation of neural crest cell differentiation
down-regulation of neural crest cell differentiation
downregulation of neural crest cell differentiation
inhibition of neural crest cell differentiation
negative regulation of neural crest cell differentiation
Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation.
up regulation of neural crest cell differentiation
up-regulation of neural crest cell differentiation
upregulation of neural crest cell differentiation
activation of neural crest cell differentiation
positive regulation of neural crest cell differentiation
Any process that modulates the frequency, rate or extent of intestinal epithelial cell development.
regulation of intestinal epithelial cell development
Any process that stops, prevents or reduces the frequency, rate or extent of intestinal epithelial cell development.
down regulation of intestinal epithelial cell development
down-regulation of intestinal epithelial cell development
downregulation of intestinal epithelial cell development
inhibition of intestinal epithelial cell development
negative regulation of intestinal epithelial cell development
Any process that activates or increases the frequency, rate or extent of intestinal epithelial cell development.
up regulation of intestinal epithelial cell development
up-regulation of intestinal epithelial cell development
upregulation of intestinal epithelial cell development
activation of intestinal epithelial cell development
positive regulation of intestinal epithelial cell development
Any process that modulates the frequency, rate or extent of cardiac myofibril assembly.
regulation of cardiac myofibril development
regulation of cardiac myofibril morphogenesis
regulation of cardiac myofibril assembly
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly.
down regulation of cardiac myofibril assembly
down regulation of cardiac myofibril development
down regulation of cardiac myofibril morphogenesis
down-regulation of cardiac myofibril assembly
down-regulation of cardiac myofibril development
down-regulation of cardiac myofibril morphogenesis
downregulation of cardiac myofibril assembly
downregulation of cardiac myofibril development
downregulation of cardiac myofibril morphogenesis
negative regulation of cardiac myofibril development
negative regulation of cardiac myofibril morphogenesis
inhibition of cardiac myofibril assembly
inhibition of cardiac myofibril development
inhibition of cardiac myofibril morphogenesis
down regulation of heart myofibril assembly
down-regulation of heart myofibril assembly
downregulation of heart myofibril assembly
negative regulation of heart myofibril assembly
negative regulation of cardiac myofibril assembly
Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly.
positive regulation of cardiac myofibril development
positive regulation of cardiac myofibril morphogenesis
up regulation of cardiac myofibril assembly
up regulation of cardiac myofibril development
up regulation of cardiac myofibril morphogenesis
up-regulation of cardiac myofibril assembly
up-regulation of cardiac myofibril development
up-regulation of cardiac myofibril morphogenesis
upregulation of cardiac myofibril assembly
upregulation of cardiac myofibril development
upregulation of cardiac myofibril morphogenesis
activation of cardiac myofibril assembly
activation of cardiac myofibril development
activation of cardiac myofibril morphogenesis
positive regulation of heart myofibril assembly
up regulation of heart myofibril assembly
up-regulation of heart myofibril assembly
upregulation of heart myofibril assembly
positive regulation of cardiac myofibril assembly
Any cell proliferation that is involved in endocardial cushion morphogenesis.
cell proliferation involved in endocardial cushion morphogenesis
Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium.
regulation of morphogenesis of an epithelium
Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium.
down regulation of epithelium morphogenesis
down regulation of morphogenesis of an epithelium
down-regulation of epithelium morphogenesis
down-regulation of morphogenesis of an epithelium
downregulation of epithelium morphogenesis
downregulation of morphogenesis of an epithelium
negative regulation of epithelium morphogenesis
inhibition of morphogenesis of an epithelium
negative regulation of morphogenesis of an epithelium
Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium.
positive regulation of epithelium morphogenesis
up regulation of epithelium morphogenesis
up regulation of morphogenesis of an epithelium
up-regulation of epithelium morphogenesis
up-regulation of morphogenesis of an epithelium
upregulation of epithelium morphogenesis
upregulation of morphogenesis of an epithelium
activation of morphogenesis of an epithelium
positive regulation of morphogenesis of an epithelium
The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.
A process in which a protein is transported to, or maintained in, a location within a presynapse.
Any process that modulates the frequency, rate or extent of protein localization to presynapse.
regulation of protein localisation in presynapse
regulation of protein localisation to presynapse
regulation of protein localization in presynapse
regulation of recruitment of presynaptic proteins
regulation of protein localization to presynapse
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse.
down regulation of protein localisation in presynapse
down regulation of protein localisation to presynapse
down regulation of protein localization in presynapse
down regulation of protein localization to presynapse
down regulation of recruitment of presynaptic proteins
down-regulation of protein localisation in presynapse
down-regulation of protein localisation to presynapse
down-regulation of protein localization in presynapse
down-regulation of protein localization to presynapse
down-regulation of recruitment of presynaptic proteins
downregulation of protein localisation in presynapse
downregulation of protein localisation to presynapse
downregulation of protein localization in presynapse
downregulation of protein localization to presynapse
downregulation of recruitment of presynaptic proteins
negative regulation of protein localisation in presynapse
negative regulation of protein localisation to presynapse
negative regulation of protein localization in presynapse
negative regulation of recruitment of presynaptic proteins
inhibition of protein localisation in presynapse
inhibition of protein localisation to presynapse
inhibition of protein localization in presynapse
inhibition of protein localization to presynapse
inhibition of recruitment of presynaptic proteins
negative regulation of protein localization to presynapse
Any process that activates or increases the frequency, rate or extent of protein localization to presynapse.
positive regulation of protein localisation in presynapse
positive regulation of protein localisation to presynapse
positive regulation of protein localization in presynapse
positive regulation of recruitment of presynaptic proteins
up regulation of protein localisation in presynapse
up regulation of protein localisation to presynapse
up regulation of protein localization in presynapse
up regulation of protein localization to presynapse
up regulation of recruitment of presynaptic proteins
up-regulation of protein localisation in presynapse
up-regulation of protein localisation to presynapse
up-regulation of protein localization in presynapse
up-regulation of protein localization to presynapse
up-regulation of recruitment of presynaptic proteins
upregulation of protein localisation in presynapse
upregulation of protein localisation to presynapse
upregulation of protein localization in presynapse
upregulation of protein localization to presynapse
upregulation of recruitment of presynaptic proteins
activation of protein localisation in presynapse
activation of protein localisation to presynapse
activation of protein localization in presynapse
activation of protein localization to presynapse
activation of recruitment of presynaptic proteins
positive regulation of protein localization to presynapse
Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
regulation of neuropeptide-mediated retrograde trans-synaptic signaling
regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
down regulation of retrograde trans-synaptic signaling by neuropeptide
down-regulation of retrograde trans-synaptic signaling by neuropeptide
downregulation of retrograde trans-synaptic signaling by neuropeptide
inhibition of retrograde trans-synaptic signaling by neuropeptide
inhibition of neuropeptide-mediated retrograde trans-synaptic signaling
negative regulation of neuropeptide-mediated retrograde trans-synaptic signaling
negative regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.
up regulation of retrograde trans-synaptic signaling by neuropeptide
up-regulation of retrograde trans-synaptic signaling by neuropeptide
upregulation of retrograde trans-synaptic signaling by neuropeptide
activation of retrograde trans-synaptic signaling by neuropeptide
positive regulation of neuropeptide-mediated retrograde trans-synaptic signaling
positive regulation of retrograde trans-synaptic signaling by neuropeptide
Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation.
regulation of myeloid progenitor cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation.
down regulation of myeloid progenitor cell differentiation
down-regulation of myeloid progenitor cell differentiation
downregulation of myeloid progenitor cell differentiation
inhibition of myeloid progenitor cell differentiation
negative regulation of myeloid progenitor cell differentiation
Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation.
up regulation of myeloid progenitor cell differentiation
up-regulation of myeloid progenitor cell differentiation
upregulation of myeloid progenitor cell differentiation
activation of myeloid progenitor cell differentiation
positive regulation of myeloid progenitor cell differentiation
Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
regulation of vascular smooth muscle cell apoptotic process
regulation of vascular associated smooth muscle cell apoptosis
regulation of vascular smooth muscle cell apoptosis
regulation of vascular associated smooth muscle cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
down regulation of VSMC apoptotic process
down regulation of vascular associated smooth muscle cell apoptotic process
down regulation of vascular smooth muscle cell apoptotic process
down-regulation of VSMC apoptotic process
down-regulation of vascular associated smooth muscle cell apoptotic process
down-regulation of vascular smooth muscle cell apoptotic process
downregulation of VSMC apoptotic process
downregulation of vascular associated smooth muscle cell apoptotic process
downregulation of vascular smooth muscle cell apoptotic process
negative regulation of VSMC apoptotic process
negative regulation of vascular smooth muscle cell apoptotic process
down regulation of vascular associated smooth muscle cell apoptosis
down regulation of vascular smooth muscle cell apoptosis
down-regulation of vascular associated smooth muscle cell apoptosis
down-regulation of vascular smooth muscle cell apoptosis
downregulation of vascular associated smooth muscle cell apoptosis
downregulation of vascular smooth muscle cell apoptosis
inhibition of vascular associated smooth muscle cell apoptosis
inhibition of vascular associated smooth muscle cell apoptotic process
inhibition of vascular smooth muscle cell apoptosis
inhibition of vascular smooth muscle cell apoptotic process
negative regulation of vascular associated smooth muscle cell apoptosis
negative regulation of vascular smooth muscle cell apoptosis
negative regulation of vascular associated smooth muscle cell apoptotic process
Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.
positive regulation of VSMC apoptotic process
positive regulation of vascular smooth muscle cell apoptotic process
up regulation of vascular associated smooth muscle cell apoptotic process
up regulation of vascular smooth muscle cell apoptotic process
up-regulation of vascular associated smooth muscle cell apoptotic process
up-regulation of vascular smooth muscle cell apoptotic process
upregulation of vascular associated smooth muscle cell apoptotic process
upregulation of vascular smooth muscle cell apoptotic process
activation of vascular associated smooth muscle cell apoptosis
activation of vascular associated smooth muscle cell apoptotic process
activation of vascular smooth muscle cell apoptosis
activation of vascular smooth muscle cell apoptotic process
positive regulation of vascular associated smooth muscle cell apoptosis
positive regulation of vascular smooth muscle cell apoptosis
up regulation of vascular associated smooth muscle cell apoptosis
up regulation of vascular smooth muscle cell apoptosis
up-regulation of vascular associated smooth muscle cell apoptosis
up-regulation of vascular smooth muscle cell apoptosis
upregulation of vascular associated smooth muscle cell apoptosis
upregulation of vascular smooth muscle cell apoptosis
positive regulation of vascular associated smooth muscle cell apoptotic process
Any process that modulates the frequency, rate or extent of protein localization to membrane.
regulation of protein localisation in membrane
regulation of protein localization in membrane
regulation of protein localization to membrane
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane.
down regulation of protein localisation in membrane
down regulation of protein localization in membrane
down regulation of protein localization to membrane
down-regulation of protein localisation in membrane
down-regulation of protein localization in membrane
down-regulation of protein localization to membrane
downregulation of protein localisation in membrane
downregulation of protein localization in membrane
downregulation of protein localization to membrane
negative regulation of protein localisation in membrane
negative regulation of protein localization in membrane
inhibition of protein localisation in membrane
inhibition of protein localization in membrane
inhibition of protein localization to membrane
negative regulation of protein localization to membrane
Any process that activates or increases the frequency, rate or extent of protein localization to membrane.
positive regulation of protein localisation in membrane
positive regulation of protein localization in membrane
up regulation of protein localisation in membrane
up regulation of protein localization in membrane
up regulation of protein localization to membrane
up-regulation of protein localisation in membrane
up-regulation of protein localization in membrane
up-regulation of protein localization to membrane
upregulation of protein localisation in membrane
upregulation of protein localization in membrane
upregulation of protein localization to membrane
activation of protein localisation in membrane
activation of protein localization in membrane
activation of protein localization to membrane
positive regulation of protein localization to membrane
Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve.
up regulation of branching morphogenesis of a nerve
up-regulation of branching morphogenesis of a nerve
upregulation of branching morphogenesis of a nerve
activation of branching morphogenesis of a nerve
positive regulation of branching morphogenesis of a nerve
Any process that activates or increases the frequency, rate or extent of fertilization.
Any process that modulates the frequency, rate or extent of blood vessel branching.
regulation of branching involved in blood vessel morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching.
down regulation of branching involved in blood vessel morphogenesis
down regulation of patterning of blood vessels
down-regulation of branching involved in blood vessel morphogenesis
down-regulation of patterning of blood vessels
downregulation of branching involved in blood vessel morphogenesis
downregulation of patterning of blood vessels
negative regulation of branching involved in blood vessel morphogenesis
inhibition of branching involved in blood vessel morphogenesis
inhibition of patterning of blood vessels
Any process that activates or increases the frequency, rate or extent of blood vessel branching.
positive regulation of branching involved in blood vessel morphogenesis
up regulation of branching involved in blood vessel morphogenesis
up regulation of patterning of blood vessels
up-regulation of branching involved in blood vessel morphogenesis
up-regulation of patterning of blood vessels
upregulation of branching involved in blood vessel morphogenesis
upregulation of patterning of blood vessels
activation of branching involved in blood vessel morphogenesis
activation of patterning of blood vessels
positive regulation of blood vessel branching
Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly.
regulation of mitotic nuclear envelope breakdown
regulation of mitotic nuclear envelope catabolism
regulation of mitotic nuclear envelope degradation
regulation of mitotic nuclear envelope disassembly
Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly.
down regulation of mitotic nuclear envelope breakdown
down regulation of mitotic nuclear envelope catabolism
down regulation of mitotic nuclear envelope degradation
down regulation of mitotic nuclear envelope disassembly
down-regulation of mitotic nuclear envelope breakdown
down-regulation of mitotic nuclear envelope catabolism
down-regulation of mitotic nuclear envelope degradation
down-regulation of mitotic nuclear envelope disassembly
downregulation of mitotic nuclear envelope breakdown
downregulation of mitotic nuclear envelope catabolism
downregulation of mitotic nuclear envelope degradation
downregulation of mitotic nuclear envelope disassembly
negative regulation of mitotic nuclear envelope breakdown
negative regulation of mitotic nuclear envelope catabolism
negative regulation of mitotic nuclear envelope degradation
inhibition of mitotic nuclear envelope breakdown
inhibition of mitotic nuclear envelope catabolism
inhibition of mitotic nuclear envelope degradation
inhibition of mitotic nuclear envelope disassembly
negative regulation of mitotic nuclear envelope disassembly
Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly.
positive regulation of mitotic nuclear envelope breakdown
positive regulation of mitotic nuclear envelope catabolism
positive regulation of mitotic nuclear envelope degradation
up regulation of mitotic nuclear envelope breakdown
up regulation of mitotic nuclear envelope catabolism
up regulation of mitotic nuclear envelope degradation
up regulation of mitotic nuclear envelope disassembly
up-regulation of mitotic nuclear envelope breakdown
up-regulation of mitotic nuclear envelope catabolism
up-regulation of mitotic nuclear envelope degradation
up-regulation of mitotic nuclear envelope disassembly
upregulation of mitotic nuclear envelope breakdown
upregulation of mitotic nuclear envelope catabolism
upregulation of mitotic nuclear envelope degradation
upregulation of mitotic nuclear envelope disassembly
activation of mitotic nuclear envelope breakdown
activation of mitotic nuclear envelope catabolism
activation of mitotic nuclear envelope degradation
activation of mitotic nuclear envelope disassembly
positive regulation of mitotic nuclear envelope disassembly
Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation.
regulation of vascular endothelial cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation.
down regulation of vascular endothelial cell proliferation
down-regulation of vascular endothelial cell proliferation
downregulation of vascular endothelial cell proliferation
inhibition of vascular endothelial cell proliferation
negative regulation of vascular endothelial cell proliferation
Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation.
up regulation of vascular endothelial cell proliferation
up-regulation of vascular endothelial cell proliferation
upregulation of vascular endothelial cell proliferation
activation of vascular endothelial cell proliferation
positive regulation of vascular endothelial cell proliferation
Any process that modulates the frequency, rate or extent of presynapse assembly.
regulation of presynaptic terminal assembly
Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly.
down regulation of presynapse biogenesis
down regulation of presynaptic terminal assembly
down-regulation of presynapse biogenesis
down-regulation of presynaptic terminal assembly
downregulation of presynaptic terminal assembly
negative regulation of presynapse biogenesis
negative regulation of presynaptic terminal assembly
inhibition of presynaptic terminal assembly
negative regulation of presynapse assembly
Any process that activates or increases the frequency, rate or extent of presynapse assembly.
positive regulation of presynapse biogenesis
positive regulation of presynaptic terminal assembly
up regulation of presynaptic terminal assembly
up-regulation of presynaptic terminal assembly
upregulation of presynaptic terminal assembly
activation of presynaptic terminal assembly
positive regulation of presynapse assembly
Any process that modulates the frequency, rate or extent of serotonin biosynthetic process.
regulation of serotonin biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process.
down regulation of serotonin biosynthesis
down regulation of serotonin biosynthetic process
down-regulation of serotonin biosynthesis
down-regulation of serotonin biosynthetic process
downregulation of serotonin biosynthesis
downregulation of serotonin biosynthetic process
negative regulation of serotonin anabolism
negative regulation of serotonin biosynthesis
negative regulation of serotonin formation
negative regulation of serotonin synthesis
inhibition of serotonin biosynthetic process
negative regulation of serotonin biosynthetic process
Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process.
positive regulation of serotonin anabolism
positive regulation of serotonin biosynthesis
positive regulation of serotonin formation
positive regulation of serotonin synthesis
up regulation of serotonin biosynthetic process
up-regulation of serotonin biosynthetic process
upregulation of serotonin biosynthetic process
activation of serotonin biosynthetic process
positive regulation of serotonin biosynthetic process
Any process that modulates the frequency, rate or extent of protein localization to chromatin.
regulation of protein localisation to chromatin
regulation of protein localization to chromatin
Any process that modulates the frequency, rate or extent of artery morphogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis.
down regulation of arterial morphogenesis
down-regulation of arterial morphogenesis
downregulation of arterial morphogenesis
negative regulation of arterial morphogenesis
negative regulation of artery morphogenesis
Any process that activates or increases the frequency, rate or extent of artery morphogenesis.
positive regulation of arterial morphogenesis
positive regulation of artery morphogenesis
The disaggregation of a nucleus into its constituent components.
Any microtubule bundle that is part of a cytoplasm.
A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule.
protein localisation to cytoplasmic microtubule
protein localization to cytoplasmic microtubule
Any process that modulates the frequency, rate or extent of mesodermal cell differentiation.
regulation of mesoderm cell differentiation
regulation of mesodermal cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation.
down regulation of mesoderm cell differentiation
down regulation of mesodermal cell differentiation
down-regulation of mesoderm cell differentiation
down-regulation of mesodermal cell differentiation
downregulation of mesoderm cell differentiation
downregulation of mesodermal cell differentiation
negative regulation of mesoderm cell differentiation
inhibition of mesoderm cell differentiation
inhibition of mesodermal cell differentiation
negative regulation of mesodermal cell differentiation
Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation.
positive regulation of mesoderm cell differentiation
up regulation of mesoderm cell differentiation
up regulation of mesodermal cell differentiation
up-regulation of mesoderm cell differentiation
up-regulation of mesodermal cell differentiation
upregulation of mesoderm cell differentiation
upregulation of mesodermal cell differentiation
activation of mesoderm cell differentiation
activation of mesodermal cell differentiation
positive regulation of mesodermal cell differentiation
Any process that modulates the frequency, rate or extent of synapse pruning.
Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning.
Any process that activates or increases the frequency, rate or extent of synapse pruning.
Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization.
negative regulation of synapse development
negative regulation of synapse organisation
down regulation of synapse morphogenesis
down regulation of synapse organization and biogenesis
down-regulation of synapse morphogenesis
down-regulation of synapse organization and biogenesis
downregulation of synapse organization and biogenesis
inhibition of synapse organization and biogenesis
negative regulation of synapse morphogenesis
negative regulation of synapse organization and biogenesis
negative regulation of synapse organization
Any process that activates or increases the frequency, rate or extent of chromosome condensation.
positive regulation of eukaryotic chromosome condensation
positive regulation of nuclear chromosome condensation
up regulation of chromosome condensation
up regulation of eukaryotic chromosome condensation
up regulation of nuclear chromosome condensation
up-regulation of chromosome condensation
up-regulation of eukaryotic chromosome condensation
up-regulation of nuclear chromosome condensation
upregulation of eukaryotic chromosome condensation
upregulation of nuclear chromosome condensation
activation of eukaryotic chromosome condensation
activation of nuclear chromosome condensation
positive regulation of chromosome condensation
Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation.
down regulation of microtubule nucleation
down-regulation of microtubule nucleation
downregulation of microtubule nucleation
negative regulation of microtubule nucleation
Any process that modulates the frequency, rate or extent of protein localization to cell leading edge.
regulation of protein localisation in cell leading edge
regulation of protein localisation to cell leading edge
regulation of protein localization in cell leading edge
regulation of protein localization to cell leading edge
Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge.
down regulation of protein localisation in cell leading edge
down regulation of protein localisation to cell leading edge
down regulation of protein localization in cell leading edge
down regulation of protein localization to cell leading edge
down-regulation of protein localisation in cell leading edge
down-regulation of protein localisation to cell leading edge
down-regulation of protein localization in cell leading edge
down-regulation of protein localization to cell leading edge
downregulation of protein localisation in cell leading edge
downregulation of protein localisation to cell leading edge
downregulation of protein localization in cell leading edge
downregulation of protein localization to cell leading edge
negative regulation of protein localisation in cell leading edge
negative regulation of protein localisation to cell leading edge
negative regulation of protein localization in cell leading edge
inhibition of protein localisation in cell leading edge
inhibition of protein localisation to cell leading edge
inhibition of protein localization in cell leading edge
inhibition of protein localization to cell leading edge
negative regulation of protein localization to cell leading edge
Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge.
positive regulation of protein localisation in cell leading edge
positive regulation of protein localisation to cell leading edge
positive regulation of protein localization in cell leading edge
up regulation of protein localisation in cell leading edge
up regulation of protein localisation to cell leading edge
up regulation of protein localization in cell leading edge
up regulation of protein localization to cell leading edge
up-regulation of protein localisation in cell leading edge
up-regulation of protein localisation to cell leading edge
up-regulation of protein localization in cell leading edge
up-regulation of protein localization to cell leading edge
upregulation of protein localisation in cell leading edge
upregulation of protein localisation to cell leading edge
upregulation of protein localization in cell leading edge
upregulation of protein localization to cell leading edge
activation of protein localisation in cell leading edge
activation of protein localisation to cell leading edge
activation of protein localization in cell leading edge
activation of protein localization to cell leading edge
positive regulation of protein localization to cell leading edge
Any process that modulates the frequency, rate or extent of oogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis.
Any process that activates or increases the frequency, rate or extent of oogenesis.
Any process that modulates the frequency, rate or extent of smooth muscle tissue development.
regulation of smooth muscle tissue development
Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development.
down regulation of smooth muscle tissue development
down-regulation of smooth muscle tissue development
downregulation of smooth muscle tissue development
inhibition of smooth muscle tissue development
negative regulation of smooth muscle tissue development
Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development.
up regulation of smooth muscle tissue development
up-regulation of smooth muscle tissue development
upregulation of smooth muscle tissue development
activation of smooth muscle tissue development
positive regulation of smooth muscle tissue development
Any process that modulates the frequency, rate or extent of mesoderm formation.
Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation.
negative regulation of mesoderm formation
Any process that activates or increases the frequency, rate or extent of mesoderm formation.
positive regulation of mesoderm formation
Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process.
regulation of acetylcholine biosynthesis
regulation of acetylcholine biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine biosynthetic process.
down regulation of acetylcholine anabolism
down regulation of acetylcholine biosynthesis
down regulation of acetylcholine biosynthetic process
down regulation of acetylcholine formation
down regulation of acetylcholine synthesis
down-regulation of acetylcholine anabolism
down-regulation of acetylcholine biosynthesis
down-regulation of acetylcholine biosynthetic process
down-regulation of acetylcholine formation
down-regulation of acetylcholine synthesis
downregulation of acetylcholine anabolism
downregulation of acetylcholine biosynthesis
downregulation of acetylcholine biosynthetic process
downregulation of acetylcholine formation
downregulation of acetylcholine synthesis
negative regulation of acetylcholine anabolism
negative regulation of acetylcholine biosynthesis
negative regulation of acetylcholine formation
negative regulation of acetylcholine synthesis
inhibition of acetylcholine biosynthesis
inhibition of acetylcholine biosynthetic process
negative regulation of acetylcholine biosynthetic process
Any process that activates or increases the frequency, rate or extent of acetylcholine biosynthetic process.
positive regulation of acetylcholine anabolism
positive regulation of acetylcholine biosynthesis
positive regulation of acetylcholine formation
positive regulation of acetylcholine synthesis
up regulation of acetylcholine anabolism
up regulation of acetylcholine biosynthesis
up regulation of acetylcholine biosynthetic process
up regulation of acetylcholine formation
up regulation of acetylcholine synthesis
up-regulation of acetylcholine anabolism
up-regulation of acetylcholine biosynthesis
up-regulation of acetylcholine biosynthetic process
up-regulation of acetylcholine formation
up-regulation of acetylcholine synthesis
upregulation of acetylcholine biosynthesis
upregulation of acetylcholine biosynthetic process
activation of acetylcholine biosynthesis
activation of acetylcholine biosynthetic process
positive regulation of acetylcholine biosynthetic process
Any process that modulates the frequency, rate or extent of germ cell proliferation.
Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation.
down regulation of germ cell proliferation
down-regulation of germ cell proliferation
downregulation of germ cell proliferation
negative regulation of germ cell proliferation
Any process that activates or increases the frequency, rate or extent of germ cell proliferation.
up regulation of germ cell proliferation
up-regulation of germ cell proliferation
positive regulation of germ cell proliferation
Any process that modulates the frequency, rate or extent of gonad development.
Any process that stops, prevents or reduces the frequency, rate or extent of gonad development.
negative regulation of gonad development
Any process that activates or increases the frequency, rate or extent of gonad development.
positive regulation of gonad development
Any process that modulates the frequency, rate or extent of lipid localization.
Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization.
negative regulation of lipid localisation
negative regulation of lipid localization
Any process that activates or increases the frequency, rate or extent of lipid localization.
positive regulation of lipid localisation
positive regulation of lipid localization
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis.
down regulation of endothelial tube morphogenesis
down-regulation of endothelial tube morphogenesis
downregulation of endothelial tube morphogenesis
inhibition of endothelial tube morphogenesis
negative regulation of endothelial tube morphogenesis
Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis.
up regulation of endothelial tube morphogenesis
up-regulation of endothelial tube morphogenesis
upregulation of endothelial tube morphogenesis
activation of endothelial tube morphogenesis
positive regulation of endothelial tube morphogenesis
Any apoptotic process in a retinal cell.
induction of retinal programmed cell death
Any apoptotic process in a compound eye retinal cell.
compound eye retinal cell apoptotic process
The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
extracellular vesicular exosome secretion
multi-vesicular body fusion with plasma membrane
A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.
A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.
An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).
Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis.
The multiplication or reproduction of cholangiocytes, resulting in the expansion of the cholangiocyte population. A cholangiocyte is an epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water.
Any process carried out at the cellular level that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry of the large intestine, exclusive of the rectum. The colon is that part of the large intestine that connects the small intestine to the rectum.
The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products.
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine.
small intestine smooth muscle contraction
A process in which a protein is transported to, or maintained in, the cell periphery.
Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell.
The multiplication or reproduction of acinar cells, resulting in the expansion of a cell population. An acinar cell is a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini (singular acinus).
The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.
vascular smooth muscle cell proliferation
vascular associated smooth muscle cell proliferation
A macromolecular complex that contains both RNA and protein molecules.
Any process that modulates the frequency, rate or extent of multicellular organismal development.
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of animal organ morphogenesis.
regulation of histogenesis and organogenesis
regulation of animal organ morphogenesis
Any process that modulates the frequency, rate or extent of stem cell division.
Any process that modulates the frequency, rate or extent of pancreatic B cell development.
regulation of pancreatic B cell development
regulation of pancreatic beta cell development
regulation of type B pancreatic cell development
Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development.
negative regulation of pancreatic B cell development
negative regulation of pancreatic beta cell development
negative regulation of type B pancreatic cell development
Any process that activates or increases the frequency, rate or extent of pancreatic B cell development.
positive regulation of pancreatic B cell development
positive regulation of pancreatic beta cell development
positive regulation of type B pancreatic cell development
Any process that modulates the frequency, rate or extent of leukocyte apoptotic process.
regulation of leukocyte apoptotic process
Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process.
negative regulation of leukocyte apoptosis
negative regulation of leukocyte apoptotic process
Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process.
positive regulation of leukocyte apoptosis
positive regulation of leukocyte apoptotic process
Any process that modulates the frequency, rate or extent of establishment of cell polarity.
regulation of bud site selection/establishment of cell polarity
regulation of establishment of cell polarity
Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
regulation of cell proliferation involved in heart morphogenesis
Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
negative regulation of cell proliferation involved in heart morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
positive regulation of cell proliferation involved in heart morphogenesis
Any process that modulates the frequency, rate or extent of cell motility.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
negative regulation of movement of a cell
Any process that activates or increases the frequency, rate or extent of cell motility.
positive regulation of movement of a cell
Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve.
regulation of branching morphogenesis of a nerve
Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve.
negative regulation of branching morphogenesis of a nerve
Any process that modulates the frequency, rate or extent of neural precursor cell proliferation.
regulation of neural precursor cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation.
negative regulation of neural precursor cell proliferation
Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation.
positive regulation of neural precursor cell proliferation
Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis.
negative regulation of blood vessel morphogenesis
Any process that modulates the frequency, rate or extent of phosphate transmembrane transport.
regulation of phosphate membrane transport
regulation of phosphate transmembrane transport
Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport.
negative regulation of phosphate membrane transport
negative regulation of phosphate transmembrane transport
Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport.
positive regulation of phosphate membrane transport
positive regulation of phosphate transmembrane transport
Any process that modulates the frequency, rate or extent of female gonad development.
Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
negative regulation of ovarian development
negative regulation of ovary development
negative regulation of female gonad development
Any process that activates or increases the frequency, rate or extent of female gonad development.
positive regulation of ovarian development
positive regulation of ovary development
positive regulation of female gonad development
Any process that modulates the frequency, rate or extent of pancreatic A cell differentiation.
regulation of pancreatic alpha cell differentiation
regulation of pancreatic A cell differentiation
Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic A cell differentiation.
negative regulation of pancreatic alpha cell differentiation
negative regulation of pancreatic A cell differentiation
Any process that activates or increases the frequency, rate or extent of pancreatic A cell differentiation.
positive regulation of pancreatic alpha cell differentiation
positive regulation of pancreatic A cell differentiation
Any process that modulates the frequency, rate or extent of reproductive process.
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
negative regulation of reproductive process
Any process that activates or increases the frequency, rate or extent of reproductive process.
positive regulation of reproductive process
Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or maintenance of neuroblast polarity.
negative regulation of establishment and/or maintenance of neuroblast cell polarity
negative regulation of establishment or maintenance of neuroblast polarity
Any process that modulates the frequency, rate or extent of fibroblast apoptotic process.
regulation of fibroblast apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process.
negative regulation of fibroblast apoptosis
negative regulation of fibroblast apoptotic process
Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process.
positive regulation of fibroblast apoptosis
positive regulation of fibroblast apoptotic process
Any process that modulates the frequency, rate or extent of DNA biosynthetic process.
Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.
negative regulation of DNA biosynthetic process
Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process.
regulation of amino acid biosynthetic process
regulation of cellular amino acid anabolism
regulation of cellular amino acid biosynthesis
regulation of cellular amino acid formation
regulation of cellular amino acid synthesis
regulation of cellular amino acid biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process.
negative regulation of amino acid anabolism
negative regulation of amino acid biosynthesis
negative regulation of amino acid formation
negative regulation of amino acid synthesis
negative regulation of cellular amino acid biosynthetic process
negative regulation of amino acid biosynthetic process
Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process.
positive regulation of amino acid anabolism
positive regulation of amino acid biosynthesis
positive regulation of amino acid formation
positive regulation of amino acid synthesis
positive regulation of cellular amino acid biosynthetic process
positive regulation of amino acid biosynthetic process
Any process that activates or increases the frequency, rate or extent of myotome development.
positive regulation of myotome development
Any process that activates or increases the frequency, rate or extent of myoblast proliferation.
positive regulation of myoblast proliferation
Any process that modulates the frequency, rate or extent of myotome development.
Any process that modulates the frequency, rate or extent of myoblast proliferation.
Any process that modulates the frequency, rate or extent of defecation.
Any process that stops, prevents or reduces the frequency, rate or extent of defecation.
Any process that activates or increases the frequency, rate or extent of defecation.
Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process.
regulation of apoptosis of endothelial cells
regulation of endothelial cell programmed cell death by apoptosis
regulation of killing of endothelial cells
regulation of programmed cell death of endothelial cells by apoptosis
regulation of programmed cell death, endothelial cells
regulation of endothelial cell apoptosis
regulation of endothelial cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
negative regulation of apoptosis of endothelial cells
negative regulation of endothelial cell programmed cell death by apoptosis
negative regulation of killing of endothelial cells
negative regulation of programmed cell death of endothelial cells by apoptosis
negative regulation of programmed cell death, endothelial cells
negative regulation of endothelial cell apoptosis
negative regulation of endothelial cell apoptotic process
Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
positive regulation of apoptosis of endothelial cells
positive regulation of endothelial cell programmed cell death by apoptosis
positive regulation of killing of endothelial cells
positive regulation of programmed cell death of endothelial cells by apoptosis
positive regulation of programmed cell death, endothelial cells
positive regulation of endothelial cell apoptosis
positive regulation of endothelial cell apoptotic process
Any process that modulates the frequency, rate or extent of oxygen metabolic process.
regulation of diatomic oxygen metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process.
negative regulation of diatomic oxygen metabolic process
negative regulation of oxygen metabolism
negative regulation of oxygen metabolic process
Any process that activates or increases the frequency, rate or extent of oxygen metabolic process.
positive regulation of diatomic oxygen metabolic process
positive regulation of oxygen metabolism
positive regulation of oxygen metabolic process
Any process that modulates the frequency, rate or extent of mesoderm development.
Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development.
negative regulation of mesoderm development
Any process that activates or increases the frequency, rate or extent of mesoderm development.
positive regulation of mesoderm development
Any process that modulates the frequency, rate or extent of ectoderm development.
Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development.
negative regulation of ectoderm development
Any process that activates or increases the frequency, rate or extent of ectoderm development.
positive regulation of ectoderm development
Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
regulation of cell proliferation involved in compound eye morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
negative regulation of cell proliferation involved in compound eye morphogenesis
Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.
positive regulation of cell proliferation involved in compound eye morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation.
Any process that activates or increases the frequency, rate or extent of gastrulation.
Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
positive regulation of DNA biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation.
negative regulation of stem cell proliferation
Any process that activates or increases the frequency, rate or extent of stem cell proliferation.
positive regulation of stem cell proliferation
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity.
regulation of sodium transporter activity
regulation of sodium ion transmembrane transporter activity
Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity.
negative regulation of sodium transporter activity
negative regulation of sodium ion transmembrane transporter activity
Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transporter activity.
positive regulation of sodium transporter activity
positive regulation of sodium ion transmembrane transporter activity
Any process that modulates the frequency, rate or extent of motor neuron apoptotic process.
regulation of motor neuron apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process.
negative regulation of motoneuron apoptosis
negative regulation of motor neuron apoptosis
negative regulation of motor neuron apoptotic process
Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process.
positive regulation of motoneuron apoptosis
positive regulation of motor neuron apoptosis
positive regulation of motor neuron apoptotic process
Any process that modulates the frequency, rate or extent of type B pancreatic cell apoptotic process.
regulation of pancreatic B cell apoptosis
regulation of pancreatic beta cell apoptosis
regulation of type B pancreatic cell apoptosis
regulation of type B pancreatic cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell apoptotic process.
negative regulation of pancreatic B cell apoptosis
negative regulation of pancreatic beta cell apoptosis
negative regulation of type B pancreatic cell apoptosis
negative regulation of type B pancreatic cell apoptotic process
Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process.
positive regulation of pancreatic B cell apoptosis
positive regulation of pancreatic beta cell apoptosis
positive regulation of type B pancreatic cell apoptosis
positive regulation of type B pancreatic cell apoptotic process
Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
regulation of myocardial precursor cell differentiation
regulation of cardiac myoblast differentiation
regulation of cardiac muscle cell myoblast differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
negative regulation of myocardial precursor cell differentiation
negative regulation of cardiac myoblast differentiation
negative regulation of cardiac muscle cell myoblast differentiation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation.
positive regulation of myocardial precursor cell differentiation
positive regulation of cardiac myoblast differentiation
positive regulation of cardiac muscle cell myoblast differentiation
Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation.
regulation of cardiomyocyte differentiation
regulation of heart muscle cell differentiation
regulation of cardiac muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation.
negative regulation of cardiomyocyte differentiation
negative regulation of heart muscle cell differentiation
negative regulation of cardiac muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation.
positive regulation of cardiomyocyte differentiation
positive regulation of heart muscle cell differentiation
positive regulation of cardiac muscle cell differentiation
Any process that modulates the frequency, rate or extent of stem cell differentiation.
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation.
negative regulation of stem cell differentiation
Any process that activates or increases the frequency, rate or extent of stem cell differentiation.
positive regulation of stem cell differentiation
Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
regulation of mesenchymal cell proliferation involved in lung development
Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
negative regulation of mesenchymal cell proliferation involved in lung development
Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.
positive regulation of mesenchymal cell proliferation involved in lung development
Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.
regulation of epithelial cell proliferation involved in lung morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.
negative regulation of epithelial cell proliferation involved in lung morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation.
negative regulation of myoblast proliferation
Any process that modulates the frequency, rate or extent of heart morphogenesis.
Any process that modulates the frequency, rate or extent of steroid hormone secretion.
Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion.
negative regulation of steroid hormone secretion
Any process that activates or increases the frequency, rate or extent of steroid hormone secretion.
positive regulation of steroid hormone secretion
Any process that modulates the frequency, rate or extent of androgen secretion.
Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion.
negative regulation of androgen secretion
Any process that activates or increases the frequency, rate or extent of androgen secretion.
positive regulation of androgen secretion
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state.
mesenchymal cell differentiation involved in urinary system development
mesenchymal cell differentiation involved in urinary tract development
mesenchymal cell differentiation involved in renal system development
Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation.
regulation of skeletal muscle cell differentiation
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation.
negative regulation of skeletal muscle cell differentiation
Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation.
positive regulation of skeletal muscle cell differentiation
Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process.
regulation of mesenchymal cell apoptosis
regulation of mesenchymal cell apoptotic process
Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process.
negative regulation of mesenchymal cell apoptosis
negative regulation of mesenchymal cell apoptotic process
Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process.
positive regulation of mesenchymal cell apoptosis
positive regulation of mesenchymal cell apoptotic process
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
Any process that modulates the frequency, rate or extent of vasculogenesis.
Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis.
negative regulation of vascular morphogenesis
Any process that activates or increases the frequency, rate or extent of vasculogenesis.
positive regulation of vascular morphogenesis
Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.
regulation of apoptotic signalling pathway
regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.
negative regulation of apoptotic signalling pathway
negative regulation of apoptotic signaling pathway
Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
positive regulation of apoptotic signalling pathway
positive regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.
negative regulation of chromosome organisation
negative regulation of chromosome organization and biogenesis
negative regulation of maintenance of genome integrity
negative regulation of nuclear genome maintenance
negative regulation of chromosome organization
Any process that activates or increases the frequency, rate or extent of chromosome organization.
positive regulation of chromosome organisation
positive regulation of chromosome organization and biogenesis
positive regulation of maintenance of genome integrity
positive regulation of nuclear genome maintenance
positive regulation of chromosome organization
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
A directive information entity that describes an action the bearer will take.
action specification
data item
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
information content entity
A generically dependent continuant that is about some thing.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
directive information entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
data set
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
image
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
plan specification
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
measurement datum
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
figure
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
time stamped measurement datum
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
time sampled measurement data set
A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]
The act of moving any of the tissues and hard structures surrounding the mouth other than teeth, jaws or filter structures [NBO:AC]
The act of repeated grinding, tearing, and or crushing with teeth or jaws [NBO:SMAC]
chew
gnaw
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
"Movement behavior of the body or its parts."
"Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795]
regulation of behavior
Saccharomyces cerevisiae 'var. diastaticus'
A process that realizes a plan which is the concretization of a plan specification.
planned process
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
container
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position.
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A composite chromatic quality composed of hue, saturation and intensity parts.
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
A chromatic property that is the relative position of different hues or degrees of saturation.
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
A physical quality inhering in a bearer by virtue of the bearer's orientation in space.
A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.
A physical quality inhering in a bearer by virtue of the bearer's molecules being are aerially dispersed and perceived by an odorant receptor.
A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
The number of entities of this type that are part of the whole organism.
A physical quality of a process inhering in a bearer by virtue of the size of the bearer's maximum displacement from the 'normal' position, when periodic motion is taking place.
A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A physical quality of the thermal energy of a system.
A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
A quality in which events occur in sequence.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development.
A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers.
An achromatic color of maximum brightness; the color of objects that reflect nearly all light of all visible wavelengths.
A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency.
A color quality inhering in a bearer by virtue of the bearer's lacking color.
A directional quality inhering in a bearer by virtue of the bearer's direction from a higher to a lower point.
A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces east.
A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces west.
A directional quality inhering in a bearer by virtue of the bearer's direction from a lower to a higher point.
A hardness quality of being rigid and resistant to pressure.
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals).
A shape quality inhering in a bearer by virtue of the bearer's having parallel chains in undulate fashion on the border.
A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend.
A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature.
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
A quality of a single process inhering in a bearer by virtue of the bearer's once or in or a few unpredictable instances.
A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation.
A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement.
A quality inhering in a bearer by virtue of the bearer's existence.
A length quality which is relatively large.
A length quality which is relatively small.
A size quality which is relatively high.
A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view.
A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view.
A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view.
A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided.
A positional quality inhering in a bearer by virtue of the bearer's being overfilled.
A positional quality inhering in a bearer by virtue of the bearer's being upright in position or posture.
A positional quality inhering in a bearer by virtue of the bearer's having mistakenly taken course, way, or passage; ill-routed.
A positional quality inhering in a bearer by virtue of the bearer's being stretched out and lying at full length along the ground.
A spatial pattern inhering in a bearer by virtue of the bearer's involvement of only one part or side.
A structural quality inhering in a bearer by virtue of the bearer's being merged with another entity.
A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
A quality of a single process inhering in a bearer by virtue of the bearer's being marked by breaks or interruptions.
A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities.
A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
A shape quality inhering in a bearer by virtue of the bearer's having a somewhat elongated form with approximately parallel sides.
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
A color consisting of dark orange, red, of very low intensity.
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
A shape quality inhering in a bearer by virtue of the bearer's having a sinuate margin and rippled surface.
A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
A permeability quality inhering in a bearer by virtue of the bearer's being incapable of being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
A porosity quality inhering in a bearer by virtue of the bearer's being incapable of admitting the passage of gas or liquid through pores or interstices.
A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
A physical quality inhering in a bearer by virtue of the bearer's velocity multiplied by its mass.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction.
A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input.
A physical quality that exists by virtue of the rate of flow of the bearer across a given surface.
A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way.
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration.
A concentration which is higher relative to the normal or average.
A concentration which is lower relative to the normal or average.
A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density.
An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way.
An elasticity quality inhering in a bearer by virtue of the bearer's inability to recover its size and shape after deformation in any way.
A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the middle relative to another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity.
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter Y.
An odor quality inhering in a bearer by virtue of the bearer's lacking odour.
A variability quality inhering in a bearer by virtue of whether the bearer exhibits variation or change.
A quality inhering in a bearer by virtue of the bearer's power or force.
A spatial quality inhering in a bearer by virtue of the bearer's being located further from a more centrally located entity.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality that is independent of the EM wavelength range.
A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation.
A reflective quality restricted to a particular wavelength.
A scalar optical quality which obtains by the magnitude of the light emitted by the bearer.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given area.
A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given volume.
A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity.
A shape quality inhering in a bearer by virtue of the bearer's having thin filamentous extensions at its edge.
A surface feature shape quality inhering in a bearer by virtue of the bearer's having deeply undulating edges forming lobes.
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
A monadic quality of continuant that exists at the cellular level of organisation.
A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types.
A cellular potency that is the capacity to produce only one differentiated cell type.
Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.
A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity.
Less potent than multipotent, often thought of as precursor or progenitor cell status.
A cellular potency that is the capacity to form multiple differentiated cell types.
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body.
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel.
A structural quality inhering in a bearer by virtue of the bearer's having distinct structure.
A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure.
A physical quality inhering in a bearer by virtue of the rate of the bearer's angular movement about an axis; the angle rotated in a given time.
A physical quality inhering in a bearer by virtue of the bearer's disposition to rise or float in a fluid medium such as water or air.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base.
An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions.
An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions.
A quality inhering in a bearer by virtue of the bearer's decomposition into component parts.
A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity.
A structural quality inhering in a bearer by virtue of whether the bearer includes all its components.
A structural quality inhering in a bearer by virtue of the bearer's components no longer being in a single contiguous unit.
A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311).
An attachment quality inhering in a bearer by virtue of the bearer's lacking connection or association with another entity.
A sensitivity quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
A quality inhering in a bearer by virtue of the bearer's dependence on oxygen.
A quality inhering in a bearer by virtue of the bearer's independence on oxygen.
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together.
A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter).
A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s).
A functionality quality held by the bearer when the latter is able to perform a regular function(s).
A physical quality inhering in sound by virtue of the bearer's travelling speed in a given medium under specified conditions.
A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid.
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking.
A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s).
A mass which is lower than normal or average.
A mass which is higher than normal or average.
A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up.
A physical quality inhering in a bearer by virtue of the bearer's motion characteristic.
A physical quality that is the ability to contract or shrink.
A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium.
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
A concave quality inhering in a bearer by virtue of the bearer's forming or resembling an arch.
A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
A depth quality which is relatively high.
A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary.
A spatial pattern inhering in a bearer by virtue of the bearer's being marked by, consisting of, or diversified with patches.
A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form.
A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s).
A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s).
A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole.
A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary into the surface or boundary of another entity.
A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary and outwards in relation to the physical space occupied by another entity.
An 1-D extent quality which is equal to the length of the closed curve of a circle.
A spatial quality inhering in a bearer by virtue of the bearer's spatial positioning with respect to an additional entity.
An alignment quality inhering in a bearer by virtue of the bearer's being in a proper spatial positioning with respect to an additional entity.
An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning with respect to an additional entity.
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
A distribution which is relatively high.
An efficiency quality inhering in a bearer by virtue of the bearer's having efficiency.
A physical quality inhering in a bearer by virtue of the bearer's disposition to exert an attractive or repulsive force on other entities.
A magnetic quality inhering in a bearer by virtue of the bearer's ability to exert magnitism.
A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface.
A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted.
This refers to the disposition of the bearer.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it.
An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process.
A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts.
A quality inhering in a plant by virtue of the bearer's disposition to shed foliage.
A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part.
A quality inhering in a plant by virtue of the bearer's disposition to retain foliage.
A quality inhering in a plant by virtue of the bearer's disposition to being between evergeen and deciduous.
A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids.
A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate.
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave.
A conductivity quality inhering in a bearer by virtue of the bearer's disposition to spontaneous transfer of thermal energy from a region of higher temperature to a region of lower temperature.
A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity.
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
A thickness quality which lacks pattern.
A density which is higher relative to the normal or average.
A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome.
A density which is lower relative to the normal or average.
A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops.
A shape quality inhering in a bearer by virtue of the bearer's exhibiting disturbance of its smoothness or regularity.
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid.
A wetness quality that is relatively high.
A wetness quality that is relatively low.
A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions).
A structural quality inhering in a bearer by virtue of the bearer's being entwined and difficult to unravel.
A spatial pattern inhering in a bearer by virtue of the bearer's being situated at right angles to the horizon.
A positional quality inhering in a bearer by virtue of the bearer's being in the plane of the horizon.
A shape quality in a bearer by virtue of the bearer's curving inward.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter U.
A physical quality inhering in a bearer by virtue the bearer's disposition to being water-repellent; tending to repel and not absorb water.
A quality inhering in a bearer by virtue of the bearer's lacking affinity for water; tending to repel and not absorb water; tending not to dissolve in or mix with or be wetted by water.
A physical quality inhering in a bearer by virtue the bearer's disposition to having an affinity for water; it is readily absorbing or dissolving in water.
A quality inhering in a bearer by virtue of the bearer's disposition to having a strong affinity for water; tending to dissolve in, mix with, or be wetted by water.
A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being divided into three branches.
A circumference which is relatively low.
A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the south when it faces north.
A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces south.
A directional quality inhering in a bearer by virtue of the bearer's having one direction only.
A directional quality inhering in a bearer by virtue of the bearer's having two directions.
A directional quality inhering in a bearer by virtue of the bearer's direction approximating the shape of a circle.
A physical quality inhering in a bearer by virtue of the bearer's participation in movement.
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell.
A positional quality inhering in a bearer by virtue of the bearer's being positioned on opposite sides on the same plane.
A shape quality inhering in a bearer by virtue of the bearer's being roundish, a little inclining to be oblong.
A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change.
A variability of size which is relatively low.
A variability of size which is relatively high.
A shape quality inhering in a bearer by virtue of the bearer's parts or projections being interlocked; for example, the fingers of two hands that are clasped.
A shape quality inhering in a bearer by virtue of the bearer's having at least one salient angle on the margin.
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
A quality inhering in a bearer by virtue of the bearer's passing into solution.
A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance.
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
A quality that inheres in an entire organism or part of an organism.
Surface shape that refers to the inward or outward curvature of the surface.
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
Use this term or an is_a child of this term when the entire shape of the object is known.
A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave.
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers).
A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.
A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure.
A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical.
A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes.
A spatial pattern inhering in a bearer by virtue of the bearer's layered configuration.
A spatial pattern inhering in a bearer by virtue of the bearer's exhibiting a layered configuration.
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
A broken quality inhering in a bearer by virtue of the bearer's being separated into two contiguous wholes.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions.
A structural quality inhering in a bearer by virtue of the bearer's penetrating or permeating another substance or area.
A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity.
A spatial pattern inhering in a bearer by virtue of the bearer's structure resembling an irregular meshwork with cross-linking struts.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be eaten.
A physical quality inhering in a bearer by virtue of the bearer being suitable for use as food.
A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as food.
An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning towards an additional entity.
An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning away from an additional entity.
A shape quality inhering in a bearer by virtue of the bearer's being free of curves, bends, or angles.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
A quality inhering in a bearer by virtue of its constitution.
A shape quality inhering in a bearer by virtue of the bearer's being small or narrow in circumference or width in proportion to length or height.
A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle.
A quality inhering in a bearer that is shaped in the form of a fan.
An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of the letter V.
A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
A spatial quality inhering in a bearer by virtue of the bearer's being located far (not close to) in space in relation to another entity.
A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position.
A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
A quality inhering in a bearer by virtue of the bearer's being roundish, flattish shape, possibly with a slightly angled edge.
A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane.
Becoming flat but not necessarily completely flat.
Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels.
A quality inhering in a bearer by virtue of the bearer's being partially upright in position or posture.
A shape that inheres in a 3 dimensional entity.
A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges.
A structural quality of the collection or massing of one physical object within another physical object.
An increased number of physical objects that are accumulated within another physical object usually as a result of a failure to break down or remove objects in a timely manner.
A spatial quality inhering in a bearer by virtue of the bearer's being located at the same continuous distance relative to another object.
A structural quality inhering in a bearer by virtue of the bearer's underlying structure being capable of change.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is increased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter.
Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope).
Having a fringe or border of hairlike or fingerlike projections.
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
A temporal distribution pattern of process occurrences within a regulation/reference process.
A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the base of an organism relative to another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the stalk of an organism relative to another entity.
A quality inhering in a bearer by virtue of the bearer's upper parts die back to the rootstock at the end of the growing season.
A quality inhering in a bearer by virtue of the bearer's width being notably higher than its length.
Recurrent and often more or less cyclic alteration.
A concave 3-D shape that inheres in the bearer by virtue of the bearer's shape that is wider at one end and narrow in the middle.
Flattened from above downward; below the normal level or the level of the surrounding parts.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions.
Eosin stains acidophilic structures, hence eosinophilic is the same as acidophilic.
Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry.
Open to view or not covered by another entity.
A surface feature shape marked by large amounts of relief, often with multiple ridges and grooves in close association. Topographically complex.
A positional quality inhering in a bearer by virtue of the bearer touching another entity along a border or with a projecting part.
A positional quality inhering in a bearer by virtue of the bearer's position being displaced from a reference point.
A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures.
A surface feature shape in which the bearer's surface is highly topographical with ridges, pits, rugosity or other surface structures.
A positional quality inhering in a bearer by virtue of the bearer's being located at the same level as another entity.
A structural quality inhering in a bearer by virtue of the bearer bring gradually worn away.
A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen.
A positional quality inhering in a bearer by virtue of some aspect of the bearer extending to the position of another entity.
A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching.
A physical quality inhering in a bearer by virtue of the bearer's increased rate of change of the position.
A physical quality inhering in a bearer by virtue of the bearer's decreased rate of change of the position.
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer.
Positional quality in which an entity is located outside of another entity.
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
A positional quality inhering in a bearer by virtue of the bearer's having a slanting direction (neither perpendicular nor parallel) relative to another entity.
A positional quality inhering in a bearer by virtue of the bearer being level or even with another surface.
A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a funnel.
A variability quality inhering in the bearer by virtue of the bearer having a variable number or count of an entity.
Shape quality inhering in a bearer expanding outward, or having parts expanding outward, from a center point.
A positional quality inhering in a bearer by virtue of the bearer possessing an uninterrupted or unbroken connection or spatial distribution relative to the position of another entity.
A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other.
A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array.
A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline.
A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen.
A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids.
A shape that ineres in a bearer by virtue of the bearer's mass being distributed in a feather-like fashion.
A shape quality inhering in a bearer by virtue of the bearer's having an ornamental border consisting of short straight or twisted threads or strips hanging from cut or raveled edges or from a separate band.
A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a bowl.
A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio.
A high nuclear/cytolasmic ratio is 70% or higher.
A quality of an object that has a value that is normal or average.
A position which is relatively normal or average
A pressure which is relatively normal or average
A size quality which is relatively normal or average
An area which is relatively normal or average
A depth quality which is relatively normal or average
A volume which is relatively normal or average
A width which is relatively normal or average
A speed which is relatively normal or average
A velocity which is relatively normal or average
The four cardinal directions or cardinal points are the directions north, east, south, and west, commonly denoted by their initials, N, E, S, W. East and west are at right angles to north and south, with east being in the clockwise direction of rotation from north and west being directly opposite east.
North is one of the four compass points or cardinal directions. It is the opposite of south and is perpendicular to east and west.
East is one of the four cardinal directions or points of the compass. It is the opposite direction from west.
South is one of the four cardinal directions or compass points. South is the polar opposite of north and is perpendicular to east and west.
West is one of the four cardinal directions or points of the compass. It is the opposite direction from east.
The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute)
A rate of occurrence that is relatively high.
A rate of occurrence that is relatively low.
A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.
A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions.
A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
quality of interaction of a substance with electromagnetic radiation
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
May be of the same or different species.
collection of organisms
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.
multispecies community
Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.
ecological community
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
A multi-species collection of organisms that consists of two or more microbes from at least two species.
multi-species collection of microbes
An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness.
A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22
microbiota
The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another.
microbial community
An embryonic plant structure (PO:0025099) that is the body of a developing plant embryo (PO:0009009) attached to the maternal tissue in an plant ovule (PO:0020003) by a suspensor (PO:0020108).
The embryo proper is the entire embryo exclusive of the suspensor.
A microsporangium wall (PO:0025307) that is part of an anther (PO:0009066).
Has an outer epidermis (exothecium) and an endothecium and may have additional layers. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A plant structure (PO:0005679) which is a whole organism.
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
A plant structure (PO:0009011) that is grown or maintained in vitro.
estructura vegetal in vito (Spanish, exact)
In vitro growth is defined as microbe-free growth in a sterile, culture environment, usually in the laboratory. An example of a sterile culture environment is growth on or in a nutrient medium in a Petri dish, culture flask or test tube. Microbes may be intentionally added to the culture environment, such as in co-culture with Agrobacterium.
A plant cell (PO:0009002) that is grown or maintained in vitro.
Includes isolated plant cells and small plant cell aggregates that proliferate while suspended in sterile liquid medium or spread on a solid agar medium.
A cultured plant cell from which the entire plant cell wall has been removed.
The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase. The cultured plant cell may be in suspension culture or from callus culture on solid media.
A cultured plant cell that was derived from leaf tissue.
c&#233lula cultivada de hoja (Spanish, exact)
May be derived from cultured plant callus or plant protoplast that was induced from a segment of leaf. In the case of the plant protoplast, after the re-establishment cell walls.
A cultured plant cell that was derived from root tissue.
c&#233lula cultivada de ra&#237z (Spanish, exact)
May be derived from cultured plant callus or plant protoplasts induced from a segment of root. In the case of the plant protoplast, after the re-establishment plant cell walls.
A plant callus (PO:0005052) grown or maintained in vitro.
Cultured plant callus may induced to form from plant protoplasts or cultured plant cells in suspension culture. After supplementation with the appropriate plant growth regulators, further differentiation may lead to the development of plant tissues, plant organs and ultimately, a whole plant.
A plant embryo (PO:0009009) that is grown or maintained in vitro.
Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).
A somatic plant embryo grown and maintained in vitro.
embri&#243n som&#225tico cultivado (Spanish, exact)
Cultured somatic plant embryos are commonly induced after the formation of callus from an explant and treatment with plant growth regulators.
Hook-like structure which develops at the apical part of the hypocotyl in dark-grown seedlings in dicots.
A vascular leaf (PO:0009025), borne on the stem (PO:0009047).
In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches. May ocur singly or pairs/whorls of leaves.
A vascular leaf (PO:0009025) born in a circular pattern around a stem (PO:0009047) with compressed stem internodes (PO:0020142).
Arabidopsis, vegetative development is characterized by the production of the rosette leaves.
A phyllome primordium (PO:0025128) that develops from a cotyledon anlagen (PO:0025432) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a cotyledon (PO:0020030).
portion of cotyledon primordium tissue (exact)
primordio de cotiled&#243n (Spanish, exact)
A root primordium (PO:0005029) that is part of a root (PO:0009005) and is committed to the development of a lateral root (PO:0020121).
portion of lateral root primordium tissue (exact)
primordio de ra&#237z lateral (Spanish, exact)
A lateral root primordium may arise from cells of a pericycle (PO:0006203) in a root, as in most seed plants (pericyclic lateral root primordium; PO:0025492), or from cells of an endodermis (PO:0000252) or other tissue in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493). Transition from lateral root primordium to lateral root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147), which can occur before the lateral root penetrates the exterior of the parent root.
A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025).
portion of vascular leaf primordium tissue (exact)
A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003).
portion of ovule primordium tissue (exact)
The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210).
A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
portion of gynoecium primordium tissue (exact)
Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).
A phyllome primordium (PO:0025128) that develops from a petal anlagen (PO:0025484) and is committed to the development of a petal (PO:0009032).
portion of petal primordium tissue (exact)
primordio de p&#233talo (Spanish, exact)
A portion of plant substance (PO:0025161) composed of cutin (PO:0025385), a polyester matrix of hydroxy- and hydroxy epoxy fatty acids C16 and C18 chains, embedded and overlayed with cuticular wax (PO:0025386) and forming a layer on the surface of a plant epidermis (PO:0005679).
The plant cuticle is produced in and secreted by epidermal cells (PO:0004013) of leaves (PO:0025034), stems (PO:0009047), fruits (PO:0009001), and other aerial plant structures. It has as parts an inner cuticle proper (PO:0025387) and an outer layer of epicuticular wax (PO:0025388).
A cardinal organ part (PO:0025001) which is the apical portion of the root (PO:0009005), and includes the root apical meristem (PO:0020147) and root cap (PO:0020123).
The portion of the primary root including the meristem and root cap.
punta de la ra&#237z primaria (Spanish, exact)
A root tip (PO:0000025) of a lateral root (PO:0020121).
punta de la ra&#237z lateral (Spanish, exact)
A collective organ part structure composed of two or more layers of various tissues that is a partition that divides a cavity formed by the fusion of two or more organs.
A septum is formed by the fusion of the walls of two adjacent organs (ovary walls or anther walls), for example, the partition between two sections of an orange, seen in cross-section.
A portion of periderm tissue (PO:0005046) characterized by the presence of intercellular spaces between the cells of the phellem (PO:0004003) and phelloderm (PO:0005050)
Lenticels are produced by the cork cambium (PO:0005599) and facilitate gas exchange.
A portion of plant tissue consisting of four microspores that remained joined together shortly after meiosis. Each cell will give rise to a male gametophyte.
t&#233trada de las microsporas (Spanish, exact)
A valve that is a part of a fruit that splits apart when the fruit dehisces.
A valve may develop from an entire carpel (as in Brassicaceae) or from part of a carpel (as in Fabaceae). If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A maximal portion of vascular tissue (PO:0009015) in a whole plant (PO:0000003), collective plant structure (PO:0025497), multi-tissue plant structure (PO:0025496), or cardinal part of multi-tissue plant structure (PO:0025498).
A vascular system consist of the totality of the portions of vascular tissue in their specific arrangement in a plant structure. May include other portions of plant tissue or plant cells (PO:0009002) of other types, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).
A vascular system (PO:0000034) that is part of a cotyledon (PO:0020030).
sistema vascular del cotiled&#243n (Spanish, exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a vascular leaf (PO:0009025).
sistema vascular de la hoja (Spanish, exact)
A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
&#225pice del epiblasto (epiblastema) (Spanish, exact)
Cell produced by the fusion of sperm cell nucleus and two polar nuclei of the central cell (or diploid secondary endosperm nucleus, in cases where two polar nuclei fuse together before double fertilization). The first cell of the endosperm, often triploid.
c&#233lula primaria del endosperma (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a shoot axis (PO:0025029).
sistema vascular del eje del epiblasto (epiblastema) (Spanish, exact)
Enlargement or swelling at position of dormant adventitious root primordium (on the stem), inhabited by nitrogen-fixing bacteria.
n&#243dulo de la ra&#237z adventicia (Spanish, exact)
Unlike the root nodules, these contain functioning chloroplasts in the nodule cortex and are therefore capable of carbon fixation. Note: stem nodule is commonly used term for this structure, although the nodules are formed at positions of dormant adventitious root primordia.
One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with silica cell.
c&#233lula de corcho epid&#233rmica (Spanish, exact)
c&#233lula suber&#237 epid&#233rmica (Spanish, exact)
Developmentally different from periderm cork cell (i.e., phellem), produced by cork cambium. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025).
A root (PO:0009005) that develops from shoot axis (PO:0025029) tissue.
epiblasto (epiblastema) que se origina en la ra&#237z (Spanish, exact)
A shoot-borne nodal root (PO:0003005) formed at a stem base (PO:0008039).
A shoot-borne nodal root (PO:0003005) formed at a stem node (PO:0020141) above the ground and growing directly into the soil.
This term is perhaps best defined functionally to prop the plant up, but sometimes prop roots may also act as breathing roots. Compare to pneumatophore (PO:0025357), which is a lateral root that grows upwards from below the soil or water surface.
A root (PO:0009005) that is initiated in a developing plant embryo (PO:0009009).
ra&#237z embri&#243nica (Spanish, exact)
An embryo root (PO:0000045) formed within the scutellar node (PO:0004708) of the plant embryo (PO:0009009) in some monocotyledonous plants.
A portion of leaf epidermis (PO:0006016) that is part of a leaf lamina (PO:0020039).
epidermis de la l&#225mina de la hoja (Spanish, exact)
If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a leaf lamina (PO:0020039).
sistema vascular de la l&#225mina de la hoja (Spanish, exact)
A portion of leaf lamina epidermis (PO:0000047) that covers the abaxial/lower surface of a leaf lamina (PO:0020039).
epidermis abaxial de la l&#225mina de la hoja (Spanish, exact)
A portion of leaf lamina epidermis (PO:0000047) that covers the adaxial/upper surface of a leaf lamina (PO:0020039).
epidermis adaxial de la l&#225mina de la hoja (Spanish, exact)
A portion of leaf epidermis (PO:0006016) that is part of a petiole (PO:0020038).
epidermis del pec&#237olo (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a petiole (PO:0020038).
sistema vascular del pec&#237olo (Spanish, exact)
A portion of cortex (PO:0005708) that is part of a petiole (PO:0020038).
cortex (corteza) del pec&#237olo (Spanish, exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a petal (PO:0025218).
sistema vascular de p&#233talo (Spanish, exact)
An undeveloped shoot system (PO:0009006).
A bud that develops into an inflorescence.
A bud (PO:0000055) that develops into a vegetative shoot system (PO:0025607).
An initial cell (PO:0004011) that is part of a root apical meristem (PO:0020147) and by division gives rise to two cells, one of which remains in the meristem, while the other is produces different root cells.
c&#233lula inicial de la ra&#237z (Spanish, exact)
A root initial cell (PO:0000059) that produces root cortex (PO:0000258) and root endodermis (PO:0005059). In direct contact with quiescent center (PO:0020149).
c&#233lula inicial del cortex/endodermis de la ra&#237z (Spanish, exact)
root cortex-endodermis stem cell (exact)
A root initial cell (PO:0000059) that produces lateral root cap cells and root epidermis (PO:0006036).
c&#233lula inicial del caliptra de la ra&#237z lateral (Spanish, exact)
lateral root-cap epidermal initial (exact)
lateral root-cap-epidermal stem cell (exact)
An plant epidermal initial cell (PO:0000349) that undergoes several rounds of uneven division, each time giving rise to a larger daughter cell that differentiates into an epidermal ground cell and a smaller daughter cell that remains meristematic, until the meristematic cell (PO:0004010) differentiates into a guard mother cell (PO:0000351).
inicial estom&#225tica (meristemoide inicial) (Spanish, exact)
A procambial cell (PO:0025258) that is part of a leaf procambium (PO:0025259).
c&#233lula procambial de la hoja (Spanish, exact)
Leaf procambial cells may be derived from the shoot apical meristem or can arise throughout the mesophyll of a developing leaf.
A pericycle cell that is adjacent to the protoxylem of a vascular bundle.
c&#233lula del polo xilem&#225tico del periciclo (Spanish, exact)
Xylem pole pericycle cells are cells in the pericycle that are adjacent to the protoxylem pole of a vascular bundle. Pericycle cells that are adjacent to other xylem cells in the vascular bundle are not considered xylem pole pericycle cells. Xylem pole pericycle cells may retain some meristematic activity and are the site of lateral root initiation.
A pericycle cell that is adjacent to the protophloem of a vascular bundle.
c&#233lula del polo floem&#225tico del periciclo (Spanish, exact)
Phloem pole pericycle cells are cells in the pericycle that are adjacent to the protophloem pole of a vascular bundle. Pericycle cells that are adjacent to other phloem cells in the vascular bundle are not considered phloem pole pericycle cells. Phloem pole pericycle cells are distinct from xylem pole pericycle cells in that they display cytoplasmic characteristics of a more differentiated status.
A parenchyma cell of the mesophyll of a hydathode found between the xylem endings and the epidermis.
Proposed to be involved in the retrieval of solutes from the xylem sap.
A root (PO:0009005) that forms one or more clusters of closely spaced lateral roots (PO:0020121) of limited growth along its length.
The terms proteoid root, cluster root, and root cluster have all been used in the literature to describe either the proteoid root axis or clusters of rootlets, and caution should be taken when comparing studies because the definitions of these terms vary (Watts and Evans, 1999; Plant Physiology).
A parenchyma cell (PO:0000074) that is adjacent to a sieve tube element (PO:0000289) and arises from the same phloem mother cell (PO:0000400) as the sieve tube element.
c&#233lula acompa&#241iante (Spanish, exact)
Companion cells are connected to sieve tube elements through plasmodesmata and function in phloem loading of small molecules, including photosynthate (either sucrose or raffinose-family oligosaccharides). May participate in phloem sucrose loading (GO:0009915). Molecules can be loaded into the companion cells from surrounding cells through either symplastic (via plasmodesmata) or apoplastic (transmembrane) transport. Unlike sieve tube elements, companion cells retain their nuclei and other organelles at maturity. A sieve tube element may have one or more or no companion cells associated with it. This term should not be used for other types of parenchyma cells (PO:0000074) that do not arise from the same phloem mother cell as a sieve tube element. Companion cells are found in angiosperms, as compared to albuminous cells (PO:0025412), which are found in non-angiosperm vascular plants. Companion cells may be specialized as transfer companion cells (PO:0025458), ordinary companion cells (PO:0025459), or intermediary companion cells (PO:0025460). Multiple types of companion cells may be found in the same plant.
A relatively unspecialized ground tissue cell with a nucleate protoplast.
c&#233lula parenquim&#225tica (Spanish, exact)
An elongated plant cell with unevenly thickened non-lignified primary walls that is alive at maturity.
c&#233lula colenquim&#225tica (Spanish, exact)
A parenchyma cell containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue.
c&#233lula clorenquim&#225tica (Spanish, exact)
A ground tissue cell (PO:0025030) with a lignified secondary cell wall.
c&#233lula esclerenquim&#225tica (Spanish, exact)
May be dead at maturity. The secondary cell wall of a sclerenchyma cell is often thicker than other cell types in the same plant structure, but it is not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Compare with collenchyma cells (PO:0000075) that are always alive at maturity, have irregularly thickened primary cell walls, and do not have lignified secondary cell walls. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness. Sclerenchyma cells include plant fiber cells (PO:0025407) and sclerid cells (PO:0025418).
A cell with wall ingrowths (or invaginations) that increase the surface of the plasmalemma.
c&#233lula de transferencia (Spanish, exact)
Appear to be specialized for short-distance transfer of solutes. Transfer cells can occur anywhere there is a junction between two individuals, such as between a sporophyte and a gametophyte, or between a parasitic plant and its host.
An elongated cambial initial cell (PO:0000295) with approximately wedge-shaped ends that is part of the vascular cambium (PO:0005598) and gives rise to axial cells.
c&#233lula inicial fusiforme (Spanish, exact)
A cambial initial cell (PO:0000295) that gives rise to ray cells of the secondary xylem (PO:0005848) and secondary phloem (PO:0005043).
c&#233lula inicial de rayo (Spanish, exact)
A gamete (PO:0025006) produced by an antheridium (PO:0025125) or a microgametophyte (PO:0025280).
c&#233lula esperm&#225tica o esperma (Spanish, exact)
The sperm cell is usually smaller than the egg cell. Male gametes may be defined as the motile gamete, rather than the smaller gamete. Plant sperm cells lack a cell wall.
A portion of shoot system epidermis (PO:0006035) that is part of a shoot axis (PO:0025029).
epidermis del eje del tallo (Spanish, exact)
A shoot epidermal cell (PO:0025165) that surrounds a trichome (PO:0000282) and provides its support.
cell located at the base of the trichome (related)
A portion of plant tissue (PO:0009007) that has as part a separation layer (PO:0006211) and a protective layer (PO:0006212), and is involved in the abscission (GO:0009838) of a fruit (PO:0009001), flower (PO:0009046), leaf (PO:0025034) or other plant structure (PO:0009011).
Cell, usually two in number, in the micropylar end of the embryo sac of angiosperms associated with the egg in the egg apparatus.
A portion of endosperm (PO:0009089) tissue in which at least the first karyokinesis is not followed by cytokinesis.
endosperma con n&#250cleos libres (Spanish, exact)
A portion of endosperm (PO:0009089) in which the first karyokinesis event is accompanied by cytokinesis.
A portion of plant tissue (PO:0009007) that is the region of the endosperm closest to the micropyle of the seed.
endosperma micr&#243pilar (Spanish, exact)
A portion of plant tissue (PO:0009007) that is the part of the endosperm (PO:0009089) nearest the chalazal region of the plant ovule (PO:0020003) and forming a cyst-like structure.
Not in current literature. More like an attribute.
A portion of shoot system epidermis (PO:0006035) that is part of a nectary (PO:0009035) .
A portion of cortex (PO:0005708) that is part of a shoot axis (PO:0025029).
cortex del eje del epiblasto (epiblastema) del tallo (Spanish, exact)
portion of shoot axis cortex tissue (exact)
An area of densely packed cells in the shoot apex that divide infrequently.
Functions as a population of stem cells that replenishes the meristem.
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
The region of the shoot apical meristem that lies below the central zone and is flanked by the peripheral zone.
A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
A meristem that gives rise to an inflorescence.
meristema de la inflorescencia (Spanish, exact)
A shoot system meristem (PO:0006079) formed in an axil (PO:0025224).
meristema de yema axilar (Spanish, exact)
A megaspore(s) that forms an embryo sac.
If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
In monosporic and bisporic megasporogenesis: the megaspore(s) that would not participate in megagametogenesis.
A portion of ground tissue (PO:0025059) that is the inner most layer of a cortex (PO:0005708) and has a casparian strip in its anticlinal cell walls.
Forms a sheath around the vascular system. It may have secondary walls later, part_of cortex.
A root epidermal cell (PO:0025164) that develops from a trichoblast (PO:0000262) and has as part a root hair (GO:0035618).
c&#233lula del pelo de la ra&#237z (Spanish, exact)
Compare with non-hair root epidermal cell (PO:0000263). This term is for an entire epidermal cell that contains a root hair extension. To describe only the cell extension, see root hair (GO:0035618) or root hair tip (GO:0035619).
A portion of cortex (PO:0005708) that is part of a root (PO:0009005).
In dicots and gymnosperms, the cortex consists of mainly parenchyma cells. In monocots sclerenchyma develops in addition to parenchyma.
A root epidermal cell (PO:0025164) that is the smaller cell produced by the asymmetric division of an epidermal intial cell (PO:0000349) and gives rise to a root hair (GO:0035618).
A root epidermal cell (PO:0025164) that develops from an epidermal initial (PO:0000349) and does not have as part a root hair (GO:0035618).
Compare to root hair cell (PO:0000256), which develops from a trichoblast (PO:0000262).
A portion of primary xylem (PO:0000272) tissue that has as part one or more protoxylem tracheary elements (PO:0025575) embedded in parenchyma (PO:0005421) tissue.
Develops while the vascular tissue (PO:0009015) is still elongating. When protoxylem tracheary elements (PO:0025575) are destroyed they may become obliterated by surrounding parenchyma cells (PO:0000074). Protoxylem has smaller elements than the metaxylem (PO:0000372).
A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.
It may be difficult to distinguish xylem fiber cells, especially fiber tracheids (PO:0000355), from tracheary elements (PO:0000290). Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading to the cell lumen through the cell wall.
A unicellular or multicellular plant structure (PO:0009011) that forms a non-sclerified outgrowth from the epidermis (PO:0005679).
This class is the union of unicellular trichome (PO:0025537) and multicellular trichome (PO:0025162). A trichome can vary in length and shape and may be branched or unbranched. It may be glandular or non-secretory.
A native plant cell (PO:0025606) that markedly differs in form, size, or contents from other cells in the same tissue.
Often contains deposit of minerals or products of secondary metabolism. May have a specialized function.
A shoot epidermal cell (PO:0025165) associated with a stomatal pore (PO:0008032) and at least morphologically distinguishable from the other epidermal cells.
c&#233lula subsididaria (Spanish, exact)
助細胞,副細胞（気孔）(auxiliary cell, synergid) (Japanese, exact)
A sieve element (PO:0025406) that is part of a sieve tube (PO:0025416) and has as parts sieve areas aggregated into sieve plates (GO:0097218).
miembro del tubo criboso (Spanish, exact)
Sieve tube elements have sieve areas that are specialized into those with wide pores in sieve plates and those with narrow pores in lateral sieve areas. Sieve tube elements may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells (PO:0025415), which have less pronounced specialization of sieve areas and no sieve plates.
A native plant cell (PO:0025606) that has a lignified cell wall with secondary thickening and bordered pits.
Tracheary elements are dead at maturity, are more or less elongated, and have pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).
A shoot epidermal cell (PO:0025165) that is one of a pair of cells flanking the stomatal pore (PO:0008032).
They cause the opening and closing of the pore by changes in turgor.
An initial cell (PO:0004011) that is part of the vascular cambium (PO:0005598) or cork cambium (PO:0005599), and by periclinal divisions, produces cells to the outside or inside of the cambial axis.
c&#233lula inicial del cambium (Spanish, exact)
A tracheary element (PO:0000290) that has no perforations in its cell wall.
May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003), it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).
A portion of parenchyma tissue (PO:0005421) that is part of a nectary (PO:0009035).
par&#233nquima nectarifero (Spanish, exact)
A shoot epidermal cell (PO:0025165) that is relatively unspecialized at maturity.
c&#233lula del pavimento epidermal (Spanish, exact)
May have sinuous anticlinal cell walls that overall give a jigsaw like appearance to the epidermis. Pavement cells are epidermal cells that are not directly associated with a stomatal complex or trichome at maturity, but they share similar developmental origins.
An initial cell (PO:0004011) that is part of an plant epidermis (PO:0005679) and gives rise to specialized cells.
c&#233lula inicial de la epidermis (Spanish, exact)
A shoot epidermal cell (PO:0025165) that divides to produce the guard cells (PO:0000293).
c&#233lula madre de la c&#233lula guardiana (Spanish, exact)
A cell containing glucosinolates ("mustard oil glucosides") and myrosinases, enzymes hydrolyzing the glucosinolates.
A ground tissue cell that is part of an exodermis or an endodermis and remains thin walled when the associated cells develop thick secondary walls.
A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.
Fiber tracheids generally have pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading to the cell lumen through the cell wall.
A portion of primary xylem (PO:0005849) tissue that has as part one or more metaxylem tracheary elements (PO:0025576) embedded in parenchyma (PO:0005421) tissue and may contain xylem fiber cells (PO:0000274).
Metaxylem has larger tracheary elements (PO:0000290) than the protoxylem (PO:0000272), and develops after the formation of the protoxylem, once elongation of the plant axis (PO:0025004) has completed.
A cambial initial cell (PO:0000295) which is destined to differentiate into secondary phloem.
c&#233lula madre del floema (Spanish, exact)
Phloem islands can be formed in the middle of the xylem.
A native plant cell (PO:0025606) which is a whole plant (PO:0000003) in the plant zygote stage (PO:0001097).
A plant zygote is a whole plant that is a single cell formed by fertilization (syngamy).
A sporocyte (PO:0006204) that produces four haploid (1n) megaspores (PO:0020019).
A multi-tissue plant structure development stage (PO:0025571) that has as primary participant a single fruit (PO:0009001).
stage 17 flower in Arabidopsis (related)
stage 18 flower in Arabidopsis (related)
stage 19 flower in Arabidopsis (related)
stage 20 flower in Arabidopsis (related)
Defined by characteristic morphological, structural, histological or other visible features of a fruit. Includes as subclasses fruit formation stage (PO:0025501) and fruit ripening stage (PO:0025502). May have as part a seed development stage (PO:0001170). This stage applies to an individual fruit. For development stages of a whole plant (PO:0000003) based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.
A vascular leaf initiation stage (PO:0007040) during which the vascular leaf founder cells (PO:0025592) of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).
vascular leaf founder cell formation stage (exact)
The initial stage of leaf development when cells in the shoot apical meristem (PO:0020148) are already determined to form a vascular leaf primordium (PO:0000017), but the primordium is not yet morphologically distinguishable.
Stages of development of the anther defined by characteristic morphological, cytological, histological or other visible features.
An initial stage during which archesporial cells arise in four corners of L2 layer. Change in shape of primordia to more oval.
Stage during which the microsporocytes become conspicuous.
A microgametophyte development stage (PO:0025602) during which the pollen (PO:0025281) develops.
pollen development in Arabidopsis (related)
Stage during which diploid pollen mother cells become separated from each other and from tapetum by a callose wall.
C callose wall formation in pollen mother cells stage
Stage during which pollen mother cells undergo meiosis to form tetrads of microspores.
Stage of microgametophyte development during which the callose wall between the tetrads breaks down and haploid microspores are released and lie freely in locules.
An initial stage during which the archesporial cells divide to give rise to primary parietal and sporogenous cells.
Stage of microgametophyte development during which the microspores round up and small vacuoles appear in their cytoplasm. The microspore walls thicken due to the formation of the exine.
Stage of microgametophyte development during which a large vacuole is formed in each microspore causing a rapid increase in size and a displacement of the nucleus to one side.
Stage of microgametophyte development during which the asymmetric, first mitotic division of the microspores occurs producing a large vegetative cell and small generative cell, located near pollen wall.
A pollen development stage (PO:0001007) during which the generative cell (PO:0020097) undergoes mitotic division to form two male gametes, the pollen sperm cells (PO:0025121).
tricellular pollen development stage (exact)
In taxa with mature two-celled pollen (PO:0025281), the second mitotic division takes place after pollen germination (GO:0009846), in the germinating pollen tube cell (PO:0025195). Note: This term overlaps with the GO BP term: generative cell mitosis (GO:0055047): The process in which the generative cell divides by mitosis to form two haploid cells. These will subsequently differentiate into sperm cells.
Stage of microgametophyte development during which the pollen reaches mature stage and desiccates.
pollen stage 10 in Arabidopsis (related)
Mature pollen stages is reached at three-celled pollen in some angiosperms (maize, rice and Arabidopsis), while in others, the maturepollen has two haploid cells (tobacco, snapdragon).
The final stage in the life cycle of the male gametophyte. Upon rehydration, mature pollen grain forms a tubular outgrowth, the pollen tube, which carries the male gametes.
germinated pollen grain in Arabidopsis (related)
Stage during which the primary parietal and primary sporogenous layers are derived from archesporial cells.
B formation of primary parietal and sporogenous cells stage
A vascular leaf initiation stage (PO:0001051) during which a vascular leaf primordium (PO:0000017) forms in the peripheral zone (PO:0000225) of the vegetative shoot apical meristem (PO:0020148).
The vascular leaf primordium (PO:0000017) develops from the vascular leaf anlagen (PO:0025431).
vascular leaf primordium formation stage
Stage of leaf development when a hood-shaped primordium is formed, partially enclosing P1 and SAM, as in Poaceae.
A vascular leaf expansion stage (PO:0001052) when conical P3 leaf completely encloses SAM, and the ligule (PO:0020105) primordium is visible.
A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf lamina (PO:0020039) occurs.
rapid elongation of vascular leaf lamina stage
A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf sheath (PO:0020104) occurs.
Stage during which the four-lobed anther pattern with two developing stomium regions (notch) are formed.
Stage during which the four clearly defined locules are established. All anther cell types present and microspore mother cells appear.
Stage immediately following meiosis, during which the tetrads of microspores are still hold together, enclosed by the callose wall.
The stage at which a root is elongating.
Benfey's stage 2 of root development (related)
In some plant species this stage is subdivided into distal and proximal elongating zones.
An anther development stage (PO:0001004) during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.
Microspores within single locule are at unicellular stage.
E anther wall tapetum degeneration initiated stage
Stage during which anther becomes bilocular, after degeneration and breakage of septum below stomium.
Stage during which the dehiscence of anthers occurs. Anther breaks along stomium and pollen is released.
Stage during which the senescence of anther and stamen occurs. Shrinkage of cells and anther structure takes place.
A seed development stage (PO:0001170) during which the mature seed reaches a low moisture content.
The initial stage of endosperm development during which the chalazal and micropilar domains are established.
chalazal and micropylar domain establishment stage
Stage of endosperm development during which the functional specialization of the maturing endosperm occurs.
functional specialization of the endosperm stage
Stage of calyx development defined by differentiation and expansion of sepal.
sepal differentiation and expansion stage
Stage of calyx development when sepal is fully expanded.
A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).
A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).
A phyllome development stage (PO:0025579) that has as a primary participant a lodicule (PO:0009036).
A phyllome development stage (PO:0025579) during which the development of vascular leaves (PO:0009025) and non-vascular leaves (PO:0025075) occurs.
leaf development in Arabidopsis (related)
A vascular leaf development stage (PO:0025570) which begins with the onset of the vascular leaf anlagen formation stage (PO:0001003) and ends with the termination of the vascular leaf primordium polarity determination stage (PO:0001052).
leaf initiation in Arabidopsis (related)
Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.
A vascular leaf development stage (PO:0025570) during which vascular leaf size increases primarily through cell expansion.
leaf expansion stage in Arabidopsis (related)
During this stage leaf shaping (GO:0010358) occurs which is defined as the developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.
A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and ends with the onset of the vascular leaf senescence stage (PO:0001054).
fully expanded leaf stage in Arabidopsis (related)
A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.
leaf senescence stage in Arabidopsis (related)
Stage of lemma development that begins when the lemma primordia arise.
The lemma primordium forms in 1/2 alternate phylotaxy in rice spikelet.
Stage of lemma development defined by differentiation and expansion of lemma.
lemma differentiation and expansion stage
Stage of lemma development when lemma is fully expanded.
Stage of palea development that begins when the palea primordia arise.
The palea primordium forms in 1/2 alternate phylotaxy in rice spikelet.
Stage of microgametophyte development during which the small generative cell moves inward, becoming completely surrounded by the cytoplasm of the vegetative cell.
Stage of palea development defined by differentiation and expansion of palea.
palea differentiation and expansion stage
Stage of palea development when palea is fully expanded.
Stage of lodicule development that begins when the lodicule primordia arise.
Two lodicules form on the side of the lemma in rice spikelet.
Stage of microgametophyte development during which the generative cell undergoes a mitotic division to form two male gametes, the sperm cells.
N second mitotic division stage in germinating pollen
Stage of lodicule development defined by differentiation and expansion of lodicule.
lodicule differentiation and expansion stage
A plant embryo development stage (PO:0007631) that occurs during the interval between the beginning of rapid elongation of the plant embryo axis (PO:0019018) and plant embryo cotyledons (PO:0025470), and the onset of a plant embryo true leaf formation stage (PO:0001095), when present, or a mature plant embryo stage (PO:0001081).
curled cotyledon stage in Arabidopsis (related)
During this stage, the plant embryo (PO:0009009) continues to undergo a process of developmental growth (as a result of both cell division (GO:0051301) and cell expansion (GO:0016049), which ends with the onset of a mature plant embryo stage (PO:0001081). For species that develop true leaves in the plant embryo, (vascular leaves (PO:0009025) that develop after the cotyledons (PO:0020030) or coleoptile (PO:0020033)), growth may continue in the plant embryo true leaf formation stage (PO:0001095). For other species, the plant embryo transitions directly from a plant embryo cotyledonary stage (PO:0001078) to a mature plant embryo stage (PO:0001081).
Stage of lodicule development when lodicule is fully expanded.
A plant embryo development stage (PO:0007631) during the interval between when a plant embryo (PO:0009009) has stopped developmental growth involved in morphogenesis (GO:0060560) and one of the following: the beginning of the seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
In some seed plants, this occurs some time after the fruit ripening stage (PO:0025502) and after the dispersal of the seed (PO:0009010). This stage may be very short in plants that do not enter a plant embryo dormant stage (PO:0025377).
A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
A plant embryo development stage (PO:0007631) that occurs during the interval between the beginning of elongation of the plant embryo axis (PO:0019018), with the formation of a plant embryo coleoptile (PO:0025286), a plant embryo shoot apical meristem (PO:0006362) and root apical meristem (PO:0020147), and ends with the onset of a plant embryo true leaf formation stage (PO:0001095), when present, or a mature plant embryo stage (PO:0001081).
SAM and radicle formation stage (related)
This stage occurs in grasses and other monocots.
A plant embryo development stage (PO:0007631) that occurs during the interval between the beginning of the formation of the first vascular leaf primordium (PO:0000017) in the plant embryo proper (PO:0000001), and the onset of a mature plant embryo stage (PO:0001081).
A true leaf is vascular leaf (PO:0009025) that forms after the formation of the cotyledons (PO:0020030) or a coleoptile (PO:0020033). Not all species form true leaves in the plant embryo development stage (PO:0007631). If it occurs, a plant embryo true leaf formation stage is preceded by either a plant embryo cotyledonary stage (PO:0001078) or a plant embryo coleoptilar stage (PO:0001094), depending upon the species.
One cell stage that takes place following the fertilization, produced by the fusion of sperm cell nucleus and one or more polar nuclei.
A sporophyte development stage (PO:0007134) that occurs during the interval between fertilization and the first cell division of the plant zygote (PO:0000423).
Precedes the sporophyte vegetative stage (PO:0007134). Refers to the GO biological process term fertilization (GO:0009566).
Differentiation of aleurone layer, the outermost endosperm tissue, and the internal starchy tissue.
formation of aleurone and starchy layers stage
A multi-tissue plant structure development stage (PO:0025571) that has as primary participant a seed (PO:0009010).
seed development in Arabidopsis (related)
Includes the stages of seed development, from fertilization to the dry or quiescent state. May have as part an embryo development stage.
A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).
eight-celled stage in Arabidopsis (related)
two-celled stage in Arabidopsis (related)
In the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), or other embryos that arise through apogamy, the plant proembryo stage (PO:0001180) begins after the division of a single cell that is not a zygote. The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034) epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).
A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry (with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).
dermatogen stage in Arabidopsis (related)
late globular stage in Arabidopsis (related)
mid-globular stage in Arabidopsis (related)
During the plant embryo globular stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
Stage of calyx development that begins when the developing sepals enclose the floral meristem.
stage 4 flower in Arabidopsis (related)
Stage of calyx development that begins when the sepals enclose the floral bud.
stage 6 flower in Arabidopsis (related)
A portion of shoot system epidermis (PO:0006035) that has as parts two guard cells (PO:0000293) and a stomatal pore (PO:0008032). May also contain subsidiary cells (PO:0000284).
complejo estom&#225tico (Spanish, exact)
A native plant cell (PO:0025606) that is the lower-most cell formed after the first division of the plant zygote (PO:0000423) and is part of a plant embryo (PO:0009009).
The zygote divides to form an embryo apical cell and an embryo basal cell.
A tracheary element (PO:0000290) that is part of a xylem vessel (PO:0025417) and has as parts perforation plates.
Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fibers (PO:0004520) and fiber tracheids are present, the libriform fibers usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.
A cardinal part of multi-tissue plant structure (PO:0025498) which is composed of the shriveled remains of the silk (PO:0006488), and the base of the style (PO:0009074), and is located on the distal end of a developing or mature kernel (caryopsis fruit; PO:0030104).
A region of the root between the meristem and the region of rapid elongation in which isodiametric growth (cell expansion) occurs.
A shoot-borne root (PO:0000042) that forms at a shoot axis node (PO:0005004).
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a root (PO:0009005).
sistema vascular de la ra&#237z (Spanish, exact)
This term was brought back from OBSOLETE node (original reason for OBSOLETE: synonym of term stele). Since stele encompasses both vascular system and the pith, in roots with pith, vascular system and stele are not synonymous.
A root differentiation zone that is part of a primary root.
zona de diferenciaci&#243n de la ra&#237z primary (Spanish, exact)
A root differentiation zone that is part of a lateral root.
zona de diferenciaci&#243n de la ra&#237z lateral (Spanish, exact)
A root cap that is part of a primary root tip.
caliptra de la ra&#237z primary (Spanish, exact)
A root cap that is part of a lateral root tip.
caliptra de la ra&#237z lateral (Spanish, exact)
A central root cap that is part of a root cap of lateral root.
caliptra de la ra&#237z central de la ra&#237z lateral (Spanish, exact)
A lateral root cap that is part of a root cap of lateral root.
caliptra de la ra&#237z lateral de la ra&#237z lateral (Spanish, exact)
A central root cap that is part of a root cap of primary root.
caliptra de la ra&#237z central de la ra&#237z primaria (Spanish, exact)
A lateral root cap (PO:0020131) that is part of a root cap (PO:0020123) of a primary root (PO:0020127).
caliptra de la ra&#237z lateral de la ra&#237z primaria (Spanish, exact)
A cardinal organ part (PO:0025001) that is an outgrowth of a root (PO:0009005) and is inhabited by nitrogen-fixing bacteria.
n&#243dulo de la ra&#237z (Spanish, exact)
Root nodules are a symbiosis between a plant (often, but not exclusively, of the Fabaceae) and bacteria of the genus Rhizobium, Bradyrhizobium, or Azorhizobium.
A branch (PO:0025073) that is prostrate or trailing, and produces adventitious nodal roots (PO:0003005) and sometimes erect shoots.
The stolon develops from an axillary bud (PO:0004709) and produces adventitious roots (PO:0003005) at the nodes and a terminal aerial stem. That stem then sends out one or more stolons from its axillary buds and the process is reiterated. Stolons may be above ground, as with strawberries, or below ground as in potatoes.
An enlarged more or less thin-walled leaf pavement cell, present, with other similar cells, in longitudinal rows in leaves of monocots.
Also called motor cell because of its presumed participation in the mechanism of rolling and unrolling of leaves. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A portion of ground tissue (PO:0025059) centrifugally derived from cork cambium (PO:0005599), non-living at maturity, and having suberized walls.
Protective in function because the walls are highly impervious to water.
A chlorenchyma cell that is part of a mesophyll.
c&#233lula del mes&#243filo (Spanish, exact)
Cells with deposits of silica in them. One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with epidermal cork cell.
c&#233lula sil&#237cica (Spanish, exact)
One of two types of short cells in the epidermis of grasses. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025).
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
c&#233lula meristem&#225tica (Spanish, exact)
A meristematic cell (PO:0004010) that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.
Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic.
A native plant cell (PO:0025606) that is part of a portion of epidermis (PO:0005679).
c&#233lula epid&#233rmica (Spanish, exact)
A vascular leaf expansion stage (PO:0001052) at which a leaflet primordium (PO:0025481) is initiated on the leaf rachis (PO:0020055) of a compound leaf (PO:0020043).
formation of vascular leaflet primordia stage
Stage of gynoecium development defined by differentiation and expansion of carpels.
gynoecium differentiation and expansion stage
Stage of gynoecium development defined by the closure of the carpel(s).
Closure of the carpel can occur in various ways, by fusion or secretion.
Epidermal cells at the top of developing style differentiate stigma.
Stage of ovule development defined by differentiation and expansion of ovules.
ovule differentiation and expansion stage
The earliest stage of seed development immediately following double fertilization.
Stage of seed development characterized by seed growth and differentiation.
A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of either the plant embryo cotyledonary stage (PO:0001078) or the plant embryo coleoptilar stage (PO:0001094).
A plant embryo bilateral stage is commonly known as the heart stage in dicotyledonous plants and the transition stage in monocots. Preceded by a plant embryo globular stage (PO:0001185).
A trichome (PO:0000282) that secretes or sequesters a portion of plant substance (PO:0025161).
A trichome that develops from seed coat epidermis.
A portion of secondary xylem (PO:0005848) that lacks living secondary xylem parenchyma cells (PO:0004525).
Heartwood has ceased to function in storage and conduction, and the reserve materials have been removed or converted into heartwood substances. It is generally darker colored than sapwood (PO:0004513) and is found in the center of a shoot axis (PO:0025029) or root (PO:0009005), interior to the sapwood. Heartwood forms at the end of a cell death stage of secondary xylem (PO:0025466).
A portion of secondary xylem (PO:0005848) that has as parts living secondary xylem parenchyma cells (PO:0004525).
Sapwood contains reserve materials and may function in the conduction of water and minerals (xylem sap (PO:0025539)). It is generally lighter colored than the heartwood (PO:0004512) and is located between the heartwood and the vascular cambium (PO:0005598) of a shoot axis (PO:0025029) or root (PO:0009005). Sapwood forms during a secondary xylem development stage (PO:0025427).
A portion of secondary xylem (PO:0005848) that has as parts a single layer of early wood (PO:0004515) and a single layer of late wood (PO:0004516) from the same growth season and is part of a shoot axis (PO:0025029) or root (PO:0009005).
Appears as a ring in a transverse section of plant axis (PO:0025004). May be an annual ring (one growth ring per year) or a false annual ring (more or less than one growth ring per year).
A portion of secondary xylem (PO:0005848) that is a part of a growth ring (PO:0004514) formed during the early part of a growing season, has lower density than late wood (PO:0004516) of the same growth ring, and has as parts early wood tracheary elements (PO:0025461) with generally larger lumens than the late wood tracheary elements (PO:0025462) of the same growth ring.
The transition from early wood to late wood may be gradual and is not always easy to distinguish.
A portion of secondary xylem (PO:0005848) that is a part of a growth ring (PO:0004514) formed during the later part of a growing season, has higher density than early wood (PO:0004515) of the same growth ring, and has as parts late wood tracheary elements (PO:0025462) with generally smaller lumens than the early wood tracheary elements (PO:0025461) of the same growth ring.
A portion of secondary xylem (PO:0005848) that includes the last-formed late wood (PO:0004516) of one growth ring (PO:0004514) and the earliest-formed early wood (PO:0004515) of the next growth ring.
l&#237mite del anillo de crecimiento (Spanish, exact)
Used to describe the boundary area between two adjacent growth rings, which may be distinct or indistinct.
A portion of plant tissue (PO:0009007) outside the vascular cambium (PO:0005598) or the xylem (PO:0005352); in older trees may be divided into dead outer bark and living inner bark, which consists of secondary phloem (PO:0005043).
A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.
A xylem fiber cell (PO:0000274) with simple pits.
Libriform fiber cells have simple (unbordered) pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exist and are generally classified as fiber tracheids (PO:0000355). If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.
A plant fiber cell (PO:0025407) with thin transverse walls (septa), which are formed when mitosis occurs within the cell after development of a secondary cell wall (GO:0009531).
A septate fiber septum is composed of the adjacent primary cell walls of two internal cells that arise from mitosis within the septate fiber cell after it has formed a secondary cell wall (GO:0009531).
Cambium at the outer margin of the xylem cylinder.
cambium vascular externo (Spanish, exact)
cambium vascular interno (Spanish, exact)
A portion of secondary phloem tissue produced by included vascular cambium.
A parenchyma cell (PO:0000074) that is part of a portion of secondary xylem parenchyma (PO:0004532).
c&#233lula parenquim&#225tica de la madera (Spanish, exact)
A secondary xylem parenchyma cell (PO:0004525) that is part of a portion of axial secondary xylem parenchyma (PO:0004533).
c&#233lula parenquim&#225tica axial de la madera (Spanish, exact)
A parenchyma cell (PO:0000074) that develops from a ray initial (PO:0000082) and is part of a portion of ray secondary xylem parenchyma (PO:0004534).
c&#233lula parenquim&#225tica de rayo de la madera (Spanish, exact)
A ray secondary xylem parenchyma cell (PO:0004527) that is oriented with its longest dimension parallel to the plant axis (PO:0025004) in which it is found.
rayo par&#233nquim&#225tico vertical de la madera (Spanish, exact)
upright ray wood parenchyma cell (exact)
upright ray secondary xylem parenchyma cell
A ray secondary xylem parenchyma cell (PO:0004527) that is oriented with its longest dimension radial to the plant axis (PO:0025004) in which it is found.
c&#233lula procumbente del rayo de la madera (Spanish, exact)
procumbent ray wood parenchyma cell (exact)
procumbent ray secondary xylem parenchyma cell
Empty upright ray cell of approximately the same height as the procumbent ray cell and occurring in indeterminate horizontal series usually interspersed among the procumbent cells.
c&#233lula de baldoza B (Spanish, exact)
Cell on the margin of, and tending to form a sheath around, the procumbent cells of a multi-seriate ray as seen in tangential section.
A portion of parenchyma (PO:0005421) tissue that is part of a portion of secondary xylem (PO:0005848) and has as parts secondary xylem parenchyma cells (PO:0004525).
par&#233nquima de la madera (Spanish, exact)
A portion of secondary xylem parenchyma (PO:0004532) that is part of an axial system (PO:0025410) and has as parts axial secondary xylem parenchyma cells (PO:0004526).
par&#233nquima axial de la madera (Spanish, exact)
A portion of secondary xylem parenchyma (PO:0004532) that is part of a ray system (PO:0025411) and has as parts ray secondary xylem parenchyma cells (PO:0004527).
par&#233nquima de rayo de la madera (Spanish, exact)
Occurs in bands or rays of variable width and height that extend radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005043) of a plant axis (PO:0025004).
A portion of placenta tissue (PO:0025078) that is part of a fruit (PO:0009001) and to which seeds (PO:0009010) are attached.
If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A fruit pedicel (PO:0030114) that bears a fruit (PO:0009001) in an infructescence (PO:0006342).
An infructescence fruit pedicel is the ultimate shoot axis (PO:0025029) in an infructescence (PO:0006342).
A somatic plant embryo derived directly from nucellus cells.
A root nodule characterized by a persistent meristem, presence of vascular transfer cells, and cell division in the inner cortex with non-dividing infected cells and bacteria.
n&#243dulo indeterminable (Spanish, exact)
Nodule is persistent and may continue to grow after a physiological stress.
A root nodule characterized by a dividing infected cells and bacteria, vascular transfer cells absent and cell division is in the outer cortex.
A columella (PO:0025230) that forms the central axis of a fruit.
A swollen shoot axis (PO:0025029) that grows horizontally at or below the substrate surface and produces shoots above and roots or rhizoids below.
In ferns and many monocots, a rhizome is a primary axis (stem), while in other species, it is a branch. Usually produces scale-like leaves.
A shoot axis (PO:0025029) that develops from a branch (PO:0025073) and is radially enlarged for storage.
Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species. Use the term tuberous root tuber (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.
A shoot system that is initiated from a root.
sistema de epiblasto (epiblastema) que nace en la ra&#237z (Spanish, exact)
A shoot system that is initiated from a shoot.
sistema de epiblasto (epiblastema) que nace en el epiblasto (epiblastema) (Spanish, exact)
A shoot-borne shoot system (PO:0004546) developing from a stem (PO:0009047).
A shoot axis tuber (PO:0004543) that develops below ground.
tub&#233rculo subterr&#225neo (Spanish, exact)
A shoot axis tuber (PO:0004543) that develops above ground.
tub&#233rculo a&#233reo (Spanish, exact)
A portion of ground tissue (PO:0025059) directly internal to an anther wall endothecium (PO:0020002) that develops from an anther wall secondary parietal cell layer (PO:0006007).
May be a single or double layer. Usually crushed by the endothecium and therefore almost invariably degenerates early during anther development. In some angiosperms, including Arabidopsis, it develops from an anther wall outer secondary parietal cell layer. In other angiosperms, it develops directly from an anther wall primary parietal cell layer, while in still others, two layers of the middle layer may develop from both an anther wall outer secondary parietal cell layer and an anther wall inner secondary parietal cell layer.
Shoot system in which the internodes elongate little or at all, bearing reproductive structures and/or leaves.
epiblasto (epiblastema) corto (Spanish, exact)
Shoot system in which all or most of the internodes elongate.
epiblasto (epiblastema) largo (Spanish, exact)
A phyllome primordium (PO:0025128) that develops from a carpel anlagen (PO:0006005) and is committed to the development of a carpel (PO:0009030).
portion of carpel primordium tissue (exact)
A phyllome primordium (PO:0025128) that develops from a sepal anlagen (PO:0025485) and is committed to the development of a sepal (PO:0009031).
portion of sepal primordium tissue (exact)
primordio de s&#233palo (Spanish, exact)
A phyllome primordium (PO:0025128) that develops from a stamen anlagen (PO:0025486) and is committed to the development of a stamen (PO:0009029).
portion of stamen primordium tissue (exact)
A dehiscence zone (PO:0025092) that is part of a fruit.
zona de dehiscencia del fruto (Spanish, exact)
Upon fruit maturation by drying, undergoes cell separation, allowing the valves to detach from the replum and seeds to be dispersed. If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A stem node (PO:0020141) that is part of a plant embryo axis (PO:0019018) where the scutellum (PO:0020110) is attached.
Found in grasses where no hypocotyl is present. The scutellar node may represent a reduction of the hypocotyl and cotyledonary node.
A bud (PO:0000055) that develops from an axillary bud meristem (PO:0000232).
An axillary bud that develops into a flower.
An axillary reproductive bud that develops into an inflorescence.
yema de inflorescencia axilar (Spanish, exact)
An axillary bud (PO:0004712) that develops into a shoot system (PO:0009006) that has as organ parts only vegetative organs.
A bud that develops from a shoot apical meristem.
A terminal bud that develops into a flower.
A terminal reproductive bud develops into an inflorescence.
yema de inflorescencia terminal (Spanish, exact)
A terminal bud (PO:0004713) that develops into a shoot system (PO:0009006) that has as organ parts only vegetative organs.
yema vegetativa terminal (Spanish, exact)
A more or less rectangular leaf pavement cell in which the proximodistal dimension is several times longer than the transverse dimension.
In the leaf epidermis of Poaceae and Joinvilleaceae, long cells and short cells often alternate in longitudinal rows. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A canal (PO:0025132) that is a longitudinal groove in the testa through a prominent hilum (PO:0020063) of a seed (PO:0009010).
A portion of cortex (PO:0005708) that is part of a higher order inflorescence axis (PO:0009081), also called a paraclade.
cortex (corteza) del paraclado (Spanish, exact)
portion of paraclade cortex tissue (exact)
A portion of cortex (PO:0005708) that is part of a pedicel (PO:0030112).
cortex (corteza) del pedicelo (Spanish, exact)
portion of pedicel cortex tissue (exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a sepal (PO:0009031).
sistema vascular del s&#233palo (Spanish, exact)
A cardinal organ part (PO:0025001) that is the part of a plant axis (PO:0025004) where a radicle (PO:0020031) joins a hypocotyl (PO:0020100).
union del hipoc&#243tile con la ra&#237z (Spanish, exact)
A portion of vascular leaf primordium (PO:0000017) that is distal to the axis of the shoot apical meristem (PO:0020148) and develops into the abaxial side of the leaf lamina (PO:0020039).
lado abaxial del primordio de hoja (Spanish, exact)
While the abaxial side of the leaf is usually the lower surface, the vascular leaves (PO:0009025) of some plants may not have an obvious adaxial or abaxial side such as the leaves of many xerophytic (arid-adapted) species. The adaxial and abaxial side may appear considerably more rounded and this could be due to early activity of the vascular leaf adaxial meristem (PO:0025401) and/or leaf abaxial meristem (PO:0025401). In other cases, such as Alstromeria, the leaves may be twisted or resupinate.
A portion of vascular leaf primordium (PO:0000017) that is proximal to the axis of the shoot apical meristem (PO:0020148) and develops into the adaxial side of the leaf lamina (PO:0020039).
lado adaxial del primordio de la hoja (Spanish, exact)
While the adaxial side of the leaf is usually the upper surface, the vascular leaves (PO:0009025) of some plants may not have an obvious adaxial or abaxial side such as the leaves of many xerophytic (arid-adapted) species. The adaxial and abaxial side may appear considerably more rounded and this could be due to early activity of the vascular leaf adaxial meristem (PO:0025401) and/or leaf abaxial meristem (PO:0025401). In other cases, such as Alstromeria, the leaves may be twisted or resupinate.
An axillary shoot system (PO:0006343) that is part of a stem base (PO:0008039).
epiblasto (epiblastema) axilar basal (Spanish, exact)
An axillary branch that forms from a leaf above the very base of the shoot.
epiblasto (epiblastema) axilar caulinar (Spanish, exact)
The genetic distinction between cauline axillary branches and tillers may or may not be unique to the Poaceae. There are no data for other plant families.
A trichome that is part of a shoot axis epidermis.
eje de tricoma del epiblasto (epiblastema) (Spanish, exact)
A cardinal organ part (PO:0025001) of a shoot axis (PO:0025029) where a bud (PO:0000055) may form and develop into a branch (PO:0025073), leaf (PO:0025034), flower (PO:0004541), inflorescence (PO:0009049) or nodal root (PO:0003005).
nodo del epiblasto (epiblastema) (Spanish, exact)
A cardinal organ part (PO:0025001) of a shoot axis (PO:0025029) that is between two shoot axis nodes (PO:0005004).
internodo del epiblasto (epiblastema) (Spanish, exact)
A portion of secretory tissue (PO:0005656) that has as parts articulated laticifer cells (PO:0006221).
latic&#237fero articulado (Spanish, exact)
portion of articulated laticifer tissue (exact)
The articulated laticifer cells are joined longitudinally to form a tube, with cross-walls that may be partially to fully perforated.
A septum (PO:0000030) that is part of an anther dehiscence zone (PO:0005011).
A dehiscence zone (PO:0025092) that is part of an anther (PO:0009066).
zona de dehiscencia de la antera (Spanish, exact)
Extends along the entire length of the anther and is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break open and pollen to be released.
A shoot axis vascular system (PO:0000039) that includes the totality of the portions of vascular tissue in their specific arrangement in a pedicel (PO:0030112).
sistema vascular del pedicelo (Spanish, exact)
A portion of stem epidermis (PO:0025178) which is the outermost primary cell layer of the hypocotyl (PO:0020100).
epidermis del hipoc&#243tile (Spanish, exact)
A portion of cortex (PO:0005708) that is part of a plant embryo (PO:0009009).
cortex (corteza) del emrbion (Spanish, exact)
A portion of endodermis (PO:0000252) that is part of an plant embryo (PO:0009009).
endodermis del embri&#243n (Spanish, exact)
A shoot system vascular system (PO:0025205) that includes the totality of the portions of vascular tissue in their specific arrangement in a flower (PO:0009046).
sistema vascular de la flor (Spanish, exact)
Because a vascular system is defined as the totality of the portions of vascular tissue in a plant structure, the vascular systems of floral parts are part of the flower vascular system.
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a stamen (PO:0009029).
sistema vascular del estambre (Spanish, exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a carpel (PO:0009030).
sistema vascular del carpelo (Spanish, exact)
A portion of vascular tissue (PO:0009015) that is a unit strand of the vascular system (PO:0000034) and has as part xylem (PO:0005352) or phloem (PO:0005417).
May also contain portions of ground tissue (PO:0025059). The bundle sheath (PO:0006023) can also be part of a vascular bundle, if it is present.
A phyllome margin (PO:0025018) which is part of a sepal (PO:0009031).
A portion of plant tissue (PO:0009007) that is composed of plant ovary outer epidermis (PO:0005023), plant ovary inner epidermis (PO:0005024), and a plant ovary wall middle layer (PO:0005025)
A portion of plant ovary epidermis (PO:0006063) which is the outer surface of a plant ovary (PO:0009072).
epidermis externo del ovario (Spanish, exact)
A portion of plant ovary epidermis (PO:0006063) which is the inner surface of a plant ovary (PO:0009072).
epidermis interno del ovario (Spanish, exact)
A portion of chlorenchyma tissue (PO:0005426) that is part of the plant ovary wall (PO:0005022) and is composed of mesophyll cells (PO:0004006).
capa media de la pared del ovario (Spanish, exact)
middle layer of plant ovary wall (exact)
In some species, such as Arabidopsis, there may be a distinct subepidermal adaxial cell layer. The cells in the mesophyll layer(s) may not differentiate similar to the spongy and palisade cells found in the leaf mesophyll.
Multinucleate cell developed by a series of events involving kayokinesis but not cytokinesis of the initial feeding cell. The events are induced by root knot nematodes (e.g., Meloidogyne sp. ) entering the feeding cells (any cells) of the root vascular system.
c&#233lula gigante de la ra&#237z (Spanish, exact)
Multinucleate cell developed by a series of events involving fusion with the neighboring dividing cells. The events are induced by cyst nematodes (e.g. Heterodera schachtii) entering the feeding cells (any cells) of the root vascular system.
c&#233lula ??? de la ra&#237z (Spanish, exact)
A shoot system vascular system (PO:0025205) that includes the totality of the portions of vascular tissue in their specific arrangement in an inflorescence (PO:0009049).
sistema vascular de inflorescencia (Spanish, exact)
A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
portion of root primordium tissue (exact)
A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
A glandular trichome (PO:0004509) that synthesizes terpenophenolic resins and prenylflavonoids.
One of the major chalconoids from hops is xanthohumol (CHEBI:66331).
A strobilus (PO:0025083) that bears only pollen (PO:0025281).
A strobilus (PO:0025083) that bears only plant ovules (PO:0020003).
A shoot lateral meristem (PO:0006344) that is part of a shoot axis (PO:0025029) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).
meristema de engrosamiento primario (Spanish, exact)
Contributes to primary thickening of a shoot axis (PO:0025029), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
A portion of pith (PO:0006109) that is part of a root stele (PO:0020124).
m&#233dula de la ra&#237z (Spanish, exact)
A portion of pith (PO:0006109) that is part of a shoot axis (PO:0025029).
m&#233dula del eje del epiblasto (epiblastema) (Spanish, exact)
A portion of phloem (PO:0005417) tissue that develops from a vascular cambium (PO:0005598).
portion of secondary phloem tissue (exact)
Secondary phloem develops as part of secondary growth (GO:0080117).
A peripheral portion of ground tissue (PO:0025059) in a plant axis (PO:0025004) that is composed of cork cambium (phellogen; PO:0005599), phellem (PO:0004003), and phelloderm (PO:0005050).
After secondary growth, the periderm may replace the epidermis in stems and roots, rarely in other organs. In some cases, the epidermis is retained after periderm development. Periderm is derived from lateral meristem and may contain secondary phloem.
A portion of periderm tissue (PO:0005046) that is part of a root (PO:0009005).
peridermis de la ra&#237z (Spanish, exact)
A portion of periderm tissue (PO:0005046) that is part of a shoot axis (PO:0025029).
peridermis del eje del epiblasto (epiblastema) (Spanish, exact)
A portion of ground tissue (PO:0025059) often resembling cortical parenchyma produced centripetally by the cork cambium.
A portion of ground tissue (PO:0025059) that is the outermost layer of a portion of cortex (PO:0005708).
A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.
A portion of plant tissue (PO:0009007) that consists of mass of undifferentiated plant cells (PO:0009002).
Consists primarily of parenchyma cells but may contain other cell types as the callus begins to differentiate. May be formed as a result of wounding or may develop in culture.
A portion of shoot axis hypodermis (PO:0005057) that is part of a stem cortex (PO:0000223).
hipodermis del eje del epiblasto (epiblastema) (Spanish, exact)
A portion of endodermis (PO:0000252) that is part of a shoot axis cortex (PO:0000223).
endodermis de eje del epiblasto (epiblastema) (Spanish, exact)
A portion of endodermis that is part of a root cortex.
endodermis de la ra&#237z (Spanish, exact)
A portion of endodermis that is part of a vascular leaf.
Often found in the leaf of Gymnosperms and elsewhere.
A portion of vascular tissue (PO:0009015) that has as part one or more tracheary elements (PO:0000290).
Functions in the translocation of water and solutes from roots (PO:0009005) to the shoot system (PO:0009006) and in support. Tracheary elements have lignified cell walls with secondary thickening and are dead at maturity.
A portion of plant tissue (PO:0009007) that is the outermost layer of endosperm (PO:0009089) in a seed (PO:0009010), its cells being characterized by presence of protein bodies (GO:0042735).
Occurs in cereals and many other taxa. The protein bodies (GO:0042735) contain seed storage proteins and enzymes involved with endosperm digestion (Esau, 1977).
A portion of seed storage parenchyma that is part of an endosperm.
par&#233nquima endosp&#233rmico (Spanish, exact)
A portion of vascular tissue (PO:0009015) that has as parts sieve elements (PO:0025406).
Functions in the conduction of organic substances in vascular plants.
A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.
portion of parenchymatous tissue (exact)
Parenchyma contains relatively unspecialized cells.
A portion of ground tissue (PO:0025059) which comprises living tissue composed of more or less elongated cells with thick, non-lignified primary cell walls.
Chloroplast-containing parenchyma tissue.
A portion of ground tissue (PO:0025059) which comprises supporting tissue composed of plant fiber cells (PO:0025407) or sclereid cells (PO:0025418).
portion of sclerenchymatous tissue (exact)
A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.
This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).
A cambium (PO:0005597) that is located between and gives rise to secondary xylem (PO:0005848) and secondary phloem (PO:0005043).
A vascular cambium produces cells in both directions, centrifugally and centrifically, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).
A cambium (PO:0005597) that is part of a periderm (PO:0005046) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis (PO:0025004).
The chloroplast-containing, photosynthetic parenchymatous tissue situated between the two epidermal layers of the foliage leaf.
mes&#243filo de la hoja (Spanish, exact)
Leaf mesophyll parenchyma characterized by little elongated cells, that are not closely packed and have conspicuous intercellular spaces.
Parenchyma containing closely packed elongated chlorenchymatous cells oriented perpendicular to the leaf surface and which are active in photosynthesis.
mes&#243filo en empalizada (Spanish, exact)
A portion of plant tissue (PO:0009007) that form specialized structures producing a secretion.
porci&#243n del tejido secretor (Spanish, exact)
The synonym gland does not imply non-secretory 'glands'.
A cardinal organ part that releases water through a hydathode pore.
Hydathodes may have one or more pores that are similar to stomata but lack the ability to open and close. Hydathodes are involved in the release of water or xylem sap through pores via guttation or secretion. Generally, hydathodes are located at the end of a minor vein in a phyllome. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.
A specialized tissue where excess salt absorbed in water from the soil is concentrated, being stores or excreted.
A crust of salt forms on leaves which tastes bad and the white surfaces act to reflect light. Example, as is Mangrove vegetation.
A canal (PO:0025132) of schizogenous origin, lined with secretory resin cells (PO:0025604) and containing plant resin (PO:0025603).
A gland or a cavity lined with cells that secrete oils.
A portion of plant tissue (PO:0009007) composed of epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011).
A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011).
The epidermis can be composed of one or more layers of cells. In some species of vascular plants, the epidermis, which is a primary tissue, is replaced by periderm, which is secondary tissue, later in development. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids.
A portion of parenchyma tissue containing particularly large intercellular spaces of schizogenous or lysigenous origin.
As applied to an intercellular space, originating by one or a combination of two processes, separation and degradation of cell walls.
A maximal portion of ground tissue (PO:0025059) between the vascular system (PO:0000034) and the epidermis (PO:0005679) in a plant.
The sub-epidermal layer or layers of cells of the root similar in structure and cytochemical characteristics of the endodermis, the outermost layer or layers of cells of the cortex.
The cell walls are thickened and contain suberin. Absent in pteridophytes, fibrous in Phoenix and accompanied by sclerenchyma in Ananas.
A portion of xylem (PO:0005352) tissue that develops from a vascular cambium (PO:0005598).
portion of secondary xylem tissue (exact)
Secondary xylem develops as part of secondary growth (GO:0080117). Secondary xylem is the wood of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial (PO:0025410) and ray (PO:0025411) systems. Secondary xylem is often part of a shoot axis (PO:0025029) or a root (PO:0009005) but may occur in other organs. Some monocots have a primary thickening meristem (PO:0005039), located near the shoot apical meristem (PO:0020148), that gives the appearance of secondary growth and may produce lignified tissue that appears woody but is not composed of secondary xylem. Tracheary elements in secondary xylem (PO:0000290) have lignified cell walls with secondary thickening and are dead at maturity.
A portion of xylem (PO:0005352) tissue that develops from the procambium (PO:0025275).
Primary xylem develops as part of primary growth (request for primary growth has been made to GO) and is not differentiated into axial (PO:0025410) and ray (PO:0025411) systems. Tracheary elements (PO:0000290) have lignified cell walls with secondary thickening and are dead at maturity.
A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea.
A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
A glume that is the proximal/basal of the two glumes subtending a pair of florets.
A phyllome that is reduced in size relative to a vascular leaf on the same plant and is often associated with a perennating or dormant bud or a vegetatively propagating organ such as a rhizome.
May be photosynthetic or non-photosynthetic. Some species have vascular leaves that are scale-like (such as Juniperus, Thuja, and Chamaecyparis). Annotations for scale-like leaves should go under vascular leaf (PO:0009025), not scale leaf.
A glume that is the apical/distal of the two glumes subtending a pair of florets.
A phyllome anlagen (PO:0025430) that will give rise to a carpel primordium (PO:0004703) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
A portion of ground tissue (PO:0025059) that is part of an anther wall (PO:0000002) and has as parts a primary parietal cell (PO:0006010) and adjacent plant cells.
capa primaria de c&#233lulas parietales (Spanish, exact)
pollen sac primary parietal cell layer (exact)
A portion of ground tissue (PO:0025059) that is part of an anther wall (PO:0000002) and develops from an anther wall primary parietal cell layer (PO:0006006).
capa secundaria de c&#233lulas parietales (Spanish, exact)
pollen sac secondary parietal cell layer (exact)
In many angiosperms, the cells of the anther wall primary parietal cell layer undergo a periclinal division, resulting in the formation of two anther wall secondary parietal layers.
anther wall secondary parietal cell layer
An anther wall secondary parietal cell layer (PO:0006007) that is formed towards the inside, after the cells of an anther wall primary parietal cell layer (PO:0006006) undergo a periclinal division.
capa interna secundaria de c&#233lulas parietales (Spanish, exact)
pollen sac inner secondary parietal cell layer (exact)
In many angiosperms, including Arabidopsis, it divides periclinally to form an anther wall middle layer externally and an anther wall tapetum internally. Alternatively, it may differentiate into a tapetum.
anther wall inner secondary parietal cell layer
An anther wall secondary parietal cell layer (PO:0006007) formed towards the outside, after an anther wall primary parietal cell layer (An anther wall secondary parietal cell layer (PO:0006006) undergoes a periclinal division.
capa externa secundaria de c&#233lulas parietales (Spanish, exact)
pollen sac outer secondary parietal cell layer (exact)
In many angiosperms, including Arabidopsis, it differentiates into the anther wall endothecium. Alternatively, it may divide periclinally to form an anther wall endothecium externally and an anther wall middle layer internally.
anther wall outer secondary parietal cell layer
A native plant cell (PO:0025606) which is formed by the division of a male archesporial cell (PO:0006014), and is part of the anther wall primary parietal cell layer (PO:0006006).
c&#233lula primaria parietal (Spanish, exact)
An unbranched second order leaf vein (PO:0020140) that runs between two adjacent primary leaf veins (PO:0025413).
Found in the leaf lamina of some monocots, particularly in Poaceae.
A thin band of intercalary meristematic tissue at the junction of a leaf blade (lamina) and a leaf sheath found in grasses.
A portion of plant tissue (PO:0009007) which is composed of highly vacuolated cells forming closely-packed, club-shaped sacs with long slender stalks and containing juice.
ves&#237cula contenedora de jugo (Spanish, exact)
Juice sac tissue is found in citrus spp. (hesperidium fruit; PO:0030109), and develops from cells of the endocarp (PO:0009086).
An archesporial cell (PO:0030056) that is part of a microsporangium (PO:0025202) and divides to gives rise to a microsporocyte (PO:0020047).
c&#233lula masculina arquesporial (Spanish, exact)
Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In seed plants, a male archesporial cell undergoes periclinal division, giving rise to an inner primary sporogenous cell layer and an outer primary parietal cell.
An archesporial cell (PO:0030056) that is part of a megasporangium (PO:0025201) and divides to give rise to a megasporocyte (PO:0000431).
c&#233lula femenina arquesporial (Spanish, exact)
Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell. In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte.
A portion of phyllome epidermis (PO:0025157) that is part of a leaf (PO:0025034).
A portion of endosperm (PO:0009089) tissue in which the first karyokinetic event is accompanied by the formation of a horizontal wall which divides the embryo sac central cell (PO:0020090) into unequal regions. The larger one is the micropylar chamber in which cytokinesis does not occur and the smaller one is the chalazal chamber.
A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf (PO:0025034).
epidermis adaxial de la hoja (Spanish, exact)
Used to refer to an adaxial epidermis of an entire leaf. More specific terms exist for leaf lamina adaxial epidermis and petiole adaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf (PO:0025034).
epidermis abaxial de la hoja (Spanish, exact)
Used to refer to an abaxial epidermis of an entire leaf. More specific terms exist for leaf lamina abaxial epidermis and petiole abaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A root apical meristem (PO:0020147) that gives rise to a lateral root (PO:0020121).
meristema apical de la ra&#237z lateral (Spanish, exact)
apical meristem of lateral root (related)
This is different from root lateral meristem.
A root apical meristem (PO:0020147) that gives rise to a shoot-borne root (PO:0000042).
adventitious root apical meristem (broad)
meristema de la ra&#237z adventicia (Spanish, exact)
A portion of ground tissue (PO:0025059) which forms a strip along the leaf veins and extending from the bundle sheath (PO:0006023) to the epidermis. It may be present on one or both sides of the vein and may consist of parenchyma or sclerenchyma.
extensi&#243n de la vaina vascular (Spanish, exact)
A portion of ground tissue (PO:0025059) which comprises a layer or layers of cells surrounding the vascular bundles (PO:0005020) of leaves. It may consist of parenchyma (PO:0005421) or sclerenchyma (PO:0005427).
A single layered, parenchymatous bundle sheath characterized by presence of large quantity of starch.
vaina parenquim&#225tica (Spanish, exact)
The inner endodermal sheath of a two layered bundle sheath. The cells are smaller in diameter compared to those in outer wall (starch sheath). The cell walls are thick and contain suberized lamellae. They are analogous to endodermis.
A cardinal organ part (PO:0025001) which is a short, abrupt, flexible point at the apex of the palea (PO:0009038).
ap&#237culo de la palea (Spanish, exact)
A cardinal organ part (PO:0025001) that is the edge of a leaflet (PO:0020049) and the area immediately internally adjacent to it.
A portion of epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020).
A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020).
epidermis del epiblasto (epiblastema) (Spanish, exact)
Often interrupted by stomatal complexes (PO:0002000) and other structures. The shoot system epidermis is different from the root epidermis (PO:0006036) in its origin, function and structure.
A portion of epidermis (PO:0005679) that is part of a root (PO:0009005).
A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005).
epidermis de la ra&#237z (Spanish, exact)
The root epidermis is different from the shoot epidermis in its origin, function and structure.
A portion of root epidermis (PO:0006036) that is part of a shoot-borne root (PO:0000042).
epidermis de la ra&#237z adventicia (Spanish, exact)
A portion of phyllome epidermis (PO:0025157) that is part of a sepal (PO:0009031).
epidermis del s&#233palo (Spanish, exact)
A portion of phyllome epidermis (PO:0025157) that is part of a petal (PO:0009032).
epidermis del p&#233talo (Spanish, exact)
A multiseriate portion of root epidermis (PO:0006036) found in aerial roots of some monocots. Most of its cells are dead and store water like a sponge.
A portion of plant epidermis (PO:0005679) that is part of an plant ovule integument (PO:0020021).
epidermis del integumento (Spanish, exact)
A portion of integument epidermis (PO:0006043) of the inner integument (PO:0020022) in a plant ovule (PO:0020003).
epidermis del integumento interior (Spanish, exact)
A portion of integument epidermis (PO:0006043) of the outer integument (PO:0020023) in a plant ovule (PO:0020003).
epidermis del integumento exterior (Spanish, exact)
A portion of plant epidermis (PO:0005679) that is part of a seed coat (PO:0009088).
epidermis de la cubierta de la semilla (Spanish, exact)
A portion of shoot system epidermis (PO:0006035) that is part of the scutellum (PO:0020110).
A portion of seed coat epidermis (PO:0006048) which is part of the seed coat (PO:0009088), and develops from the outer surface of the outer integument (PO:0020023).
exotesta/testa exterior (Spanish, exact)
外珠皮の外側の表皮から発生する外種皮 (Japanese, exact)
A portion of seed coat epidermis (PO:0006048) which is part of a seed coat (PO:0009088) and develops from the inner epidermis of the outer integument (PO:0020023).
endotesta/testa interior (Spanish, exact)
外珠皮の内側の表皮から発生する外種皮 (Japanese, exact)
A portion of petal epidermis (PO:0006041) that covers the abaxial/lower surface of a petal (PO:0009032).
epidermis abaxial del p&#233talo (Spanish, exact)
A portion of petal epidermis (PO:0006041) that covers the adaxial/upper surface of a petal (PO:0009032).
epidermis adaxial del p&#233talo (Spanish, exact)
A portion of sepal epidermis (PO:0006040) that covers the abaxial/lower surface of a sepal (PO:0009031).
epidermis abaxial del s&#233palo (Spanish, exact)
A portion of sepal epidermis (PO:0006040) that covers the adaxial/upper surface of a sepal (PO:0009031).
epidermis adaxial del s&#233palo (Spanish, exact)
A portion of leaf epidermis (PO:0006016) that is part of a cotyledon (PO:0020030).
epidermis del cotiled&#243n (Spanish, exact)
A portion of leaf epidermis (PO:0006016) which is the abaxial/lower epidermis of the cotyledon (PO:0020030).
epidermis abaxial de cotiled&#243n (Spanish, exact)
A portion of leaf epidermis (PO:0006016) which is the adaxial/upper epidermis of the cotyledon (PO:0020030).
epidermis adaxial de cotiled&#243n (Spanish, exact)
A portion of stamen epidermis (PO:0025097) that is part of a filament (PO:0009067).
epidermis del filamento (Spanish, exact)
A portion of carpel epidermis (PO:0025096) that is part of a stigma (PO:0009073).
A portion of carpel epidermis (PO:0025096) that is part of a style (PO:0009074).
A portion of plant epidermis (PO:0005679) that is part of an plant ovary wall (PO:0005022).
A portion of endodermis (PO:0000252) that is part of a hypocotyl (PO:0020100).
endodermis del hipoc&#243tile (Spanish, exact)
A portion of parenchyma tissue that is part of a petiole.
par&#233nquima del pec&#237olo (Spanish, exact)
A portion of parenchyma tissue that is part of a sepal.
par&#233nquima del s&#233palo (Spanish, exact)
A portion of parenchyma (PO:0005421) tissue that is part of a petal (PO:0009032).
par&#233nquima del p&#233talo (Spanish, exact)
The chloroplast-containing, photosynthetic parenchymatous tissue situated between the two epidermal layers of the leaf or leaf like organs.
The chloroplast-containing, photosynthetic parenchymatous tissue situated between the two epidermal layers of the petal.
mes&#243filo del p&#233talo (Spanish, exact)
The chloroplast-containing, photosynthetic parenchymatous tissue situated between the two epidermal layers of the sepal.
mes&#243filo del s&#233palo (Spanish, exact)
A shoot system meristem (PO:0006079) that is intercalated between two portions of non-meristematic tissue and results in an increase in length as part of primary growth.
See subtypes: leaf intercalary meristem (PO:0006346) and stem intercalary meristem (PO:0006347). Not known to occur in roots. Term for primary growth has been requested in GO.
A portion of phloem (PO:0005417) tissue that develops from the procambium (PO:0025275).
portion of primary phloem tissue (exact)
In stem or root it is differentiated behind the apical meristem. Primary phloem develops as part of primary growth (GO term for primary growth has been requested).
A portion of primary phloem (PO:0006075) tissue that has as parts companion cells (PO:0000071, in angiosperms) or albuminous cells (PO:0025412, in gymnosperms) associated with the sieve elements (PO:0025406) and that develops after the protophloem (PO:0006077).
Metaphloem develops after a portion of vascular tissue (PO:0009015) has stopped elongating, in the same location as the protophloem, replacing the protophloem. Sieve elements in the metaphloem are larger than in the protophloem. Develops before the secondary phloem, if any is formed.
A portion of primary phloem (PO:0006075) tissue has as parts the first-formed sieve elements (PO:0025406) at a particular location and does not have companion cells (PO:0000071, in angiosperms) or albuminous cells (PO:0025412, in gymnosperms) associated with the sieve elements.
Protophloem is the first primary phloem to develop in any particular location in a portion of vascular tissue (PO:0009015). Sieve elements in the protophloem are smaller than in the metaphloem (PO:0006076). The protophloem usually only lasts a short time before it is replaced by metaphloem.
A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
meristema del epiblasto (epiblastema) (Spanish, exact)
A root apical meristem (PO:0020147) that gives rise to a primary root (PO:0020127).
meristema apical de la ra&#237z primaria (Spanish, exact)
apical meristem of primary root (related)
A portion of protoderm (PO:0006210) tissue that is the outermost layer of the shoot apical meristem (PO:0020148), and gives rise to the leaf abaxial epidermis (PO:0006019).
portion of abaxial protoderm tissue (exact)
A portion of protoderm (PO:0006210) tissue that is the outermost layer of the shoot apical meristem (PO:0020148), and gives rise to the leaf adaxial epidermis (PO:0006018).
portion of adaxial protoderm tissue (exact)
Tissue consisting of tracheids and parenchyma cells, associated with the vascular bundle.
porci&#243n del tejido de transfusi&#243n (Spanish, exact)
A portion of meristem tissue (PO:0009013) that gives rise to a root (PO:0009005).
meristema de la ra&#237z (Spanish, exact)
A native plant cell (PO:0025606) is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.
c&#233lula espor&#243gena primaria (Spanish, exact)
A floral structure primordium (PO:0025477) that is committed to the development of an anther (PO:0009066).
portion of anther primordium tissue (exact)
A cultured plant callus that is capable of forming plant organs.
callo &#243rganog&#233nico (Spanish, exact)
Plant organs may be formed after the cultured plant callus is treated with plant growth regulators.
A cultured plant callus (PO:0000009) that is capable of forming somatic embryos.
Somatic embryos may be formed after the cultured plant callus is treated with plant growth regulators.
A maximal portion of parenchyma (PO:0005421) in the center of a shoot axis (PO:0025029) or root (PO:0009005).
A portion of vascular cambium (PO:0005598) that develops from a procambium (PO:0025275) in a vascular bundle (PO:0005020) that is part of a shoot system (PO:0009006).
Found in shoot axes (PO:0025029) and vascular leaves (PO:0009025). Portions of fascicular cambium may merge with interfascular cambium (PO:0006201) or the fascicular cambium from adjacent vascular bundles to form a cylinder, or they may remain isolated.
A portion of vascular cambium (PO:00055980) that develops from cells in an interfascicular region (PO:0006202) that is part of a shoot system (PO:0009006).
cambium interfascicular (Spanish, exact)
Portions of interfascicular cambium may merge with fascicular cambium (PO:0006200) to form a cylinder of cambium or they may remain isolated. May develop from meristematic cells (PO:0004010) that have never differentiated into another cell type or from parenchyma cells (PO:0000074) that retain some meristematic ability.
A portion of ground tissue (PO:0025059) located between vascular bundles in a shoot axis.
regi&#243n interfascicular (Spanish, exact)
A portion of ground tissue (PO:0025059) that is part of a root stele located between the phloem and endodermis.
A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017).
Irregularly-shaped, chlorenchymatous cell, separated by large air spaces.
c&#233lula del mes&#243filo esponjoso (Spanish, exact)
Usually found in the abaxial/lower part of the leaf mesophyll as in a dorsiventral leaf, but between two palisade parenchyma layers in an isobilateral leaf. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
Elongated chlorenchymatous cell oriented perpendicular to the leaf surface and which is active in photosynthesis.
c&#233lula del mes&#243filo en empalizada (Spanish, exact)
Usually found in the adaxil/upper part of the leaf mesophyll. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A short cell in the dimorphic type of exodermis with cell wall that remains non-thickened.
c&#233lula de pasaje exod&#233rmica (Spanish, exact)
Cell in the endodermal layer of the root with cell wall that remains non-thickened.
c&#233lula de pasaje endod&#233rmica (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state.
A portion of plant tissue (PO:0009007) that is part of an abscission zone (PO:0000146) and contains cells that develop an abnormal wall chemistry and swelling resulting in their easily being pulled apart along the pectin-rich middle lamella (GO:0009519).
Directly involved in the weakening process of abscission.
A portion of plant tissue (PO:0009007) composed of a layer of cells that is part of the abscission zone (PO:0000146) that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission.
Parenchyma tissue containing particularly large intercellular spaces in the tissue of roots.
aer&#233nquima de la ra&#237z (Spanish, exact)
A portion of aerenchyma that is part of a stem.
aer&#233nquima del tallo (Spanish, exact)
A portion of parenchyma tissue containing particularly large intercellular spaces in the leaf mesophyll.
aer&#233nquima de la hoja (Spanish, exact)
A portion of primary phloem tissue positioned internal to the primary xylem.
floema intraxil&#233mico (Spanish, exact)
A portion of seed coat epidermis (PO:0006048) which is part of the seed coat (PO:0009088) and develops from the outer surface of the inner integument (PO:0020022).
内珠皮の外側の表皮から発生する内種皮 (Japanese, exact)
A portion of seed coat epidermis (PO:0006048) which is part of the seed coat (PO:0009088) and develops from the inner epidermis of the inner integument (PO:0020022).
内珠皮の内側の表皮から発生する内種皮 (Japanese, exact)
A portion of plant tissue (PO:0009007) that is the central region of an endosperm (PO:0009089), composed of cells that are significantly larger than those at the periphery, especially the aleurone and sub-aleurone layers.
portion of central endosperm tissue (exact)
Also called starchy endosperm region (characteristic of some grasses).
A laticifer cell (PO:0025031) that is joined longitudinally to other articulated laticifer cells to form a tube.
c&#233lula del latic&#237fero articulado (Spanish, exact)
The walls between contiguous cells may be perforated or may disappear completely. This terms should be used for individual cells. For multiple cells joined together, use articulated laticifer (PO:0005006).
A laticifer cell (PO:0025031) that is not joined longitudinally to other laticifer cells to form a tube.
c&#233lula del latic&#237fero no articulado (Spanish, exact)
May be coenocytic (multi-nucleate) and branched and may grow intrusively between other plant cells (PO:0009002).
A portion of procambium (PO:0025275) tissue that undergoes differentiation to form the primary vascular tissue (PO:0025408) of a root (PO:0009005).
procambium de la ra&#237z (Spanish, exact)
A derivative of the root apical meristem.
A lateral meristem (PO:0020145) that is part of a root (PO:0009005).
meristema lateral de la ra&#237z (Spanish, exact)
Not to be confused with lateral root apical meristem (PO:0006020), which is an apical meristem (PO:0020144) of a lateral root (PO:0020121).
A spikelet (PO:0009051) that is part of the tassel inflorescence (PO:0020126) and bears tassel florets (PO:0006310) at maturity.
penacho (borla) de la espiguilla (Spanish, exact)
A small staminate flower (PO:0025600) that is part of a tassel spikelet (PO:0006309).
florete del penacho (borla) (Spanish, exact)
The tassel floret (PO:0006310) initiates both stamens (PO:0009029) and carpels (PO:0009030), but all carpels abort during development. Found in Zea spp.
A tassel spikelet (PO:0006309) which is the ultimate, sessile, higher order inflorescence axis (PO:0009081) of the maize tassel inflorescence (PO:0020126).
penacho (borla) s&#233sil del florete (Spanish, exact)
Develops from the tassel spikelet pair meristem (PO:0006358).
A tassel spikelet (PO:0006309) which is the ultimate, pedicellate, higher order inflorescence axis (PO:0009081) of the maize tassel inflorescence (PO:0020126).
penacho (borla) pedicelada del florete (Spanish, exact)
A tassel floret that is the lower of the two florets of a pedicellate spikelet of a tassel inflorescence.
florete inferior de la espiguilla pedicelada (Spanish, exact)
lower floret of pedicellate spikelet of tassel
A tassel floret that is one of the two florets placed above the lower floret on a pedicellate spikelet rachilla of a tassel inflorescence.
florete superior de la espiguilla pedicelada (Spanish, exact)
upper floret of pedicellate spikelet of tassel
A tassel floret that is the lower of the two florets of a sessile spikelet of a tassel inflorescence.
florete inferior de la espiguilla s&#233sil (Spanish, exact)
lower floret of sessile spikelet of tassel
A tassel floret that is one of the two florets placed above the lower floret on a sessile spikelet rachilla of a tassel inflorescence.
florete superior de la espiguilla s&#233sil (Spanish, exact)
upper floret of sessile spikelet of tassel
Inflorescence branch that terminates in a spikelet.
pedicelo de la espiguilla (Spanish, exact)
This is not a pedicel in the strict sense, but is the ultimate naked part of the inflorescence axis.
A spikelet (PO:0009051) that is part of the ear inflorescence (PO:0020136) and bears a single ear floret (PO:0006354) at maturity.
The ear spikelet forms with two ear florets (PO:0006354), but the lower one aborts during development.
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a first order inflorescence axis (PO:0025104).
eje de segundo orden de la inflorescencia (Spanish, exact)
first order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a second order inflorescence axis (PO:0006322).
eje de tercero orden de la inflorescencia (Spanish, exact)
second order inflorescence branch (exact)
An inflorescence branch (PO:0009081) arising on a first order tassel inflorescence axis (PO:0006324) or from a higher order inflorescence branch (PO:0009081) that is part of a tassel inflorescence (PO:0020126).
rama del penacho (borla) (Spanish, exact)
A first order inflorescence axis (PO:0025104) that is the primary axis of a tassel inflorescence (PO:0020126).
central axis of tassel inflorescence (exact)
espiga central del penacho (borla) de la inflorescencia (Spanish, exact)
A shoot axis node (PO:0005004) that is part of an inflorescence axis (PO:0020122).
nodo de la inflorescencia (Spanish, exact)
A shoot axis internode (PO:0005005) that is part of an inflorescence axis (PO:0020122).
internodo de la inflorescencia (Spanish, exact)
An inflorescence apical meristem that gives rise to the two or more florets of a grass inflorescence.
meristema de la espiguilla (Spanish, exact)
The meristem that produces two spikelet meristems, each of which produces two floral meristems.
par de meristemas de la espiguilla (Spanish, exact)
A shoot axis (PO:0025029) that is an elongation of the floral axis that supports the carpel (PO:0009030).
A gynophore is only present when there is an elongation of the axis between the androecium and gynoecium. Found in peanut.
A cardinal part of multi-tissue plant structure (PO:0025498) that is a ridge on a seed (PO:0009010) that develops from a raphe (PO:0020027).
A cardinal part of multi-tissue plant structure (PO:0025498) that is attached to a seed (PO:0009010) and is the remnants of a funicle (PO:0020006).
fun&#237culo de la semilla (Spanish, exact)
A remnant of the ovular chalaza that is part of the seed.
A plant anatomical space that is enclosed by and forms an opening in a seed coat at the apex of a seed and is the remnant of a micropyle.
micr&#243pila de la semilla (Spanish, exact)
An outgrowth of the seed funicle, that forms a bridge between the seed micropyle and other tissues. It is also a remnant form of the obturator found in the ovular funicle.
obturador de la semilla (Spanish, exact)
portion of seed obturator tissue (exact)
A vascular leaf that is part of a plant embryo and is one of the first few leaves to develop from the embryonic shoot apical meristem.
This term is used to described not yet fully-developed leaves that are part of an embryo.
A vascular leaf that is distinct from adult leaves, being characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
Many species have juvenile leaves at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves are at the tip of the stalk (stem), which differentiates first, with adult leaves at the base, while other grasses may have other arrangements. The first juvenile leaves in Poaceae are the embryonic leaves found in the grass kernel (caryopsis).
A vascular leaf characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
Many species have juvenile leaves at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves are at the tip of the stalk (stem), which differentiates first, with adult leaves at the base, while other grasses may have other arrangements. In some plants the juvenile leaves may go on to establish as adult leaves.
A shoot system (PO:0009006) that develops from an embryo shoot apical meristem (PO:0006362).
sistema axilar primario (Spanish, exact)
A reproductive shoot system (PO:0025082) that develops from an inflorescence (PO:0009049) and has as parts each infructescence axis (PO:0025242) and all of the fruits (PO:0009001) borne by those axes.
A shoot-borne shoot system (PO:0004545) that develops from an axillary bud (PO:0004709).
sistema axilar del epiblasto (epiblastema) (Spanish, exact)
A lateral meristem (PO:0020145) that is part of a shoot axis (PO:0025029).
meristema lateral del epiblasto (epiblastema) (Spanish, exact)
An intercalary meristem (PO:0006073) that is part of a leaf (PO:0006346) and is intercalated between two portions of non-meristematic tissue between a leaf apex (PO:0020137) and a leaf base (PO:0020040).
meristema intercalar de la hoja (Spanish, exact)
Results in an increase in length of a leaf, as part of primary growth. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf. The leaf intercalary meristem does not include a leaf plate meristem (PO:0025429) .
An intercalary meristem (PO:0006073) that is part of a stem internode (PO:0020142) and is intercalated between two portions of non-meristematic tissue.
meristema intercalar del tallo (Spanish, exact)
Results in an increase in length of a stem internode, as part of primary growth.
An ear spikelet (PO:0006320) which is the ultimate, pedicellate, higher order inflorescence axis (PO:0009081) of the maize ear inflorescence (PO:0020136).
espiga pedicelada de la espiguilla (Spanish, exact)
Develops from the ear spikelet pair meristem (PO:0006360).
An ear spikelet (PO:0006320) which is the ultimate, sessile, higher order inflorescence axis (PO:0009081) of the maize ear inflorescence (PO:0020136).
espiga s&#233sil de la espiguilla (Spanish, exact)
An ear floret that is the upper of the two florets of a pedicellate spikelet rachilla of an ear inflorescence.
florete superior de la espiguilla pedicelada de la espiga (Spanish, exact)
The upper floret on the ear usually develops into a functional one.
upper floret of pedicellate spikelet of ear
An ear floret that is the lower of the two florets on a sessile spikelet of an ear inflorescence.
florete inferior de la espiguilla pedicelada de la espiga (Spanish, exact)
This floret does not usually develop into a functional one.
An ear floret that is one of the two florets placed above the lower floret on a sessile spikelet rachilla of an ear inflorescence.
florete superior de la espiguilla s&#233sil de la espiga (Spanish, exact)
This floret usually develops into a functional one.
An ear floret that is the lower of the two florets of a pedicellate spikelet rachilla of an ear inflorescence.
florete inferior de la espiguilla s&#233sil de la espiga (Spanish, exact)
The lower floret on the ear does not usually develop into a functional one.
lower floret of pedicellate spikelet of ear
A small, pistillate flower (PO:0025599) that is part of a ear spikelet (PO:0006320).
The ear floret (PO:0006354) initiates both carpels (PO:0009030) and stamens (PO:0009029), but all stamens abort during development. Found in Zea spp.
The meristem present on short tassel branch that produces two spikelet meristems, each of which produces two floral meristems in a maize tassel.
par de meristemas del penacho (borla) de la espiguilla (Spanish, exact)
An ear inflorescence axillary meristem (PO:0009110) that produces two ear spikelet meristems (PO:0006378), each of which produces two flower meristems (PO:0000229) in an ear inflorescence (PO:0020136).
par de meristemas de la espiga de la espiguilla (Spanish, exact)
A vegetative shoot apical meristem at the apex of the embryonic axis.
meristema embri&#243nico apical del epiblasto (epiblastema) (Spanish, exact)
A glume that is part of an ear spikelet.
gluma de la espiga de la espiguilla (Spanish, exact)
A glume that is part of a tassel spikelet.
gluma del penacho (borla) de la espiguilla (Spanish, exact)
A lower glume that is part of an ear spikelet.
gluma inferior la espiga de la espiguilla (Spanish, exact)
雌穂（花）小穂の第一苞頴(first glume) (Japanese, exact)
An upper glume that is part of a tassel spikelet.
gluma superior del penacho (borla) de la espiguilla (Spanish, exact)
雄穂（花）小穂の第二苞頴(second glume) (Japanese, exact)
An upper glume that is part of an ear spikelet.
gluma superior de la espiga de la espiguilla (Spanish, exact)
雌穂（花）小穂の第二苞頴(second glume) (Japanese, exact)
A lower glume that is part of a tassel spikelet.
gluma inferior del penacho (borla) de la espiguilla (Spanish, exact)
雄穂（花）小穂の第一苞頴(first glume) (Japanese, exact)
An inflorescence apical meristem that gives rise to the maize ear.
meristema apical de la espiga (Spanish, exact)
An inflorescence apical meristem that gives rise to the maize tassel.
meristema apical del penacho (borla) (Spanish, exact)
Apical meristem that gives rise to the upper and lower florets of the maize tassel spikelets.
meristema del penacho (borla) de la espiguilla (Spanish, exact)
Apical meristem that gives rise to the upper and lower florets of the maize ear spikelet.
meristema de la espiga de la espiguilla (Spanish, exact)
The axis of the tassel spikelet, above the glumes.
raquilla del penacho (borla) de la espiguilla (Spanish, exact)
The axis of the ear spikelet, above the glumes.
raquilla de la espiga de la espiguilla (Spanish, exact)
A lower glume of tassel spikelet that is part of a tassel pedicellate spikelet.
gluma inferior de la espiguilla pedicelada del penacho (borla) (Spanish, exact)
雄穂（花）の有柄小穂の第一苞頴(first glume) (Japanese, exact)
lower glume of pedicellate spikelet of tassel
A lower glume of tassel spikelet that is part of a tassel sessile spikelet.
gluma inferior de la espiguilla s&#233sil del penacho (borla) (Spanish, exact)
雄穂（花）の無柄小穂の第一苞頴(first glume) (Japanese, exact)
lower glume of sessile spikelet of tassel
An upper glume of tassel spikelet that is part of a tassel sessile spikelet.
gluma superior de la espiguilla s&#233sil del penacho (borla) (Spanish, exact)
雄穂（花）の無柄小穂の第二苞頴(second glume) (Japanese, exact)
upper glume of sessile spikelet of tassel
An upper glume of tassel spikelet that is part of a tassel pedicellate spikelet.
gluma superior de la espiguilla pedicelada del penacho (borla) (Spanish, exact)
雄穂（花）の有柄小穂の第二苞頴(second glume) (Japanese, exact)
upper glume of pedicellate spikelet of tassel
The axis of the tassel sessile spikelet, above the glumes.
raquilla de la espiguilla s&#233sil del penacho (borla) (Spanish, exact)
The axis of the tassel pedicellate spikelet, above the glumes.
raquilla de la espiguilla pedicelada del penacho (borla) (Spanish, exact)
rachilla of pedicellate spikelet of tassel
This is the ultimate branch of the pedicellate ear spikelet.
pedicelo de la espiguilla de la espiga (Spanish, exact)
This is the ultimate branch of the pedicellate tassel spikelet.
pedicelo de la espiguilla del penacho (borla) (Spanish, exact)
A peduncle of a maize tassel, below the lowest tassel node.
ped&#250nculo del penacho (borla) (Spanish, exact)
A peduncle of a maize ear, below the lowest ear node.
ped&#250nculo de la espiga (Spanish, exact)
The axis of the ear pedicellate spikelet, above the glumes.
raquilla de la espiguilla pedicelada de la espiga (Spanish, exact)
The axis of the ear sessile spikelet, above the glumes.
raquilla de la espiguilla s&#233sil de la espiga (Spanish, exact)
A lower glume of ear spikelet that is part of an ear pedicellate spikelet.
gluma inferior de la espiguilla pedicelada de la espiga (Spanish, exact)
雌穂（花）の有柄小穂の第一苞頴(first glume) (Japanese, exact)
lower glume of pedicellate spikelet of ear
A lower glume of ear spikelet that is part of an ear sessile spikelet.
gluma inferior de la espiguilla s&#233sil de la espiga (Spanish, exact)
雌穂（花）の無柄小穂の第一苞頴(first glume) (Japanese, exact)
An upper glume of ear spikelet that is part of an ear pedicellate spikelet.
gluma superior de la espiguilla pedicelada de la espiga (Spanish, exact)
雌穂（花）の有柄小穂の第二苞頴(second glume) (Japanese, exact)
upper glume of pedicellate spikelet of ear
An upper glume of ear spikelet that is part of an ear sessile spikelet.
gluma superior de la espiguilla s&#233sil de la espiga (Spanish, exact)
雌穂（花）の無柄小穂の第二苞頴(second glume) (Japanese, exact)
A collective organ part structure (PO:0025269) that has as parts an elongated stigma (PO:0009073) with stigma papilla (GO:0090397), and an elongated style (PO:0009074).
During pollination (GO:0009856), the pollen (PO:0025281) grows down through a portion of transmitting tissue (PO:0020102) to a plant ovary ovule (PO:0025490) and a megagametophyte (PO:0025279) to effect fertilization (GO:0009566). If you are annotating to this structure for Zea spp., please also add an annotation to the corresponding floret type. Choose the most specific term possible from: ear floret (PO:0006354), or one of the child terms: upper floret of pedicellate spikelet of ear (PO:0006350), or upper floret of sessile spikelet of ear (PO:0006352).
An abscission zone (PO:0000146) at the base of a vascular leaf (PO:0009025) where it separates during leaf abscission (GO:0060866).
zona de absici&#243n de la hoja (Spanish, exact)
An abscission zone (PO:0000146) at the base of a flower (PO:0009001) where a floral organ (PO:0025395) separates during floral organ abscission (GO:0010227).
zona de absici&#243n de la flor (Spanish, exact)
An abscission zone (PO:0000146) at the base of a fruit (PO:0009001) where the fruit separates from a fruit pedicel (PO:0030114) during fruit abscission (GO:0060867).
zona de absici&#243n del fruto (Spanish, exact)
落果実 (fruit shedding zone) (Japanese, exact)
A phyllome trichome that is part of a leaf epidermis.
A first order inflorescence axis (PO:0025104) that is the primary axis of an ear inflorescence (PO:0020136).
central axis of ear inflorescence (exact)
espiga central de la espiga de la inflorescencia (Spanish, exact)
7 linear grain-filling in maize (related)
7.3 early dough stage/embryo 3 in maize (related)
8.03 Early ripening in soybean (related)
BBCH principal growth stage 83 (related)
FR.01 early stage of fruit ripening in Solanaceae (related)
early dough, kernel content soft, about 45% dry matter (related)
The stage at which 3/4 of inflorescence has emerged from flag leaf sheath.
6.04-3/4 of inflorescence emerged in barley (related)
6.04-3/4 of inflorescence emerged in oat (related)
6.04-3/4 of inflorescence emerged in wheat (related)
70% of panicle emerged in rice (related)
IE.03 3/4 of inflorescence emerged from flag leaf sheath stage
An inflorescence detectable phase during which an inflorescence has reached at its full length.
4.04 full inflorescence length reached in soybean (related)
This phase can only be used if the final length of the inflorescence is known.
IL.03 full inflorescence length reached stage
An inflorescence detectable phase during which an inflorescence has reached at least one half of its full length, but has not yet reached its full length.
4.03 1/2 of inflorescence length reached in soybean (related)
IL.02 1/2 inflorescence length reached stage
An inflorescence detectable phase during which an inflorescence is just visible, but has not yet reach one quarter of its full length.
4.01 Inflorescence just visible in soybean (related)
visible flower buds in Arabidopsis (related)
Includes the time when the inflorescence can be seen by removing outer leaves or bracts, or when the inflorescence is visible as a swelling of the outer leaves or bracts, such as booting in Zea. This phase can only be used if the final length of the inflorescence is known.
A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.
7.07 Pod 70% of final length in soybean (related)
FF.03 fruit size 70% in Solanaceae (related)
This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).
whole plant fruit formation stage 50 to 70%
The stage at which 1/2 of inflorescence has emerged from flag leaf sheath.
6.03-1/2 of inflorescence emerged in barley (related)
6.03-1/2 of inflorescence emerged in oat (related)
6.03-1/2 of inflorescence emerged in wheat (related)
first individual flowers visible (related)
middle of panicle emergence in rice (related)
IE.02 1/2 of inflorescence emerged from flag leaf sheath stage
A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.
7.02 Pod 30% of final length in soybean (related)
FF.01 fruit size 30% in Solanaceae (related)
This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505).
whole plant fruit formation stage 10 to 30%
A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
09-dough development in barley (related)
dough stage kernels yellowish, about 55% dry matter (related)
silique ripening in Arabidopsis (related)
Succeeds a whole plant fruit formation stage (PO:0007042). This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.
5.2-late booting stage in rice (related)
In rice the flag leaf sheath is more than 10cm out of the penultimate leaf sheath. Booting is a term used specifically for grasses (Poaceae).
An inflorescence detectable phase characterized by a swelling of the flag leaf sheath, caused by an increase in the size of the inflorescence as it grows up the leaf sheath.
development of vegetatively propogated organs (related)
Booting is a term used specifically for grasses (Poaceae).
A root development stage (PO:0007520) during which a radicle (PO:0020031) emerges from the seed coat (PO:0009088).
0.02-radicle emergence from seed in maize (related)
0.2 radicle emergence from seed in maize (related)
05 radicle emergence from seed coat in soybean (related)
1.04-radicle emerged from seed in Triticeae (related)
1.04-radicle emerged from seed in barley (related)
1.04-radicle emerged from seed in oat (related)
1.04-radicle emerged from seed in wheat (related)
radicle emergence in Arabidopsis (related)
radicle emergence in Solanaceae (related)
The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed. If the fruit is a caryopsis, the dry pericarp is fused with the seed coat, and emergence from the pericarp is simultaneous with emergence from the seed coat. This term is used only for seed plants.
A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.
This term is to be used for a stage of development of a whole plant. For the stages of development of an individual flower, see flower development stage (PO:0007615).
A sporophyte development stage (PO:0028002) during which a sporophyte participates in multicellular organism senescence.
10.03-kernel loosening in daytime in Triticeae (related)
10.03-kernel loosening in daytime in barley (related)
10.03-kernel loosening in daytime in oat (related)
10.03-kernel loosening in daytime in wheat (related)
10.04-overripe, straw dead and collapsing in Triticeae (related)
10.04-overripe, straw dead and collapsing in barley (related)
10.04-overripe, straw dead and collapsing in oat (related)
10.04-overripe, straw dead and collapsing in wheat (related)
The sporophyte senescent stage is often preceded by the sporophyte reproductive stage, and it ends with death of the sporophyte, either as a result of senescence or some other cause. The sporophyte senescent stage may succeed the sporophyte reproductive stage in monocarpic plants that die after reproducing, such as annuals. This stage is distinct from sporophyte dormant stage, in which organs may senesce, but some parts of the plant remain alive. Multicellular organism senescence/aging (GO:0010259) includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.
The flag leaf sheath has started to extend.
5.01-flag leaf sheath extending in barley (related)
5.01-flag leaf sheath extending in oat (related)
5.01-flag leaf sheath extending in wheat (related)
5.1-early booting stage in rice (related)
In rice the flag leaf sheath is 5cm out of the penultimate leaf sheath. Upper part of the stem is slightly thickened. Booting is a term used specifically for grasses (Poaceae).
The first awns are visible and the flag leaf sheath has opened.
5.04-flag leaf sheath extending in barley (related)
5.04-flag leaf sheath extending in oat (related)
5.04-flag leaf sheath extending in wheat (related)
Awns will be visible only in those species and varieties where they are known to be present. Booting is a term used specifically for grasses (Poaceae).
A seed germination stage (PO:0007057) during which there is absorption of water by the seed (PO:0009010).
01 Beginning of seed imbibition in soybean (related)
03 Seed imbibition complete in soybean (related)
1.02-start of imbibition in Triticeae (related)
1.02-start of imbibition in barley (related)
1.02-start of imbibition in oat (related)
1.02-start of imbibition in wheat (related)
1.03-imbibition complete in Tricticeae (related)
1.03-imbibition complete in barley (related)
1.03-imbibition complete in oat (related)
1.03-imbibition complete in wheat (related)
The stage at which the inflorescence has fully emerged from the flag leaf sheath.
6.05-emergence of inflorescence completed in barley (related)
6.05-emergence of inflorescence completed in oat (related)
6.05-emergence of inflorescence completed in wheat (related)
end of panicle emergence in rice (related)
IE.04 inflorescence fully emerged from flag leaf sheath stage
The stage at which flowering is complete.
6.09 End of flowering in soybean (related)
7.03-anthesis completed in barley (related)
7.03-anthesis completed in oat (related)
7.03-anthesis completed in wheat (related)
FL.04 end of flowering in Solanaceae (related)
Zadok scale-69, Haun scale-11.6 (related)
The stage at which the inflorescence tip is just visible above flag leaf sheath.
6.01-first spikelet of inflorescence visible in barley (related)
6.01-first spikelet of inflorescence visible in oat (related)
6.01-first spikelet of inflorescence visible in wheat (related)
Zadok scale-50, Feekes scale-10.1, Haun scale-10.2 (related)
beginning of panicle emergence in rice (related)
beginning of tassel emergence in maize (related)
IE.00 inflorescence tip just visible above flag leaf sheath stage
The stage at which the first flower(s) open.
6.00 1st flowers on main stem open in soybean (related)
7.01-anthesis beginning in Triticeae (related)
7.01-anthesis beginning in barley (related)
7.01-anthesis beginning in oat (related)
7.01-anthesis beginning in wheat (related)
FL.00 first flower(s) open in Solanaceae (related)
Stage R1 Open flower at any node on the main stem (related)
first open flower in Arabidopsis (related)
These first flowers are not necessarily the oldest flowers in the inflorescence. In some cereal plants the flowering starts in the middle of the inflorescence. This stage refers to the whole plant.
A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.
BBCH principal growth stage 75 (related)
BBCH principal growth stage 79 (related)
FF.04 final fruit size in Solanaceae (related)
Kernels in middle of cob yellowish-white (related)
kernel content milky, 40% dry matter (related)
nearly all kernels have reached final size (related)
Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).
whole plant fruit formation stage 70% to final size
5.03-flag leaf sheath extending in barley (related)
5.03-flag leaf sheath extending in oat (related)
5.03-flag leaf sheath extending in wheat (related)
A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.
7.03 Pod 50% of final length in soybean (related)
8.01-kernel watery ripe in barley (related)
8.01-kernel watery ripe in oat (related)
8.01-kernel watery ripe in wheat (related)
BBCH principal growth stage 71 (related)
FF.02 fruit size 50% in Solanaceae (related)
Zadok scale-71, Feekes scale-10.54, Haun scale-12.1 (related)
beginning of grain development, kernels at blister stage, 16% dry matter (related)
This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506).
whole plant fruit formation stage 30 to 50%
Shoot or leaf breaks through soil surface.
The stage when fruit ripening is midway.
7.4 late dough stage/embryo 4 in maize (related)
BBCH principal growth stage 85 (related)
DNA degradation (endosperm) in maize (related)
FR.02 mid stage of fruit ripening in Solanaceae (related)
Zadok scale-85, Feekes scale-11.2 (related)
A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.
7.01 Pod 10% of final length in soybean (related)
FF.00 fruit size 10% in Solanaceae (related)
This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504).
whole plant fruit formation stage up to 10%
A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
Solanaceae whole plant growth stages (SGN:0000001) (related)
cereal plant growth stage ontology (GRO:0007199) (related)
maize growth stage (GRO:0007002) (related)
plant growth stages in Arabidopsis (TAIR:0000021) (related)
rice growth stage (GRO:0007040) (related)
sorghum growth stage (GRO:0007124) (related)
wheat, barley and oat growth stage (GRO:0007156) (related)
6.02 1/4 of flowers on the main stem open in soybean (related)
FL.01 1/4 of flowers open in Solanaceae (related)
The stage at which fruit maturation begins.
8.01 Beginning of bean ripening in soybean (related)
FR.00 beginning of fruit ripening in Solanaceae (related)
beginning of whole plant fruit ripening stage
Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem.
The stage at which fruit ripening is complete.
8.09 Final ripening in soybean (related)
BBCH principal growth stage 89 (related)
FR.04 fruit ripening complete in Solanaceae (related)
fully ripe grain hard, difficult to divide by thumbnail in rice (related)
fully ripe kernels hard and shiny about 65% dry matter in maize (related)
whole plant fruit ripening complete stage
A trichome development stage that has as primary participant a leaf trichome.
An inflorescence detectable phase during which an inflorescence emerges from sheathing leaves or bracts.
06-inflorescence emergence in barley (related)
06-inflorescence emergence in oat (related)
06-inflorescence emergence in wheat (related)
Includes emergence of a Zea mays inflorescence from a flag leaf sheath, following booting. In US cornbelt maize (including B73) the tassel fully emerges about 2-3 days prior to silk emergence from husk leaves. At this time the ear and husk may still be enclosed within its leaf sheath depending on the variety and environmental conditions.
A whole plant fruit development stage (PO:0025500) that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) that is not currently participating in a whole plant fruit development stage begins a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).
5 fruit formation in Solanaceae (related)
This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit formation stages during its life. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun. Although the use of synonyms like "07-milk stage in rice" properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.
A seedling development stage (PO:0007131) during which the hypocotyl (PO:0020100) emerges from the seed coat (PO:0009088).
0.07.01 Cotyledons and hypocotyl emerge in soybean (related)
0.07.02 Hypocotyl emerges above soil in soybean (related)
hypocotyl and cotyledon emergence in Arabidopsis (related)
hypocotyl emergence in Solanaceae (related)
This term is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed (PO:0009010) is underneath a growth medium. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed.
The flag leaf sheath is just visibly swollen.
5.02-flag leaf sheath extending in barley (related)
5.02-flag leaf sheath extending in oat (related)
5.02-flag leaf sheath extending in wheat (related)
Zadok scale-45, Feekes scale-10, Haun scale-9.2 (related)
flag leaf sheath just visibly swollen (related)
In rice the flag leaf sheath is 5-10cm out of the penultimate leaf sheath. Booting is a term used specifically for grasses (Poaceae).
A sporophyte vegetative stage (PO:0007134) during which the coleoptile (PO:0020033) emerges from the seed coat (PO:0009088).
0.3 coleoptile emergence from seed in maize (related)
Occurs in Poaceae and some other monocotyledons. May occur simultaneously with coleoptile emergence from the growth medium. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed (PO:0009010) is underneath a growth medium. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed. If the fruit is a caryopsis, the dry pericarp is fused with the seed coat, and emergence from the pericarp is simultaneous with emergence from the seed coat. This terms is used only for seed plants.
An inflorescence detectable phase during which an inflorescence has reached at least one quarter of its full length, but has not yet reached one half of its full length.
4.02 1/4 of inflorescence length reached in soybean (related)
IL.01 1/4 inflorescence length reached stage
A reproductive growth stage during which an inflorescence is detectable.
3 inflorescence visible in Solanaceae (narrow)
4 Inflorescence Formation in soybean (narrow)
This includes the stage when an inflorescence starts to develop (and is detectable only by assay or with a microscope), to the stage where it is visible to the naked eye. This includes the booting stage in the grasses (Poaceae). There is no one-to-one correspondence between some of the phases of inflorescence formation in members of Poaceae (e.g., booting) with that of other families.
whole plant inflorescence detectable stage
The stage at which 1/4 of inflorescence has emerged from flag leaf sheath.
30% of panicle emerged in rice (related)
6.02-1/4 of inflorescence emerged in barley (related)
6.02-1/4 of inflorescence emerged in oat (related)
6.02-1/4 of inflorescence emerged in wheat (related)
Zadok scale-53, Feekes scale-10.2 (related)
IE.01 1/4 of inflorescence emerged from flag leaf sheath stage
A seedling development stage (PO:0007131) during which the cotyledon (PO:0020030) emerges from the seed coat (PO:0009088).
01-seedling emergence in sorghum (related)
1.00 Cotyledon visible in soybean (related)
1.01-seedling emergence in maize (related)
1.1 seedling emergence in maize (related)
2.01-first leaf through coleoptile in Triticeae (related)
2.01-first leaf through coleoptile in barley (related)
2.01-first leaf through coleoptile in oat (related)
2.01-first leaf through coleoptile in wheat (related)
Oryza first leaf through coleoptile (related)
Triticeae first leaf through coleoptile (related)
Zadok scale-10, Feekes scale-1 (related)
cotyledon emergence in Solanaceae (related)
cotyledons fully open in Arabidopsis (related)
This term is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium, especially in plants with hypogeal germination. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed.
8 leveling off of grain-filling/embryo 5 in maize (related)
9.1 physiological maturity/embryo 6 in maize (related)
BBCH principal growth stage 87 (related)
FR.03 late stage of fruit ripening in Solanaceae (related)
Stage R7 Beginning maturity in soybean (related)
leveling off of dry matter accumulation (related)
physiological maturity, black dot, about 60% dry matter in maize (related)
6.02 3/4 of flowers on main stem open in soybean (related)
FL.03 3/4 of flowers open in Solanaceae (related)
Stage R2 Open flower at one of the two uppermost nodes on the main stem with fully developed leaf in soybean (related)
6.02 1/2 of flowers on main stem open in soybean (related)
7.02-anthesis half-way in barley (related)
7.02-anthesis half-way in wheat (related)
FL.02 1/2 of flowers open in Solanaceae (related)
A seedling development stage (PO:0007131) during which the epicotyl (PO:0020035) emerges from the seed coat (PO:0009088).
Occurs in plants with hypogeal germination such as pea (pisum sativum). The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed (PO:0009010) is underneath a growth medium. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed.
Trichome initiation stage that determine numbers of trichome are formed.
A sporophyte vegetative stage (PO:0007134) which begins with the onset of a seed imbibition stage (PO:0007022) and ends with a radicle emergence stage (PO: 0007015), or a coleorhiza emergence stage (PO:0025475), as a result of the growth by the plant embryo (PO:0004537) in a seed (PO:0009010).
The stage trichome nuclei continue to replicate their DNA after mitosis and cytokinesis have ceased, and as a consequence have a DNA content much greater than 2C.
The stage at which six nodes or six internodes are visible.
3.06 6 nodes/internodes visible in soybean (related)
4.07-sixth node detectable in barley (related)
4.07-sixth node detectable in oat (related)
4.07-sixth node detectable in wheat (related)
A measure of vegetative growth, but leaf production is to be preferred.
SE.06 six nodes or internodes visible stage
The stage at which leaves at seven nodes, other than the cotyledonary node, are visible above ground.
1.07 6th trifoliolate leaf unfolded in soybean (related)
2.08-seven leaves unfolded in Triticeae (related)
2.08-seven leaves unfolded in barley (related)
2.08-seven leaves unfolded in oat (related)
2.08-seven leaves unfolded in wheat (related)
3.1 ear initiation/mid-whorl stage in maize (related)
LP.07 seven leaves visible in Solanaceae (related)
Triticeae seven leaves unfolded (related)
The leaves can be a single leaf, two, or whorls of leaves at each node.
The stage at which leaves at twelve nodes, other than the cotyledonary node, are visible above ground.
1.12 11th trifoliolate leaf unfolded in soybean (related)
12 rosette leaf in Arabidopsis (related)
3.3 mid-vegetative stage of maize (related)
The stage at which leaves at five nodes, other than the cotyledonary node, are visible above ground.
1.05 4th trifoliolate leaf unfolded in soybean (related)
2 tassel initiation/early whorl stage in maize (related)
2.06-five leaves unfolded in Triticeae (related)
2.06-five leaves unfolded in barley (related)
2.06-five leaves unfolded in oat (related)
2.06-five leaves unfolded in wheat (related)
LP.05 five leaves visible in Solanaceae (related)
Triticeae five leaves unfolded (related)
Zadok scale-15, Haun scale-4.+ (related)
tassel differentiation in maize (related)
The stage at which nine nodes or nine internodes are visible.
3.09 9 nodes/internodes visible in soybean (related)
SE.09 nine nodes or internodes visible stage
The stage at which leaves at seventeen nodes, other than the cotyledonary node, are visible above ground.
1.17 16th trifoliate leaf unfolded in soybean (related)
3.4 late vegetative stage of maize (related)
late vegetative stage of maize (related)
Rosette has reached approximately 50% of its final diameter.
mid rosette growth in Arabidopsis (related)
The stage at which eight nodes or eight internodes are visible.
3.08 8 nodes/internodes visible in soybean (related)
SE.08 eight nodes or internodes visible stage
The stage at which main shoot and axillary shoots at two nodes are visible.
2.02 Main shoot and axillary shoots visible at 2 nodes in soybean (related)
2.02 main shoot and axillary shoots visible at two nodes in Solanaceae (related)
3.03-main shoot and two tillers (related)
main shoot and second tiller visible (related)
main shoot and two tillers in barley (related)
main shoot and two tillers in oat (related)
main shoot and two tillers in wheat (related)
second axillary shoot detectable (related)
The axillary shoot can be a single shoot or a pair of axillary shoots at each node.
2.02 main shoot and axillary shoots visible at two nodes stage
The stage at which leaves at eighteen nodes, other than the cotyledonary node, are visible above ground.
VT vegetative tasseling in maize (US cornbelt) (narrow)
1.18 17th trifoliolate leaf unfolded in soybean (related)
The stage at which the axillary shoots are forming.
2 axillary Shoot Formation in soybean (related)
2 formation of axillary shoot in Solanaceae (related)
The stage at which fifteen nodes or fifteen internodes are visible.
3.15 15 nodes/internodes visible in soybean (related)
SE.15 fifteen nodes or internodes visible stage
Rosette has reached approximately 70% of its final diameter.
late rosette growth in Arabidopsis (related)
The stage at which main shoot and axillary shoots at eight nodes are visible.
2.08 Main shoot and axillary shoots visible at 8 nodes in soybean (related)
2.08 main shoot and axillary shoots visible at eight nodes in Solanaceae (related)
3.09-main shoot and eight tillers (related)
eighth axillary shoot detectable (related)
main shoot and eight tillers in barley (related)
main shoot and eight tillers in oat (related)
main shoot and eight tillers in wheat (related)
main shoot and eighth tiller visible (related)
2.08 main shoot and axillary shoots visible at eight nodes stage
Stage at which rosette no longer increases in diameter, its leaf growth and expansion having ceased.
complete rosette in Arabidopsis (related)
The stage at which the internodes begin to elongate.
3.00 stem elongation begins in soybean (related)
4.01-pseudo stem erection in barley (related)
4.01-pseudo stem erection in oat (related)
4.01-pseudo stem erection in wheat (related)
4.2-panicle differentiation stage (related)
The stage at which main shoot and axillary shoots at three nodes are visible.
2.03 Main shoot and axillary shoots visible at 3 nodes in soybean (related)
2.03 main shoot and axillary shoots visible at three nodes in Solanaceae (related)
3.04-main shoot and three tillers (related)
main shoot and third tiller visible (related)
main shoot and three tillers in barley (related)
main shoot and three tillers in oat (related)
main shoot and three tillers in wheat (related)
third axillary shoot detectable (related)
2.03 main shoot and axillary shoots visible at three nodes stage
Rosette has reached approximately 20% of its final diameter.
early rosette growth in Arabidopsis (related)
The stage at which leaves at twenty or more nodes, other than the cotyledonary node, are visible above ground.
1.20 19th trifoliolate leaf unfolded in soybean (related)
1.21 20th trifoliolate leaf unfolded in soybean (related)
1.22 21st trifoliolate leaf unfolded in soybean (related)
1.23 22nd trifoliolate leaf unfolded in soybean (related)
1.24 23rd trifoliolate leaf unfolded in soybean (related)
1.25 25 or more trifoliolate leaves unfolded in soybean (related)
LP.20 twenty or more leaves whorls visible stage
The stage at which leaves at thirteen nodes, other than the cotyledonary node, are visible above ground.
1.13 12th trifoliolate leaf unfolded in soybean (related)
13 rosette leaf in Arabidopsis (related)
The stage at which ten nodes or ten internodes are visible.
3.10 10 nodes/internodes visible in soybean (related)
SE.10 ten nodes or internodes visible stage
The stage at which leaves at fourteen nodes, other than the cotyledonary node, are visible above ground.
1.14 13th trifoliolate leaf unfolded in soybean (related)
14 rosette leaf in Arabidopsis (related)
The stage at which five nodes or five internodes are visible.
3.05 5 nodes/internodes visible in soybean (related)
4.06-fifth node detectable in barley (related)
4.06-fifth node detectable in oat (related)
4.06-fifth node detectable in wheat (related)
SE.05 five nodes or internodes visible stage
The stage at which main shoot and axillary shoot(s) at one node is (are) visible.
2.01 Main shoot and axillary shoot visible at one node in soybean (related)
2.01 main shoot and axillary shoots visible at one node in Solanaceae (related)
3.02-main shoot and one tiller (related)
Zadok scale-21, Feekes scale-2 (related)
first axillary shoot detectable (related)
main shoot and first tiller visible (related)
main shoot and one tiller in barley (related)
main shoot and one tiller in oat (related)
main shoot and one tiller in wheat (related)
2.01 main shoot and axillary shoots visible at one node stage
The stage at which main shoot and axillary shoots at four nodes are visible.
2.04 Main shoot and axillary shoots visible at 4 nodes in soybean (related)
2.04 main shoot and axillary shoots visible at four nodes in Solanaceae (related)
3.05-main shoot and four tillers (related)
fourth axillary shoot detectable (related)
main shoot and four tillers in barley (related)
main shoot and four tillers in oat (related)
main shoot and four tillers in wheat (related)
main shoot and fourth tiller visible (related)
2.04 main shoot and axillary shoots visible at four nodes stage
The stage at which the internodes elongate.
04-stem elongation stage in Triticeae (related)
05-growing point differentiation (related)
3 rapid stem elongation in maize (related)
The stage at which thirteen nodes or thirteen internodes are visible.
3.13 13 nodes/internodes visible in soybean (related)
SE.13 thirteen nodes or internodes visible stage
The stage at which one node or one internode is visible.
3.01 one node visible in soybean (related)
3.1 ear initiation/mid-whorl stage (related)
4.02-first node detectable in barley (related)
4.02-first node detectable in oat (related)
4.02-first node detectable in wheat (related)
Zadok scale-31, Feekes scale-6 (related)
SE.01 one node or internode visible stage
The stage at which four nodes or four internodes are visible.
3.04 4 nodes/internodes visible in soybean (related)
4.05-fourth node detectable in barley (related)
4.05-fourth node detectable in oat (related)
4.05-fourth node detectable in wheat (related)
SE.04 four nodes or internodes visible stage
The stage at which main shoot and axillary shoots at five nodes are visible.
2.05 Main shoot and axillary shoots visible at 5 nodes in soybean (related)
2.05 main shoot and axillary shoots visible at five nodes in Solanaceae (related)
3.06-main shoot and five tillers in Triticeae (related)
3.06-main shoot and five tillers in barley (related)
3.06-main shoot and five tillers in oat (related)
3.06-main shoot and five tillers in wheat (related)
fifth axillary shoot detectable (related)
main shoot and fifth tiller visible (related)
main shoot and five tillers in barley (related)
main shoot and five tillers in oat (related)
main shoot and five tillers in wheat (related)
2.05 main shoot and axillary shoots visible at five nodes stage
The stage at which leaves at one node, other than the cotyledonary node, are visible above ground.
1.01 Unifoliolate leaves unfolded in soybean (related)
1.02-one to two leaves in maize (related)
2.02-first leaf unfolded in Triticeae (related)
2.02-first leaf unfolded in barley (related)
2.02-first leaf unfolded in oat (related)
2.02-first leaf unfolded in wheat (related)
LP.01 one leaf visible in Solanaceae (related)
Zadok scale-11, Haun scale-1.+ (related)
In the taxa with hypogeal type germination the first leaf on the epicotyl is leaf 1, and in grasses, the coleoptile is leaf 1. The leaves can be a single leaf, two, or whorls of leaves at each node.
The stage at which leaves at eight nodes, other than the cotyledonary node, are visible above ground.
1.08 7th trifoliolate leaf unfolded in soybean (related)
2.09-eight leaves unfolded in Triticeae (related)
2.09-eight leaves unfolded in barley (related)
2.09-eight leaves unfolded in oat (related)
2.09-eight leaves unfolded in wheat (related)
8 rosette leaves in Arabidopsis (related)
LP.08 eight leaves visible in Solanaceae (related)
Triticeae eight leaves unfolded (related)
Zadok scale-18, Haun scale-7.+ (related)
The stage at which three nodes or three internodes are visible.
3.03 3 nodes/internodes visible in soybean (related)
4.04-third node detectable in barley (related)
4.04-third node detectable in oat (related)
4.04-third node detectable in wheat (related)
SE.03 three nodes or internodes visible stage
The stage at which fourteen nodes or fourteen internodes are visible.
3.14 14 nodes/internodes visible in soybean (related)
SE.14 fourteen nodes or internodes visible stage
The stage at which leaves at two nodes, other than the cotyledonary node, are visible above ground.
1.02 First trifoliolate leaf unfolded in soybean (related)
2 rosette leaves in Arabidopsis (related)
2.03-two leaves unfolded in Triticeae (related)
2.03-two leaves unfolded in barley (related)
2.03-two leaves unfolded in oat (related)
2.03-two leaves unfolded in wheat (related)
LP.02 two leaves visible in Solanaceae (related)
Zadok scale-12, Haun scale-1.+ (related)
In grasses, the plant has one leaf plus the coleoptile. The leaves can be a single leaf, two, or whorls of leaves at each node.
The stage at which the flag leaf is visible.
06-flag leaf visible in sorghum (related)
4.08-flag leaf just visible in barley (related)
4.08-flag leaf just visible in oat (related)
4.08-flag leaf just visible in wheat (related)
Zadok scale-37, Feekes scale-8 (related)
The stage at which sixteen nodes or more, or sixteen internodes or more are visible.
3.16 16 or more nodes/internodes visible in soybean (related)
SE.16 sixteen or more nodes or internodes visible stage
The stage at which leaves at nine nodes, other than the cotyledonary node, are visible above ground.
1.09 8th trifoliolate leaf unfolded in soybean (related)
2.10 nine or more leaves unfolded in Triticeae (related)
2.10 nine or more leaves unfolded in barley (related)
2.10 nine or more leaves unfolded in oat (related)
2.10 nine or more leaves unfolded in wheat (related)
LP.09 nine or more leaves whorls visible (related)
The stage at which leaves at ten nodes, other than the cotyledonary node, are visible above ground.
10 rosette leaf in Arabidopsis (related)
The stage at which leaves at fifteen nodes, other than the cotyledonary node, are visible above ground.
1.15 14th trifoliolate leaf unfolded in soybean (related)
The stage at which leaves at three nodes, other than the cotyledonary node, are visible above ground.
02-three leaf stage in sorghum (related)
1.03 2nd trifoliolate leaf unfolded in soybean (related)
1.03-three to four leaves in maize (related)
LP.03 three leaves visible in Solanaceae (related)
Zadok scale-13, Haun scale-2.+ (related)
The stage at which seven nodes or seven internodes are visible.
3.07 7 nodes/internodes visible in soybean (related)
SE.07 seven nodes or internodes visible stage
The stage at which maximum stem length is reached.
3.99 Maximum stem length reached in soybean (related)
4.09-flag leaf ligule/collar just visible in barley (related)
4.09-flag leaf ligule/collar just visible in oat (related)
4.09-flag leaf ligule/collar just visible in wheat (related)
Zadok scale-39, Feekes scale-9 (related)
The stage at which main shoot and axillary shoots at nine nodes or more are visible.
2.09 Main shoot and axillary shoots visible at 9 or more nodes in soybean (related)
2.09 main shoot and axillary shoots visible at nine or more nodes in Solanaceae (related)
3.10-main shoot and nine or more tillers in Triticeae (related)
main shoot and 9 or more tiller (related)
main shoot and nine or more tillers in barley (related)
main shoot and nine or more tillers in oat (related)
main shoot and nine or more tillers in wheat (related)
maximum number of tillers detectable in (related)
maximum number of tillers visible (related)
maximum number of tillers visible in rice (related)
nine or more axillary shoots detectable (related)
2.09 main shoot and axillary shoots visible at nine or more nodes stage
The stage at which twelve nodes or twelve internodes are visible.
3.12 12 nodes/internodes visible in soybean (related)
SE.12 twelve nodes or internodes visible stage
The stage at which vegetative structures are being produced by SAM.
1 main shoot growth in Solanaceae (related)
sorghum principal growth stage 1 (related)
In monocots each leaf stage is defined according to the uppermost leaf whose collar is visible (Handbook of plant and crop physiology).
Stages of growth based on expansion of the rosette in Arabidopsis.
The stage at which eleven nodes or eleven internodes are visible.
3.11 11 nodes/internodes visible in soybean (related)
SE.11 eleven nodes or internodes visible stage
The stage at which leaves at four nodes, other than the cotyledonary node, are visible above ground.
1.04 3rd trifoliolate leaf unfolded in soybean (related)
2.05-four leaves unfolded in Triticeae (related)
LP.04 four leaves visible in Solanaceae (related)
Zadok scale-14, Haun scale-3.+ (related)
The stage at which leaves at eleven nodes, other than the cotyledonary node, are visible above ground.
1.11 10th trifoliolate leaf unfolded in soybean (related)
11 rosette leaves in Arabidopsis (related)
3.02-late whorl stage in maize (related)
The stage at which two nodes or two internodes are visible.
3.02 2 nodes/internode visible in soybean (related)
4.03-second node detectable in barley (related)
4.03-second node detectable in oat (related)
4.03-second node detectable in wheat (related)
Zadok scale-32, Feekes scale-7 (related)
SE.02 two nodes or internodes visible stage
The stage at which main shoot and axillary shoots at six nodes are visible.
2.06 Main shoot and axillary shoots visible at 6 nodes in soybean (related)
2.06 main shoot and axillary shoots visible at six nodes in Solanaceae (related)
3.07-main shoot and six tillers (related)
Zadok scale-26, Feekes scale-3 (related)
main shoot and six tillers in barley (related)
main shoot and six tillers in oat (related)
main shoot and six tillers in wheat (related)
sixth axillary shoot detectable (related)
2.06 main shoot and axillary shoots visible at six nodes stage
The stage at which leaves at sixteen nodes, other than the cotyledonary node, are visible above ground.
1.16 15th trifoliolate leaf unfolded in soybean (related)
16 rosette leaf in Arabidopsis (related)
The stage at which leaves at nineteen nodes, other than the cotyledonary node, are visible above ground.
1.19 18th trifoliolate leaf unfolded in soybean (related)
The stage at which main shoot and axillary shoots at seven nodes are visible.
2.07 Main shoot and axillary shoots visible at 7 nodes in soybean (related)
2.07 main shoot and axillary shoots visible at seven nodes in Solanaceae (related)
3.08-main shoot and seven tillers (related)
main shoot and seven tillers in barley (related)
main shoot and seven tillers in oat (related)
main shoot and seven tillers in wheat (related)
main shoot and seventh tiller visible (related)
seventh axillary shoot detectable (related)
2.07 main shoot and axillary shoots visible at seven nodes stage
The stage at which leaves at six nodes, other than the cotyledonary node, are visible above ground.
1.06 5th trifoliolate leaf unfolded in soybean (related)
2.07-six leaves unfolded in Triticeae (related)
LP.06 six leaves visible in Solanaceae (related)
Zadok scale-16, Haun scale-5.+ (related)
A sporophyte development stage that occurs during the interval between the initiation of a sporangium and the onset of senescence.
sporophyte reproductively competent stage (exact)
B reproductive growth in Solanaceae (related)
A whole plant may continue developmental vegetative growth (GO:0080186) after it has entered the reproductive stage, and it may revert to a stage in which it is no longer producing sporangia, but once it has initiated a single sporangium, it remains in the reproductive stage until senescence or death by some other cause.
A sporophyte vegetative stage (PO:0007134) that succeeds the seed germination stage (PO:0007057) and terminates with the development of the first adult vascular leaf (PO:0006340).
This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
A sporophyte development stage during which a sporophyte participates in a dormancy process.
A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy of a plant may be preceded by the senescence of its parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a sporophyte dormant stage are the resurrection plants Selaginella lepidophylla (a lycopod) and Craterostigma plantagineum (an angiosperm) while they are dessicated, and deciduous woody plants and herbaceous perennials or biennials that have a dormant stage in response to drought or cold.
The stage at which the leaves produced by SAM are visible above the ground in a seedling or mature plant.
This stage is recommended over rosette growth or stem elongation as it is most easily observed and least ambiguous.
A sporophyte development stage (PO:0028002) that occurs during the interval between the first division of a plant zygote (PO:0000423) and the formation of a sporangium (PO:0025094).
A vegetative growth in Solanaceae (related)
Succeeds a plant zygote stage (PO:0001097). A sporophyte may begin to senesce or die from other causes before producing sporangia. Developmental vegetative growth (GO:0080186) can also occur during the reproductive stage.
The stage involved in the directionality of expansion growth.
The stage at which the root cap becomes evident.
root cap formation in crown root. (related)
root cap formation in lateral root. (related)
root cap formation in primary root. (related)
The number and origin of root cap initials that form the root cap varies among species. The root cap initials become independent from the more internally located root meristem cells by an increase in the thickness of the cell wall that separates them.
The stage at which the initial cells of crown root primordium are formed in the innermost ground meristem cells by one or two periclinal divisions.
Crown root primordia formed endogenously opposite the collateral bundles in maize.
The stage at which root primordium originates and develops at specific locations in embryonic and post embryonic roots.
The stage at which a group of cells or initials that will differentiate into the primary root become organized in the embryo .
The stage at which the root vascular cylinder becomes evident.
The first identifiable region in the differentiating vascular cylinder is the pericycle. In the xylem the differentiation of the tracheary elements begins in a centrifugal direction but is completed in the centripetal direction. The first phloem elements mature before the first xylem elements.
root vascular cylinder differentiation stage
The stage at which the fully formed root emerges.
This stage at which the transverse divisions in pericycle cells form the initials of the lateral root primordium.
The stage at which the root cortex becomes evident.
cortex differentiation of crown root. (related)
cortex differentiation of lateral root (related)
cortex differentiation of primary root. (related)
Repetitive periclinal divisions and radial enlargement of cells form the cortex layers, the innermost layers become the endodermis with the differentiation of casparian strips.
The stage at which the root epidermis becomes evident.
epidermal differentiation of lateral root. (related)
epidermal differentiation of primary root (related)
epidermial differentiation of crown root. (related)
Root hairs come to full development beyond the region of elongation zone, approximately at the level where the xylem begins to mature.
The stage at which the lateral root emerges.
Starch grains can be seen in the root cap after emergence.
The stage at which the crown root emerges.
Crown root stages are based on rice plant.
The stage at which the root hairs becomes evident.
Benfey's stage 3 of root development (related)
Stages of development of a root defined by characteristic morphological, structural, histological or other visible features.
At present the stages are described for primary, lateral and crown roots and stages for adventitious root formed by wounding or hormone treatment is not described. Finer resolution of root stages has been kept in the obsolete node as they are not consistently used in the consulted literature. These terms will be reintroduced into the ontology when there is a specific user request.
The stage at which distinct tissues become organized.
Benfey's stage 1 of root development (related)
cell differentiation stage of root development (related)
establishment of fundamental organization in adventitious root (related)
establishment of fundamental organization in primary root. (related)
establishment of fundamental organization lateral root. (related)
The stage at which the root meristem becomes evident.
Characteristic differences in meristem organization have been related to taxonomic groups. Terms for developmental zones formation are available in the obsolete node, and they will be reintroduced in the ontology when there is a specific user request for them.
A floral organ formation stage (PO:0025585) which begins with the differentiation of floral organs (PO:0025395) from the floral organ primordium (PO:0025477) and ends with the beginning of the flowering stage (PO:0007616).
3 floral organ development stages (related)
stage 6-12 flower in Arabidopsis (related)
During this stage, the process of floral organ development (GO:0048437) occurs, defined as the process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.
A floral organ formation stage (PO:0025585) which begins with the development of the floral organ meristem (PO:0000229) from a portion of meristem tissue (PO:0009013) and ends with the beginning of the floral organ primordium development stage (PO:0007602).
During this stage, the process of floral meristem growth (GO:0010451) occurs. This process is defined as the increase in size or mass of a floral meristem, a population of undifferentiated cells in a plant that gives rise to a flower.
A floral organ formation stage (PO:0025585) which begins with the appearance of the floral organ primordium (PO:0025477) and ends with the beginning of the floral organ differentiation stage (PO:0007600).
During this stage, the process of floral meristem determinacy (GO:0010582) occurs, where a floral meristem becomes determinate (i.e. ceases to produce lateral organs and may or may not terminally differentiate). This stage may be indicated by a slight indentation to the inflorescence meristem.
floral organ primordium development stage
A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).
A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).
A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
Stage of calyx development that begins when the sepal primordia arise.
Stage of corolla development that begins when the petal or petal-stamen primordia arise.
Stage of corolla development defined by differentiation and expansion of petal.
stage 10 flower in Arabidopsis (related)
stage 12 flower in Arabidopsis (related)
petal differentiation and expansion stage
Stage of corolla development when petal is fully expanded.
Stage of androecium development that begins when the stamens or petal-stamen primordia arise.
A reproductive shoot system development stage (PO:0025530) that occurs in an individual flower (PO:000904) during the interval between the onset of a flower meristem transition stage (PO:0025588) and the end of a flowering stage (PO:0007616).
flower development in Arabidopsis (related)
This term and its sub-classes apply to an individual flower (PO:000904). During this stage, a flower undergoes the process of flower development (GO:0009908), defined as the process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. For the development stage of a whole plant (PO:0000003), use whole plant flowering stage (PO:0007016).
A flower development stage (PO:0007615) that begins when pollen (PO:0025281) is released by anther dehiscence (GO:0009901) and/or the stigma (PO:0009073) is receptive and ends with the process of pollination (GO:0009856) and/or floral organ senescence (GO:0080187).
stage 13 flower in Arabidopsis (related)
stage 14 flower in Arabidopsis (related)
stage 15 flower in Arabidopsis (related)
stage 16 flower in Arabidopsis (related)
In most species, flowering stage (anthesis) is when the flower is open and ends with pollination. During this stage, the process of anther dehiscence (GO:0009901) usually occurs, defined as the dehiscence of an anther to release the pollen grains contained within it. This term applies to an individual flower (PO:000904).
Stage of gynoecium development that begins when the carpel primordia arise.
Stages of development of the ovule defined by characteristic morphological, structural, histological or other visible features.
ovule development in Arabidopsis (related)
Stage of ovule development that begins when the ovule primordia arise.
ovule stage 1-I in Arabidopsis (related)
A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.
Although megaspore and megagametophyte development are normally separate, one spore producing one gametophyte, in some flowering plants a single gametophyte may be produced from two or four spores.
Stage of ovule development that begins when the integument primordia are visible.
ovule stage 2-II in Arabidopsis (related)
ovule stage 2-III in Arabidopsis (related)
The stage of megagametophyte development when the megaspore mother cell enlarges.
ovule stage 2-I in Arabidopsis (related)
The stage of megagametophyte development when the megaspore mother cell undergoes meiosis.
ovule stage 2-IV in Arabidopsis (related)
B meiosis of megaspore mother cell stage
The product of meiosis of the megaspore mother cell.
ovule stage 2-V in Arabidopsis (related)
The stage of megagametophyte development when non-functional megaspores degenerate.
ovule stage 3-I in Arabidopsis (related)
In some plants more than one megaspore contributes to the megametophyte.
The stage of megagametophyte development when there are two nuclei.
ovule stage 3-II in Arabidopsis (related)
The stage of megagametophyte development when there are four nuclei.
ovule stage 3-IV in Arabidopsis (related)
The stage of megagametophyte development when there are eight nuclei.
ovule stage 3-V in Arabidopsis (related)
Some plants do not form an eight nucleate megametophyte.
A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following: the beginning of the seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
The plant embryo stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. No plant species undergoes all of the sub-stages of plant embryo development stage listed here.
Stage during which the seed storage products (storage proteins, lipids and starch) are being accumulated, either in the cotyledons or in the endosperm. Also, LEA proteins are accumulated and subsequently, a desiccation tolerant state is reached at the end of this stage.
seed maturation in Arabidopsis (related)
A cardinal part of multi-tissue plant structure (PO:0025498) that is the end of a fruit (PO:0009001) distal from a fruit pedicel (PO:0004536).
porci&#243n distal del fruto (Spanish, exact)
A cardinal part of multi-tissue plant structure (PO:0025498) that is the end of a fruit (PO:0009001) proximal to a fruit pedicel (PO:0004536).
porci&#243n proximal del fruto (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue (PO:0009015) in their specific arrangement in a fruit (PO:0009001).
sistema vascular del fruto (Spanish, exact)
A megasporangium exothecium (PO:0025312) that is the morphologically distinct outer layer of the nucellus (PO:0020020).
A portion of plant tissue (PO:0009007) that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis.
A portion of aleurone layer (PO:0005360) which is morphologically distinct and is located adjacent to the nucellar projection (PO:0008007).
A portion of plant tissue (PO:0009007) that is the abaxial/lower portion of the nucellus (PO:0020020) overlying vascular strands in a caryopsis fruit (PO:0030104).
proyecci&#243n nucelar abaxial (Spanish, exact)
A portion of plant tissue (PO:0009007) that is the adaxial/upper portion of the nucellus (PO:0020020) overlying vascular strands in a caryopsis fruit (PO:0030104).
proyecci&#243n nucelar adaxial (Spanish, exact)
A vascular system (PO:0000034) that is part of a plant embryo (PO:0009009) .
sistema vascular del embri&#243n (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a stigma (PO:0009073).
sistema vascular del estigma (Spanish, exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in an anther (PO:0009066).
sistema vascular de la antera (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue (PO:0009015) in their specific arrangement in a filament (PO:0009067).
sistema vascular del filamento (Spanish, exact)
A vascular system (PO:0000034) that is part of a hypocotyl (PO:0020100).
sistema vascular del hipoc&#243tile (Spanish, exact)
A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs.
meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact)
A more or less abrupt swelling, especially at the apex or base of a leaf sheath.
vaina del pulv&#237nulo de la hoja (Spanish, exact)
A vascular leaf that is part of an heteroblastic series, and is characterized by anatomical features that are intermediate between juvenile and adult leaves.
維管束植物の幼葉と成熟葉の移行期の葉 (Japanese, exact)
Many species have juvenile leaves at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves are at the tip of the stalk (stem), which differentiates first, with adult leaves at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenile and adult tissues, as in Brachypodium.
The region of the leaf lamina proximal to the stem and usually connected to it by means of a petiole.
base de la l&#225mina de la hoja (Spanish, exact)
Region that includes the widest or majority portion of leaf lamina and that does not include leaf apex and leaf lamina base.
zona central de la l&#225mina de la hoja (Spanish, exact)
A leaf lamina vein (PO:0020138) arising from a secondary leaf vein (PO:0020140).
Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms.
A leaf lamina vein (PO:0020138) arising from a tertiary leaf vein (PO:0008021).
A leaf lamina vein (PO:0020138) arising from a quaternary (PO:0008022) or other higher order leaf vein.
fifth and higher order leaf vein (related)
The region of the petiole proximal to its stem attachment site.
extremo proximal del pec&#237olo (Spanish, exact)
Regions of the petiole that does not include petiole distal end and petiole proximal end.
zona central del pec&#237olo (Spanish, exact)
The region of the petiole distal to its stem attachment site or proximal to the leaf lamina.
extremo distal del pec&#237olo (Spanish, exact)
A portion of petiole epidermis (PO:0000051) that covers the adaxial/upper surface of a petiole (PO:0020038).
epidermis adaxial del pec&#237olo (Spanish, exact)
A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
A portion of petiole epidermis (PO:0000051) that covers the abaxial/lower surface of a petiole (PO:0020038).
epidermis abaxial del pec&#237olo (Spanish, exact)
A plant cell (PO:0009002) that is part of a multicellular trichome (PO:0000282).
A plant anatomical space that forms an opening in an epidermis, flanked by two guard cells.
The size of the stomatal pore is variable and controlled by movement of the guard cells in response to environmental cues.
A meristem forming the core of the axis composed of the primary vascular tissues and associated ground tissue, such as pith and interfascicular regions.
A portion of meristem tissue that forms the cortex.
A whole plant (PO:0000003) in the seedling development stage (PO:0007131).
A young plant derived from a newly germinated seed, up until the development of the first true leaf.
A phyllome primordium (PO:0025128)that develops from a lodicule anlagen (PO:0025483) and is committed to the development of a lodicule (PO:0009036).
portion of lodicule primordium tissue (exact)
primordio del lod&#237culo (Spanish, exact)
A shoot axis internode elongation zone (PO:0025100) that is part of a stem internode (PO:0009047).
zona de elongaci&#243n del internodo del tallo (Spanish, exact)
A shoot internode differentiation zone that is part of a stem internode.
zona de diferenciaci&#243n del internodo del tallo (Spanish, exact)
Primary, not secondary, tissue differentiation occurs in a differentiation zone.
A vascular system (PO:0000034) that is part of a scutellum (PO:0020110).
sistema vascular de escutelo (Spanish, exact)
A continuous layer of cylindrical cells covering the endosperm side of the scutellum. Thought to act as a secretory and absorptive organ.
A cardinal organ part (PO:0025001) at the apex or base of a petiole, petiolule, leaf sheath, or branch that is differentiated from the remaining organ parts by its enlarged cross section.
Often glandular. Often involved in movement of a plant structure in response to touch, gravity or light. In panicoid grasses a swollen region in the stem above the intercalary meristem. Such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc. [source: APweb:Glossary].
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.
A cell which is a plant structure (PO:0009011).
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).
A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
sistema de epiblasto (epiblastema) (Spanish, exact)
The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system.
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
porci&#243n de un tejido vegetal (Spanish, exact)
A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.
A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).
A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
etapa de desarrollo de estructura vegetal (Spanish, exact)
plant growth and development stage (exact)
Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'.
A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
A portion of plant tissue (PO:0009007) that has as part one or more tracheary elements (PO:0000290) or sieve elements (PO:0025406).
porci&#243n de tejido vascular (Spanish, exact)
Functions in conduction and support. In shoot axes (PO:0025029), vascular tissue is often found as part of a shoot axis stele (PO:0025198) or as scattered vascular bundles (PO:0005020). May include other types of tissues or cells, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).
A pulvinus (PO:0009000) of an inflorescence branch (PO:0009081).
pulv&#237nulo ramificado de una inflorescencia (Spanish, exact)
A transfer cell that is part of a basal endosperm transfer layer.
c&#233lula de transferencia del endosperma basal (Spanish, exact)
Responsible for transferring nutrients to an embryo by symplastic or apoplastic methods.
A portion of meristem tissue (PO:0009013) that is the outermost layer of a shoot apical meristem (PO:0020148) and gives rise to a shoot system epidermis (PO:0006035).
The cells of the meristem L1 layer divide in a strictly anticlinical fashion.
A portion of meristem tissue (PO:0009013) directly beneath a meristem L1 layer (PO:0009020) in a shoot apical meristem (PO:0020148) which gives rise to ground tissue (PO:0025059).
Cells in the first subepidermal layer, the L2, divide in a largely anticlinal fashion, forming a completely separate population of cells from the other cell layers. Within developing organs, the meristem L2 layer divides anticlinally and periclinally.
A portion of meristem tissue (PO:0009013) beneath a meristem L2 layer (PO:0009021) in a shoot apical meristem (PO:0020148) which gives rise to internal tissues of leaf and stem.
The meristem L3 layer cells frequently divide in various orientations.
An axil that is the space between a shoot axis and a leaf that branches from the shoot axis.
A leaf (PO:0025034) in a vascular plant.
Has vascular tissue. From APweb Glossary: In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud. Occurs in the sporophytic phase of a plant life cycle.
A leaf-like organ on which one or more sporangia are borne.
A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
A structure on which one or more microsporangia are borne; in flowering plants, the stamen.
A microsporophyll bearing one or more microsporangia.
A megasporophyll, almost always at the center of a flower, its margins more or less fused together or with other carpels to enclose the ovule(s).
In some cases, a gynoecium (PO:0009062) may consist of only one carpel, in which case annotations should go on carpel (PO:0009030). The word pistil is used synonymously with gynoecium, but if a gynoecium consists of a single carpel, then pistil may be used synonymously with carpel. If carpels are fused, the gynoecium is a syncarpous gynoecium, as in Poaceae, Brassicaceae and Solanaceae. If carpels are free, the gynoecium is an apocarpous gynoecium, as in Fabaceae. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A phyllome (PO:0006001) that is usually green, and is part of the calyx (PO:0009060).
In some species the sepals (PO:0009031) may not be green for example many members of the Liliaceae family.
A phyllome (PO:0006001) that is part of the corolla (PO:0009059), and is usually colored (not green).
In some species the petal (PO:0009032) may not be colored.
A phyllome (PO:0006001) that is part of a perianth (PO:0009058) where it is not possible to distinguish between the petals (PO:0009032) and sepals (PO:0009031).
There is no differentiation between the petals (PO:0009032) and the sepals (PO:0009031) in color, placement, and size (e.g. some species of Magnolia).
A bract (PO:0009055) that subtends a perianth (PO:0009058) that is part of a flower (PO:0009046).
A portion of secretory tissue (PO:0005656) which is a multicellular glandular structure secreting a liquid containing organic substances, including sugars.
A phyllome that is part of a grass floret and is one of two or three tiny scales or flaps of tissue outside the stamens.
May represent a reduced floral structure. If you are annotating to this structure for Zea mays, please also add an annotation to the corresponding floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
The lower, usually larger, of the pair of flower bracts (PO:0009034) enclosing a (PO:0009082) spikelet floret.
lemma del florete del penacho (borla) o de la espiga (Spanish, exact)
lemma of lower floret of pedicellate spikelet of ear (narrow)
lemma of lower floret of pedicellate spikelet of tassel (narrow)
lemma of lower floret of sessile spikelet of ear (narrow)
lemma of lower floret of sessile spikelet of tassel (narrow)
lemma of upper floret of pedicellate spikelet of ear (narrow)
lemma of upper floret of pedicellate spikelet of tassel (narrow)
lemma of upper floret of sessile spikelet of ear (narrow)
lemma of upper floret of sessile spikelet of tassel (narrow)
A lemma (PO:0009037) and palea (PO:0009038) enclose an individual spikelet floret (PO:0009082). The lemma is usually the larger of the two. Since it is not clear what the lemma and palea correspond to in conventional flowers, no assumptions of homology are made. If you are annotating to this structure for Zea species an annotation can also be made to the more specific floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). Found in Found in Poaceae, Cyperaceae and other Poales.
The upper (distal), usually smaller, of the pair of flower bracts (PO:0009034) enclosing a (PO:0009082) spikelet floret.
palea of lower floret of sessile spikelet of ear (exact)
palea of lower floret of pedicellate spikelet of ear (narrow)
palea of lower floret of pedicellate spikelet of tassel (narrow)
palea of lower floret of sessile spikelet of tassel (narrow)
palea of upper floret of pedicellate spikelet of ear (narrow)
palea of upper floret of pedicellate spikelet of tassel (narrow)
palea of upper floret of sessile spikelet of ear (narrow)
palea of upper floret of sessile spikelet of tassel (narrow)
A lemma (PO:0009037) and palea (PO:0009038) enclose an individual spikelet floret (PO:0009082). The palea is usually the smaller of the two. Since it is not clear what the lemma and palea correspond to in conventional flowers, no assumptions of homology are made. If you are annotating to this structure for Zea species an annotation can also be made to the more specific floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). Found in Found in Poaceae, Cyperaceae and other Poales.
One of a pair of inflorescence bracts that is part of a spikelet and subtends the two florets.
Found in Poaceae and Cyperaceae. Glumes subtend the pair of florets while a lemma or palea subtend the individual florets.
A flower bract in the position of a lemma, but not enclosing floral organs.
An undeveloped androecium or gynoecium may or may not be detectable. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type, if known. Choose the most specific term possible from: ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
A lemma that encloses a functional flower, with androecium, gynoecium or both.
If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type, if known. Choose the most specific term possible from: ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
A phyllome that is the first organ or one of the first two organs formed at the base of an axillary shoot, often smaller and/or in a distinctively different position from leaves formed subsequently.
A prophyll is not classified as a vascular leaf, because it may not have a fully developed vascular system.
A prophyll (PO:0009042) which is borne singly or in pairs on a pedicel (PO:0030112).
Sac-like bract subtending the pistillate flower, as in Carex.
ペリギニウム、果胞、造卵器群やそれから発生した胞子体の周辺の組織が発達し肉厚で筒状となった構造 (Japanese, exact)
An inflorescence bract (PO:0009054) of an involucre (PO:0009100).
Involucre are found in plant families such as Asteraceae or Compositeae.
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form.
A shoot axis (PO:0025029) that is the primary axis of a plant.
A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic.
A reproductive shoot system (PO:0025082) that has as parts all of the shoot axes (PO:0025029) and flowers (PO:0009046; must have two or more) distal to the most distal leaf (PO:0009025).
An inflorescence is a reproductive shoot system from which at least two flowers develop. The growth pattern of an inflorescence may be monopodial (single main shoot axis), sympodial (growth only occurs from axillary meristems), or both. An inflorescence axis (PO:0020122) can be determinate or indeterminate. An inflorescence flower pedicel (PO:0009052) is the ultimate axis in an inflorescence. The flower (PO:0009046) of many plants, for example Magnolia spp., is solitary.
A reproductive shoot system (PO:0025082) that is the ultimate and congested, higher order inflorescence axis (PO:0009081) of the grasses.
It consists of one to many closely-packed spikelet florets (PO:0009082) and associated glumes (PO:0009039).
A flower pedicel (PO:0030113) that bears a flower (PO:0009046) in an inflorescence (PO:0009049).
An inflorescence flower pedicel is the ultimate shoot axis (PO:0025029) in an inflorescence (PO:0009049).
A shoot axis that extends from the last foliage leaf on a stem or branch until the next distal node.
In plants with single flowers, the peduncle ends with a flower. In plants with inflorescences, the peduncle is the basal end of the primary inflorescence axis, and it ends where the inflorescence begins to branch. The peduncle marks the axial transition from vegetative to reproductive growth. In branching inflorescences, the second order inflorescence axis from the point at which it leaves the main axis up to the point at which it branches again may be called the second order peduncle. Higher order peduncles are also possible.
A bract (PO:0009055) subtending a branch of the inflorescence (PO:0009049) or borne on the inflorescence axis (PO:0020122) below any branch (PO:0025073) or flower (PO:0009046).
br&#225ctea de la inflorescencia (Spanish, exact)
Includes the leaf subtending and acting as outer envelope of an ear in Zea mays.
A phyllome that subtends a reproductive structure.
Usually different from leaves. Often used to refer to a floral bract, but includes other kinds of bracts.
A nectary (PO:0009035) occurring on a floral organ (PO:0025395) or other part of a flower (PO:0009046).
A flower nectary may occur on a sepal (PO:0009031), petal (PO:0009032), stamen (PO:0009029), plant ovary (PO:0009072), or receptacle (PO:0009064).
A nectary (PO:0009035), not occurring on a floral organ (PO:0025395) or other part of a flower (PO:0009046).
An extrafloral nectary may occur on vegetative plant structures (PO:0009011) such as a stem (PO:0009047), leaf (PO:0009025), petiole (PO:0020038), stipule (PO:0020041) or flower pedicel (PO:0009052).
A collective phyllome structure (PO:0025023) that includes as parts the corolla (PO:0009059) and/or the calyx (PO:0009060); or one or more tepals (PO:0009033).
The perianth can consist of only the corolla (PO:0009059), only the calyx (PO:0009060) or it may have both structures in a complete flower. If the petals (PO:0009032) and sepals (PO:0009031) are indistinguishable from one another, the perianth consists of just a collective tepal structure (PO:0025021), composed of one or more tepals (PO:0009033), for example in tulip or lily flowers.
A collective phyllome structure (PO:0025023) that is composed of one or more petals (PO:0009032), comprising the inner whorl of non-reproductive floral organs (PO:0025395) and surrounds the androecium (PO:0009061) and the gynoecium (PO:0009062).
The corolla (PO:0009059) is part of the perianth (PO:0009058). This definition is based on the complete flower, which has all four whorls. In many species, and in mutants one or more of the whorls may be missing. The corolla (PO:0009059) often functions to attract pollinators.
A collective phyllome structure (PO:0025023) that is composed of one or more sepals (PO:0009031), and comprises the outer whorl of non-reproductive floral organs (PO:0025395).
The calyx is part of the perianth (PO:0009058). This definition is based on the perfect flower, which has all four whorls. In many species, and in mutants one or more of the whorls are missing.
A collective phyllome structure (PO:0025023) composed all of the stamens (PO:0009029) in a flower (PO:0009046).
androecium of upper floret of pedicellate spikelet of tassel (exact)
androecium of lower floret of pedicellate spikelet of ear (narrow)
androecium of lower floret of sessile spikelet of ear (narrow)
androecium of lower floret of sessile spikelet of tassel (narrow)
androecium of upper floret of pedicellate spikelet of ear (narrow)
androecium of upper floret of sessile spikelet of ear (narrow)
androecium of upper floret of sessile spikelet of tassel (narrow)
The androecium also has as parts any staminodes (PO:0009077) that may be present in a flower. If annotating gene expression to an androecium with a single stamen (PO:0009029), the annotation should go on stamen. If you are annotating to this structure for Zea mays, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). The development of an androecium in an ear floret of a normal maize plant is aborted and is present in a rudimentary state, while the development of an androecium in a tassel floret leads to a functional androecium.
A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
gynoecium of lower floret of pedicellate spikelet of ear (narrow)
gynoecium of lower floret of pedicellate spikelet of tassel (narrow)
gynoecium of lower floret of sessile spikelet of ear (narrow)
gynoecium of lower floret of sessile spikelet of tassel (narrow)
gynoecium of upper floret of pedicellate spikelet of ear (narrow)
gynoecium of upper floret of pedicellate spikelet of tassel (narrow)
gynoecium of upper floret of sessile spikelet of ear (narrow)
gynoecium of upper floret of sessile spikelet of tassel (narrow)
If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060).
A cardinal organ part (PO:0025001) that is the region at the distal end of either a peduncle or a pedicel where the floral appendages (e.g.: sepals, petals, stamens and pistils) are attached.
The fleshy part of a strawberry develops from a receptacle.
A cup- or tube-shaped cardinal organ part, bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary.
花床筒 、いちじく状花序 i.e.hypanthodium (Japanese, exact)
Only bears stamens or perianth segments if they are present in the flower (e.g., no stamens in a carpellate flower).
A collective plant organ structure (PO:0025007) that is the pollen-bearing part of a stamen (PO:0009029).
Generally consists of four pollen sacs (microsporangia) in two anther thecas. If you are annotating to anther or one of its parts for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A stalk (PO:0025066) that is part of a stamen (PO:0009029).
Supports the anthers. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
The part of the stamen that connects the microsporangia/pollen sacs.
If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A collective plant organ structure (PO:0025007) that is part of an anther (PO:0009066) and consists of a pair of sporangia (PO:0025094) that dehisce down a common slit.
A microsporangium tapetum (PO:0025314) that is part of an anther wall (PO:0000002).
portion of anther wall tapetal tissue (exact)
Develops from a primary or secondary parietal cell layer. Innermost part of the anther wall, involved in the nutrition of the pollen. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A plant structure (PO:0009011) that is the basal portion of a carpel (PO:0009030) or group of fused carpels (gynoecium; PO:0009062) and encloses the plant ovule(s) (PO:0020003).
A cardinal organ part (PO:0025001), usually apical, that is part of a carpel (PO:0009030) or group of fused carpels on which the pollen (PO:0025281) germinates.
A cardinal organ part (PO:0025001) which is an elongated part of a carpel (PO:0009030) or gynoecium (PO:0009062) between the plant ovary (PO:0009072) and the stigma (PO:0009073), and through which the pollen tube (GO:0090406) grows.
If you are annotating to this structure for grasses, please also add an annotation to spikelet floret (PO:0009082). For Zea spp. please use silk (PO:0006488).
The axis of the spikelet, above the glumes.
raquilla de la espiguilla (Spanish, exact)
An inflorescence axis (PO:0020122) that develops from an inflorescence axillary meristem (PO:0009105) of an inflorescence axis (PO:0020122).
A higher order inflorescence axis is any inflorescence axis (PO:0020122) that develops from another inflorescence axis (PO:0020122), and is named according to its position in an inflorescence (PO:0009049). Tenth order inflorescence axis (PO:0025111) is the greatest specific inflorescence axis order in the PO; when mapping annotations to inflorescence axes which are of an order greater than ten, or when order is ambiguous or unknown, annotate directly to higher order inflorescence axis.
A small flower (PO:0009046) that is part of a spikelet (PO:0009051).
florete de la espiguilla (Spanish, exact)
A spikelet floret (PO:0009082) is enclosed by one or both the flower bracts (PO:0009034); lemma (PO:0009037) and palea (PO:0009038) and also includes a lodicule (PO:0009036). To describe a floret of the Asteraceae, use ray flower (PO:0025331) or disk flower (PO:0025332). Found in Poaceae, Cyperaceae and other Poales.
A portion of plant tissue (PO:0009007) that is the outer layer (wall) of a fruit (PO:0009001), and develops from a plant ovary (PO:0009072) or a carpel (PO:0009030) wall.
Pericarp comprises endocarp (PO:0009086), mesocarp (PO:0009087), and exocarp (PO:0009085) layers, each of which can be fleshy or dry. If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A portion of plant tissue (PO:0009007) that is the outer layer of a pericarp (PO:0009084).
A portion of plant tissue (PO:0009007) that is the innermost differentiated layer of a pericarp (PO:0009084).
A portion of plant tissue (PO:0009007) that is the middle layer of a pericarp (PO:0009084).
A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
Used only when not specified more precisely; see testa, tegmen.
A portion of plant tissue (PO:0009007) which is a maximal portion of nutritive plant tissue in a seed (PO:0009010).
In angiosperms the endosperm is usually triploid and formed after fertilization by the fusion of one gamete with the polar nucleus (GO:0043078); sometimes diploid or polyploid.
An arilloid that is an outgrowth of a seed from a seed funicle.
Usually envelopes most of the seed and is fleshy. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.
A collective phyllome structure composed of two or more involucral bracts at the base of a cluster of flowers, as found in Asteraceae or Compositae.
The burs or bristles in Cenchrus and Pennisetum are not involucres because the fused structures are branches and not bracts.
The long branch that arise from the central spike of tassel in maize.
ramificaci&#243n lateral larga del penacho (borla) (Spanish, exact)
The very short branch that may arise from either or both the long lateral branch and the central spike of tassel in maize.
ramificaci&#243n corta del penacho (borla) (Spanish, exact)
The meristem present on either or both the long lateral branch and central spike of a maize tassel that gives rise to short tassel branch.
meristema de la ramificaci&#243n corta del penacho (borla) (Spanish, exact)
third order tassel branch meristem (related)
The meristem that gives rise to the long lateral branch in the maize tassel.
meristema de la ramificaci&#243n larga del penacho (borla) (Spanish, exact)
second order tassel branch meristem (related)
An inflorescence meristem (PO:0009108) that gives rise to a higher order inflorescence axis (PO:0009081).
meristema lateral de la inflorescencia (Spanish, exact)
Meristem that gives rise to the apical and lateral structures of the tassel inflorescence in maize.
meristema del penacho (borla) (Spanish, exact)
An inflorescence axillary meristem (PO:0009105) that gives rise to the long lateral tassel branch (PO:0009101), short tassel branch (PO:0009102), and tassel spikelets (PO:0006309) in a tassel inflorescence (PO:0020126).
meristema lateral del penacho (borla) (Spanish, exact)
A reproductive shoot apical meristem that gives rise to the apical growth of the inflorescence. It develops from the shoot apical meristem (SAM) after it undergoes transition from vegetative to reproductive phase.
meristema apical de la inflorescencia (Spanish, exact)
The meristem which gives rise to the female inflorescence or ear in maize.
An inflorescence axillary meristem (PO:0009105) that gives rise to a higher order inflorescence axis (PO:0009081) of an ear inflorescence (PO:0020136).
meristema de la espiga lateral (Spanish, exact)
pulv&#237nulo del pec&#237olo (Spanish, exact)
A plant axis (PO:0025004) that is the axial part of a plant embryo (PO:0009009).
Has as parts a hypocotyl, a root meristem and a radicle, if any of these are present.
A cardinal part of multi-tissue plant structure (PO:0025498) that is a fleshy outgrowth of a seed (PO:0009010).
Often conspicuous and found on seeds with a hard testa that are dispersed by animals. There is some variation in how different sources define the subtypes of arilloids.
An arilloid that is an outgrowth of a seed on a raphe.
A plug-like structure formed in the micropylar region of the seed coat.
op&#233rculo de la semilla (Spanish, exact)
portion of seed operculum tissue (exact)
A portion of xylem (PO:0005352) tissue that is a distinct ring-like structure composed of tracheids (PO:0000301), that is part of a seed (PO:0009010) and surrounds the hilum (PO:0020063) and forms a groove in the surface of the pericarp (PO:0009084) immediately adjacent to the hilum.
A portion of placenta tissue (PO:0025078) which is part of a plant ovary (PO:0009072), and to which plant ovary ovules (PO:0025490) are attached.
An microsporangium endothecium (PO:0025309) that part of an anther wall (PO:0000002).
endotecio de la pared the la antera (Spanish, exact)
May have secondary thickening of walls of cells that are involved in anther dehiscence. There can be more than one layer in an anther endothecium. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
An microsporangium exothecium (PO:0025311) that is part of an anther wall (PO:0000002).
exotecio de la pared de la antera (Spanish, exact)
Often with thickened cell walls. Involved in anther dehiscence. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A portion of parenchyma tissue that is part of a connective and projects into a pollen sac.
A stalk (PO:0025066) that attaches a plant ovule (PO:0020003) to a placenta (PO:0025078).
If you are annotating to this structure for an angiosperm, please add an additional annotation to plant ovary ovule (PO:0025490). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:0025491). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
The larger, in general, of the two kinds of spores produced after meiosis in the life cycle of a heterosporous plant, and on germination giving rise to the female gametophyte (embryo sac).
A megasporangium (PO:0025201) in a seed plant, composed of fleshy subepidermal tissue that is part of a plant ovule (PO:0020003) and surrounds a megasporocyte (PO:0000431).
In seed plants, the megaspores and megagametophyte are retained within the nucellus. If you are annotating to this structure for an angiosperm, please add an additional annotation to plant ovary ovule (PO:0025490). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:0025491). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
A portion of plant tissue (PO:0009007) that covers a plant ovule (PO:0020003), enveloping a nucellus (PO:0020020) and forming a micropyle (PO:0020025) at the apex.
A plant ovule integument (PO:0020021) which is the innermost of the two layers of tissue that usually cover the plant ovule (PO:0020003), contiguous to the nucellus (PO:0020020) and usually contributing to the formation of the plant ovule micropyle (PO:0020025) at the apex.
A plant ovule integument (PO:0020021) which is the outermost the two layers of tissue that usually cover the plant ovule (PO:0020003), contiguous to the nucellus (PO:0020020) and usually contributing to the formation of the plant ovule micropyle (PO:0020025) at the apex.
A portion of plant tissue (PO:0009007) which is composed of cells of the inner epidermis of the inner (or only) integument of the ovule that are radially elongated and metabolically very active.
A plant anatomical space (PO:0025117) that is enclosed by and forms an opening in an integument at the apex of a plant ovule (PO:0020003).
The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
A portion of plant tissue (PO:0009007) that is the region in a plant ovule (PO:0020003) where the integuments (PO:0020021) and the nucellus (PO:0020020) join with the funicule (PO:0020006).
カラザ（合点）=珠心と珠皮が珠柄につながるところ、珠孔の反対側 (Japanese, exact)
The chalaza is recognized as the region which initiates the two integuments at its flank. If you are annotating to this structure for an angiosperm, please add an additional annotation to plant ovary ovule (PO:0025490). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:0025491). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
A cardinal organ part (PO:0025001) that is a ridge on a plant ovule (PO:0020003) where a funicle (PO:0020006) is or was fused to the ovule.
If you are annotating to this structure for an angiosperm, please add an additional annotation to plant ovary ovule (PO:0025490). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:0025491).
A cardinal organ part (PO:0025001) that is the part of a plant ovule (PO:0020003) on the opposite side from a raphe (PO:0020027).
A portion of plant tissue (PO:0009007) which is an outgrowth of the funicle, that forms a bridge between the micropyle and other tissues.
Most commonly arising from the funicle, also developing from placenta, integument, etc.
A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
An embryo root (PO:0000045) that is the basal continuation of a hypocotyl (PO:0020100) in a plant embryo (PO:0009009) or a seedling (PO:0000003).
May develop into the primary root (PO:0020127) and eventually the root system (PO:0025025) of an adult plant. Sometimes abortive.
The shoot apex (PO:0000037) of the plant embryo (PO:0009009), above the cotyledonary node (PO:0025321).
A sheath-like plant organ (PO:0009008) that surrounds the plumule (PO:0020032) of a plant embryo (PO:0009009) or the emerging shoot apex (PO:0000037) of a seedling.
The coleoptile is an outgrowth or part of the scutellum (PO:0020110) (which is a modified, haustorial cotyledon (PO:0020030)). Develops separate from the shoot apical meristem (PO:0020148). Found in Poaceae and other monocotyledons such as Zingiberaceae. Protects the emerging shoot system (PO:0009006) as it grows through the soil.
A sheath-like plant organ (PO:0009008) that surrounds the radicle (PO:0020031) of a plant embryo (PO:0009009) or the emerging root (PO:0009005) of a seedling (PO:0000003).
Found in Poaceae and some other monocots as well as some gymnosperms. Protects the emerging radicle in a plant embryo or seedling. The parenchyma cells of both the coleorhiza and epiblast may function in storage.
The first stem internode (PO:0020142) above the cotyledonary node (PO:0025321) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
A portion of plant tissue (PO:0009007) that is a flap-like projection of the coleorhiza (PO:0020034), inserted opposite the scutellum (PO:0020110).
The parenchyma cells of both the coleorhiza and epiblast may function in storage. Some researchers consider the epiblast and coleorhiza independent structures that differentiate from the same proembryonic tissue.
A stem internode (PO:0020142) that is the part of a plant embryo axis (PO:0019018) or a seedling stem (PO:0009047) above the scutellum (PO:0020110) and below the coleoptile (PO:0020033).
Occurs in grasses. In grasses, the hypocotyl and cotyledon may not be visible and may be represented by the scutellar node and scutellum, making the mesocotyl similar to the epicotyl in other taxa. Elongation of the mesocotyl during seedling growth pushes the coleoptile above the soil surface.
A stalk (PO:0025066) of a vascular leaf (PO:0009025).
A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A phyllome base (PO:0025140) that is part of a leaf (PO:0025034).
A cardinal organ part that is an appendage at the base of a vascular leaf.
Usually one of a pair of appendages. May take the form of a spine (PO:0025174) or may be bristled or brush-like. Stipules may occur on the opposite side of the shoot axis from the leaf they are associated with, but they are still thought to arise from part of the leaf.
A leaf in which the lamina is undivided.
A leaf having two or more distinct leaflets that are evident as such from early in development.
The unifacial terete apical portion of a monocot cotyledon, sometimes also visible on other leaves.
A once-compound leaf with leaflets borne along a rachis.
The total number of leaflets may be even or odd, in which case the leaf is called even-pinnate or odd-pinnate respectively.
A once-compound leaf divided into several leaflets which arise at the same point, there being no rachis.
A sporocyte (PO:0006204) that produces four haploid (1n) microspores (PO:0020048).
The smaller, in general, of the two kinds of spores produced after meiosis in the life cycle of a heterosporous plant, and on germination giving rise to the male gametophyte.
A cardinal organ part (PO:0025001) that is one of the ultimate segments of a compound leaf (PO:0020043).
Stipule-like appendage(s) at the base of a leaflet (in unifoliolate or simple leaves, found at the top of the petiole).
A scale leaf that surrounds a dormant or perennating bud.
A stalk (PO:0025066) that is the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.
That part of the seed coat that develops from the inner integument.
内種子(internal seed coat, inner seed coat, secundine) (Japanese, exact)
That part of the seed coat that develops from the outer integument, or from the single integument when there is only one.
A portion of plant tissue (PO:0009007) which is diploid nutritive tissue in an angiosperm seed derived from nucellar tissue.
An arilloid that is an outgrowth of a seed next to the micropyle.
Often hard and generally smaller and less elaborate than a arillode.
A portion of seed coat epidermis (PO:0006048) that consists of multiple seed trichomes (PO:0004511) at the seed micropyle (PO:0006334).
A cardinal organ part that is an oil-secreting outgrowth of a seed or fruit.
May be a modified arilloid (a type of strophiole or caruncle) or may be an outgrowth of a fruit. May be attractive to ants and aid in dispersal.
A cardinal part of multi-tissue plant structure (PO:0025498) that is a scar on a seed (PO:0009010) at the place where it was attached to a funicle (PO:0020006).
A cardinal part of multi-tissue plant structure (PO:0025498) which is one carpellate unit of a schizocarp fruit (PO:0030098) consisting of pericarp (PO:0009084) and one or more seeds (PO:0009010).
A mericarp develops from one carpel of a syncarpous gynoecium. The pericarp of each carpel are fused together until maturity, at which point the carpellate units separate from one another.
An embryo sac cell (PO:0025026) that is largest cell in a mature embryo sac (PO:0025074).
In most angiosperms, the embryo sac central cell contains two polar nuclei, and, after double fertilization, develops into an endosperm. In some angiosperms, such as Illicium, the embryo sac central cell contains a single polar nucleus. Embryo sac central cell is distinct from archegonium central cell (PO:0025509).
Cell, commonly three in number as in the eight-nucleate embryo sac, located at the other end of the embryo sac from the egg cell.
More or less persistent, multiplicative or not.
A gamete (PO:0025006) produced by an archegonium (PO:0025126) or an embryo sac (PO:0025074).
The plant egg cell (megagamete) is usually larger than the plant sperm cell (PO:0000084; microgamete).
A cardinal organ part that has as parts an egg cell and two synergids and is located at the micropylar end of the embryo sac.
aparato de la ooc&#233lula (Spanish, exact)
A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) that divides to produce two pollen sperm cells (PO:0025121).
A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195).
A stem internode (PO:0020142) below the cotyledonary node (PO:0025321) and transitional to a root (PO:0009005) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
A plant anatomical space that is a slit in an anther lobe formed from when a dehiscence zone dehisces.
Pollen may be released through the stomium. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
A portion of ground tissue (PO:0025059) in the style of a carpel through which a pollen tube grows; it connects a stigma and the inside of an ovary.
porci&#243n del tejido de transmisi&#243n (Spanish, exact)
The last mature leaf before the inflorescence in a cereal crop plant.
A cardinal organ part (PO:0025001) that is the lower part of a vascular leaf (PO:0009025), and which more or less encases the stem (PO:0009047).
A leaf sheath is usually tubular shaped, and is found in the Poaceae family and other monocots.
A membranous or hairy appendage on the adaxial/upper surface of a leaf, at the junction between sheath and blade, especially in grasses.
A cardinal organ part (PO:0025001) that is an ear-shaped outgrowth of the distal part of a leaf sheath (PO:0020104).
aur&#237cula de la vaina de la hoja (Spanish, exact)
May wrap around the stem (PO:0009047) or branch (PO:0025073) to which the vascular leaf (PO:0009025) it is part of is attached. Found in some Poaceae.
An embryonic plant structure at the base of a plant embryo that develops from an embryonic basal cell and connects an embryo proper to the wall of a megagametophyte.
The suspensor often allows the embryo to penetrate deep into the endosperm. Across plant species, suspensors are morphologically diverse and may be single- or multicellular, undifferentiated or highly differentiated, and variously shaped.
A native plant cell (PO:0025606) that is the uppermost cell of a suspensor (PO:0020108) and from which part of the root (PO:0009005) and root cap (PO:0020123) in a plant embryo (PO:0009009) of angiosperms are derived.
An embryonic plant structure that is a more or less shield-shaped and absorptive portion of a plant embryo of Poaceae.
A root (PO:0009005) that develops from a lateral root primordium (PO:0000016) that is part of another root on the same plant.
A lateral root primordium may develops on any root, including a primary root (PO:0020127), on an existing lateral root (PO:0020121), or a shoot-borne root (PO:0000042). In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in its formation in some species. In ferns, lateral root primordia develop from the endodermis.
A shoot axis (PO:0025029) that is part of an inflorescence (PO:0009049).
eje de la inflorescencia (Spanish, exact)
first order inflorescence branch (related)
An inflorescence axis (PO:0020122) has either a determinate apex, which terminates in a flower meristem (PO:0000229), or has an indeterminate apex, which terminates in an inflorescence apical meristem (PO:0009108). An inflorescence pedicel (PO:0009052) is the simplest example of a determinate inflorescence axis.
A portion of root parenchyma (PO:0025095) tissue that is part of the root tip (PO:0000025) and covers the root apical meristem (PO:0020147).
caliptra de la ra&#237z (Spanish, exact)
Often composed of living and dead parenchyma cells. Protects the root apical meristem.
A stele (PO:0025197) that is part of a root (PO:0009005).
Includes the pericycle as the outermost layer of the stele.
A staminate inflorescence (PO:0025601) in Zea species that bears the tassel spikelet (PO:0006309) on a terminal inflorescence axis (PO:0020122).
penacho de la inflorescencia (Spanish, exact)
Branched inflorescence with a central axis and about 10-50 lateral branches.
A root (PO:0009005) that develops directly from a seedling radicle (PO:0020127).
The first root of a plant. In dicots and gymnosperms it becomes the tap root, the central axis of a root system (PO:0025025).
A phyllome margin (PO:0025018) that is part of a leaf (PO:0025034).
A portion of root parenchyma tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.
caliptra de la ra&#237z central (Spanish, exact)
A portion of root parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis.
caliptra lateral de la ra&#237z (Spanish, exact)
This is the general term for the lateral portion of any root cap and not the term for a root cap of lateral root (PO:0003018) or lateral root cap of lateral root (PO:0003020).
Cell that constitutes the central part of the root cap, arranged in longitudinal files.
c&#233lula de la columela del caliptra de la ra&#237z (Spanish, exact)
A root initial cell (PO:0000059) that produces columella cells in the root cap (PO:0020123). In direct contact with quiescent center (PO:0020149).
c&#233lula inicial de la columela del caliptra de la ra&#237z (Spanish, exact)
A plant axis differentiation zone that is the part of a root and is located behind a root elongation zone.
zona de diferenciaci&#243n de la ra&#237z (Spanish, exact)
Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.
A pistillate inflorescence (PO:0025598) in Zea species that is highly compacted and bears the ear spikelets (PO:0006320) on a lateral inflorescence axis (PO:0020122).
oreja de la inflorescencia (Spanish, exact)
A phyllome apex (PO:0025139) that is part of a leaf (PO:0025034).
It is not precisely defined how far toward the base from the tip a leaf apex extends. For the apical most portion of a leaf, use the term leaf tip. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048).
A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).
A leaf lamina vein (PO:0020138) arising from a primary leaf vein (PO:0025413).
A shoot axis node (PO:0005004) that is part of a stem (PO:0009047).
A shoot axis internode (PO:0005005) that is part of a stem (PO:0009047).
A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
A portion of meristem (PO:0009013) tissue located parallel to the sides of a shoot axis (PO:0025029) or root (PO:0009005) that participates in lateral growth.
A term for lateral growth has been requested in GO. Lateral meristems contribute to an increase in the cross-sectional area of a shoot axis or root. Examples of lateral meristems are: cambium (PO:0005597) (includes cork cambium (PO:0005599) and vascular cambium (PO:0005598)), shoot lateral meristem (PO:0006344) (includes primary thickening meristem (PO:0005039)), root lateral meristem (PO:0006308), and secondary thickening meristem (PO:0025414). Contrasts with apical meristem (PO:0020144), phyllome marginal meristem (PO:0025404), or intercalary meristem (PO:0006073).
A root meristem (PO:0006085) located at the root tip (PO:0000025), behind the root cap (PO:0020123).
meristema apical de la ra&#237z (Spanish, exact)
In most cases, it is involved in root elongation.
A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
meristema apical del epiblasto (epiblastema) (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is part of a root apical meristem (PO:0020147) and consists of mitotically and metabolically inactive cells and is located behind the protoderm (PO:0006210) of the root (PO:0009005).
centro de division de c&#233lulas del meristema (Spanish, exact)
If a root cap is present, the quiescent center is behind the root cap.
Stage of inflorescence development marked by the formation of the inflorescence meristem on a vegetative branch.
A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
parte de un &#243rgano cardinal (Spanish, exact)
Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
A shoot-borne internode root (PO:0025593) that arises from a part of the hypocotyl (PO:0020100).
An axillary shoot that develops from a tuber axillary bud.
epiblasto (epiblastema) lateral de tub&#233rculo (Spanish, exact)
A cardinal organ part (PO:0025001) that is the edge of a plant organ (PO:0009008) and the area immediately internally adjacent to it.
margen de un &#243rgano (Spanish, exact)
Only flattened or laminar plant organs or organ parts will have a margin.
A native plant cell (PO:0025606) that has half the chromosome complement of the sporophyte and is capable of fertilization to create a plant zygote (PO:0000423).
A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva de &#243rgano (Spanish, exact)
Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure.
A phyllome margin (PO:0025018) which is part of a petal (PO:0009032).
A leaf margin (PO:0020128) that is part of a leaf lamina (PO:0020039).
margen de la l&#225mina de la hoja (Spanish, exact)
A cardinal organ part (PO:0025001) that is the edge of a petiole lamina (PO:0025129) and the area immediately internally adjacent to it.
Petiole margins may be found in flattened (laminar) petioles, but may also occur in laminar extensions of petioles that are rounded or c-shaped in cross section.
A phyllome margin (PO:0025018) that is part of a bract (PO:0009055).
margen de la br&#225ctea (Spanish, exact)
A leaf margin (PO:0020128) that is part of a cotyledon (PO:0020030).
margen del cotiled&#243n (Spanish, exact)
A phyllome margin (PO:0025018) that is part of a prophyll (PO:0009042).
A phyllome margin (PO:0025018) that is part of scale leaf (PO:0006003).
margen de la hoja escamosa (Spanish, exact)
A phyllome margin (PO:0025018) that is part of a tepal (PO:0009033).
A phyllome margin (PO:0025018) that is part of a sporophyll (PO:0009026).
A whole plant (PO:0000003) that arises through meiosis and is contained in a spore wall.
A spore is usually single-celled in homosporous plants but may be multicellular in heterosporous plants. May have a spore wall (GO:0031160) made of sporopollenin.
A plant organ margin (PO:0025005) that is part of a phyllome lamina (PO:0025396).
Only flattened carpels can have a margin.
Only flattened stamens can have a margin.
A perianth (PO:0009058) consisting of one or more tepals (PO:0009033).
estructura colectiva del t&#233palo (Spanish, exact)
This structure is a perianth (PO:0009058) where there is no differentiation between calyx (PO:0009060) and corolla (PO:0009059).
A collective phyllome structure (PO:0025023) composed of two or more leaves (PO:0025034).
estructura colectiva de hoja (Spanish, exact)
This term replaces the obsolete term leaf whorl (PO:0008034). If you are looking for annotations for PO:0008034, please use this term instead.
A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
estructura colectiva del filoma (Spanish, exact)
A shoot axis node (PO:0005004) that is part of a branch (PO:0025073).
A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
Generally the below ground portion of a vascular plant.
A native plant cell (PO:0025606) that is part of an embryo sac (PO:0025074).
c&#233lula megagametof&#237tica (Spanish, exact)
A native plant cell (PO:0025606) that is part of a plant embryo (PO:0009009).
c&#233lula embri&#243nica vegetal (Spanish, exact)
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
eje del epiblasto (epiblastema) (Spanish, exact)
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
A native plant cell (PO:0025606) that is part of a portion of ground tissue (PO:0025059).
c&#233lula del tejido fundamental (Spanish, exact)
Includes parenchyma, collenchyma and sclerenchyma cells.
A ground tissue cell (PO:0025030) that contains latex.
c&#233lula latic&#237fera (Spanish, exact)
A native plant cell (PO:0025606) that is dead at maturity, lacks specialized wall thickenings or lignin, and has tapered ends that are thin and partially hydrolyzed.
Hydroids are water and mineral conducting cells found in bryophytes in axes and leaves in the gametophytic phase and in the seta in the sporophytic phase.
A native plant cell (PO:0025606) that resembles in structure the sieve elements (PO:0025406) of vascular plants.
A carbohydrate and amino acid conducting cell found in bryophytes in axes and leaves in the gametophyte development stage (PO:0028003) and in the seta in the sporophytic phase. Leptoids have no nucleus at maturity. Carbohydrate and amino acid conducting cells in bryophytes range from conducting parenchyma cells that are indistinguishable from other parenchyma cells to 'leptoids sensu strictu' that are structurally comparable to sieve elements in vascular plants, as well as many intermediate forms. The term leptoid is used for cells that are distinguishable from other parenchyma cells, whether they be intermediate or leptoids sensu strictu.
A phyllome (PO:0006001) that is not associated with a reproductive structure.
A portion of parenchyma (PO:0005421) specialized for carbohydrate storage.
par&#233nquima de reserva (Spanish, exact)
This tissue could be found in any organ, but often occurs in fruits or tubers. New GO term carbohydrate storage has been requested.
A portion of storage parenchyma (PO:0025035) that is part of a tuber (PO:0025522).
par&#233nquima de reserva de tub&#233rculo (Spanish, exact)
This is the flesh of a tuber. See part_of children for individual components of tuber flesh. If you are annotating to this term, please add an additional annotation to either shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
A portion of storage parenchyma that is part of a fruit.
par&#233nquima de reserva de fruto (Spanish, exact)
A portion of tuber storage parenchyma (PO:0025035) that is part of a subterranean tuber (PO:0004547).
par&#233nquima de reserva de tub&#233rculo subterr&#225neo (Spanish, exact)
This term is used to refer to potato tuber flesh. See part_of children for individual components of subterranean tuber flesh.
A portion of tuber storage parenchyma (PO:0025036) that is part of an aerial tuber (PO:0004548).
par&#233nquima de reserva de tub&#233rculo a&#233reo (Spanish, exact)
See part_of children for individual components of aerial tuber flesh.
An axillary vegetative bud (PO:0004712) that is part of a shoot axis tuber (PO:0004543).
yema vegetativa axilar de tub&#233rculo (Spanish, exact)
shoot axis tuber axillary vegetative bud
A tuber axillary vegetative bud that is part of an aerial tuber.
yema vegetativa axilar de tub&#233rculo a&#233reo (Spanish, exact)
A tuber axillary vegetative bud that is part of a subterranean tuber.
yema vegetativa axilar de tub&#233rculo subterr&#225neo (Spanish, exact)
A structure on the tuber surface that can sprout. In potatoes, axillary vegetative buds (eyes) can determine processing quality. Scale that the breeders use to rate the buds/sprouts of tubers: 1. none, 2. swollen eye, 3. sprout ca. 1/4 inch, 4. sprout ca. 1/2 inch, 5. sprout ca. 1 inch, 6. sprout ca. 2 inch, 7. sprout ca. 3 inch, 8. new top growth, 9. chain tubers.
subterranean tuber axillary vegetative bud
A portion of shoot axis periderm (PO:0005048) that is part of a shoot axis tuber (PO:0004543).
peridermis de tub&#233rculo (Spanish, exact)
A portion of tuber periderm that is part of an aerial tuber.
peridermis de tub&#233rculo a&#233reo (Spanish, exact)
A portion of tuber periderm that is part of a subterranean tuber.
peridermis de tub&#233rculo subterr&#225neo (Spanish, exact)
The skin of young potatoes is epidermis while the skin of mature potatoes is periderm.
A portion of shoot axis epidermis (PO:0000112) that is part of a shoot axis tuber (PO:0004543).
epidermis de tub&#233rculo (Spanish, exact)
A portion of shoot axis tuber epidermis (PO:0025046) that is part of an aerial tuber (PO:0004548).
epidermis de tub&#233rculo a&#233reo (Spanish, exact)
A shoot axis tuber epidermis (PO:0025046) that is part of a subterranean shoot axis tuber (PO:0004547).
epidermis de tub&#233rculo subterr&#225neo (Spanish, exact)
A tuber interfascicular region that is part of a subterranean tuber storage parenchyma.
regi&#243n interfascicular de tub&#233rculo subterr&#225neo (Spanish, exact)
Because subterranean interfascicular regions in potato tubers form before the subterranean tuber perimedullary zone expands (PO:0025063), in mature potato tubers, the subterranean tuber interfascicular regions persist as rays that extend from the central pith to the eyes or subterranean tuber axillary vegetative buds (PO:0025042).
subterranean tuber interfascicular region
An interfascicular region that is part of a tuber storage parenchyma.
regi&#243n interfascicular de tub&#233rculo (Spanish, exact)
A tuber interfascicular region that is part of an aerial tuber storage parenchyma.
regi&#243n interfascicular de tub&#233rculo a&#233reo (Spanish, exact)
A portion of pith (PO:0006109) that is part of a tuber storage parenchyma (PO:0025036).
m&#233dula del tub&#233rculo (Spanish, exact)
A portion of tuber pith (PO:0025052) that is part of a subterranean tuber storage parenchyma (PO:0025038).
m&#233dula del tub&#233rculo subterr&#225neo (Spanish, exact)
A portion of tuber pith (PO:0025052) that is part of an aerial tuber storage parenchyma (PO:0025039).
m&#233dula del tub&#233rculo a&#233reo (Spanish, exact)
A portion of cortex (PO:0005708) that is part of a tuber storage parenchyma (PO:0025036).
corteza del tub&#233rculo (Spanish, exact)
A portion of tuber cortex that is part of an aerial tuber storage parenchyma.
corteza del tub&#233rculo a&#233reo (Spanish, exact)
A portion of tuber cortex that is part of a subterranean tuber storage parenchyma.
corteza del tub&#233rculo subterr&#225neo (Spanish, exact)
A portion of parenchyma (PO:0005421) that is the outer layer of the pith (PO:0006109).
The term perimedullary zone is only used when the outer layer of the pith is distinct from the inner layer.
Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).
porci&#243n del tejido fundamental (Spanish, exact)
Develops from the ground meristem (PO:0025594).
A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat.
A perimedullary zone (PO:0025058) that is part of a tuber pith (PO:0025052).
zona perimedular del tub&#233rculo (Spanish, exact)
A tuber perimedullary zone that is part of an aerial tuber pith.
zona perimedular del tub&#233rculo a&#233reo (Spanish, exact)
A tuber perimedullary zone that is part of a subterranean tuber pith.
zona perimedular del tub&#233rculo subterr&#225neo (Spanish, exact)
A perimedullary zone (PO:0025058) that is part of a shoot axis pith (PO:0005041).
zona perimedular de eje del epiblasto (epiblastema) (Spanish, exact)
A perimedullary zone that is part of a root pith.
zona perimedular de la ra&#237z (Spanish, exact)
A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part.
tallo de alto orden (secundario, terciario, etc) (Spanish, exact)
A portion of storage parenchyma that is part of a seed.
par&#233nquima de reserva de la semilla (Spanish, exact)
An axillary bud meristem (PO:0000232) that is part of a shoot axis tuber (PO:0004543).
meristema axilar de yema de tub&#233rculo (Spanish, exact)
As the bud grows, the meristem switches from being an axillary meristem to being a shoot apical meristem.
A tuber axillary bud meristem that is part of an aerial tuber.
meristema axilar de yema de tub&#233rculo a&#233reo (Spanish, exact)
A tuber axillary bud meristem that is part of a subterranean tuber.
meristema axilar de yema de tub&#233rculo subterr&#225neo (Spanish, exact)
subterranean tuber axillary bud meristem
A terminal bud that develops into a reproductive structure.
yema terminal reproductiva (Spanish, exact)
An axillary bud (PO:0004709) that develops into an reproductive shoot system (PO:0025082).
yema axilar reproductiva (Spanish, exact)
A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.
A megagametophyte (PO:0025279) that is located in a plant ovary ovule (PO:0025490).
Produces an embryo sac egg cell (PO:0025123).
A leaf (PO:0025034) in a non-vascular plant.
Non-vascular leaves occur in the gametophyte development stage (PO:0028003) of Bryophytes, plants such as moss and liverwort.
An axillary reproductive bud that develops into a strobilus.
yema de estr&#243bilo axilar (Spanish, exact)
A terminal reproductive bud that develops into a strobilus.
yema de estr&#243bilo terminal (Spanish, exact)
A portion of plant tissue (PO:0009007) at the interface between two plant structures, one of which is in a gametophyte development stage (PO:0028003) and one of which is in a sporophyte development stage (PO:0028002), and that has as parts transfer cells (PO:0000078).
The transfer cells aid in nutrient transport. Examples include ovary placenta (PO:0020001) and fruit placenta (PO:0004535).
An axillary shoot that develops from an aerial tuber axillary bud.
epiblasto (epiblastema) axilar de tub&#233rculo a&#233reo (Spanish, exact)
A shoot axis internode (PO:0005005) that is part of a branch (PO:0025073).
internodo de una ramificaci&#243n (Spanish, exact)
An axillary shoot that develops from a subterranean tuber axillary bud.
epiblasto (epiblastema) axilar de tub&#233rculo subterr&#225neo (Spanish, exact)
See also subterranean tuber axillary bud (PO:0025042).
A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
sistema de brote reproductivo (Spanish, exact)
A reproductive shoot system (PO:0025082) consisting of a number of sporophylls (PO:0009026) or plant ovule (PO:0020003)-bearing modified leaves (PO:0025034) grouped terminally on a stem (PO:0009047).
May be simple or compound. Found in lycophytes such as Selaginella and Lycopodium, sphenophytes such as Equisetum, gymnosperms such as cycad, conifers, gnetophytes and the pollen producing structures of Gingko. The term cone is often used for strobili that are woody. Flowers are sometimes considered bisexual strobili. Some flowering plants such as Alnus have inflorescences called catkins that resemble strobili, but are not.
A bud that develops into a reproductive shoot system.
A gynoecium in the early stages of development, characterized as a ridge on the abaxial surface of the floral meristem that develops from a gynoecium primordium.
gynoecium ridge of lower floret of pedicellate spikelet of ear (narrow)
gynoecium ridge of lower floret of sessile spikelet of ear (narrow)
gynoecium ridge of upper floret of pedicellate spikelet of ear (narrow)
gynoecium ridge of upper floret of sessile spikelet of ear (narrow)
Common in monocots, including species of Poaceae such as Zea mays. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). In Zea mays, development of the gynoecium ridge of the upper floret of pedicellate spikelet of ear occurs via continued overgrowth of the shoot apex (which becomes the ovule primordium) by a ring of gynoecial tissue, leading to the formation of a stylar canal that is detected as a slight protuberance on the mature ovary. Early development of the gynoecium ridge of the lower floret of pedicellate spikelet of ear is very similar to that of the upper floret of the pedicellate spikelet of ear, except the development does not proceed beyond the early ridge stage.
A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.
A dehiscence zone (PO:0025092) that is part of a spore capsule.
anillo de la c&#225psula de musgos (Spanish, exact)
Found in bryophytes. The capsule annulus is located at the base of an operculum. Upon capsule maturation, cell separation in the annulus allows the operculum to separate from the capsule, aiding in spore dispersal.
A plant organ (PO:0009008) in which plant spores (PO:0025017) are produced.
In bryophytes, particularly in mosses, a sporangium is referred to as a capsule. In seed plants, a sporangium is located in a sporophyll. In pteridophytes, a sporangium is located on the surface of a sporophyll or fertile leaf or borne on a sporangiophore. May be unicellular in some algae.
A portion of parenchyma tissue (PO:0005421) that is part of a root (PO:0009005).
par&#233nquima de la ra&#237z (Spanish, exact)
A portion of phyllome epidermis (PO:0025157) that is part of a carpel (PO:0009030).
A portion of carpel epidermis (PO:0025096) that covers the abaxial surface of a carpel (PO:0009030). (broad)
A portion of phyllome epidermis (PO:0025157) that is part of a stamen (PO:0009029).
A phyllome trichome that is part of a bract epidermis.
A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009).
estructura vegetal embri&#243nica (Spanish, exact)
Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).
A plant axis elongation zone (PO:0025180) that is part of a shoot axis internode (PO:0005005).
zona de elongaci&#243n del internodo de epiblasto (epiblastema) (Spanish, exact)
A shoot axis internode elongation zone (PO:0025100) that is part of a branch internode (PO:0025080).
zona de elongaci&#243n de la ramificaci&#243n del internodo (Spanish, exact)
A plant axis differentiation zone that is part of a shoot axis.
zona de diferenciaci&#243n del internodo del epiblasto (epiblastema) (Spanish, exact)
A shoot internode differentiation zone that is part of a branch internode.
zona de diferenciaci&#243n de la ramificaci&#243n del internodo (Spanish, exact)
An inflorescence axis (PO:0020122) that is the primary or main axis of an inflorescence (PO:0009049).
primer orden del eje de la inflorescencia (Spanish, exact)
Monopodial inflorescences, such as a raceme inflorescence (PO:0030115), have a centrally-located main axis; this axis is a first order inflorescence axis. In contrast, sympodial inflorescences, such as the riphidium inflorescence (PO:0030131), do not have a centrally-located main axis. The basal-most portion of a first order inflorescence axis is referred to as a peduncle (PO:0009053).
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a third order inflorescence axis (PO:0025105).
eje de cuarto orden de la inflorescencia (Spanish, exact)
third order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a fourth order inflorescence axis (PO:0025106).
eje de quinto orden de la inflorescencia (Spanish, exact)
fourth order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a fifth order inflorescence axis (PO:0025107).
eje de sexto orden de la inflorescencia (Spanish, exact)
fifth order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a sixth order inflorescence axis (PO:0025108).
eje de séptimo orden de la inflorescencia (Spanish, exact)
sixth order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a seventh order inflorescence axis (PO:0025109).
eje de octavo orden de la inflorescencia (Spanish, exact)
seventh order inflorescence branch (exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a eighth order inflorescence axis (PO:0025110).
eighth order inflorescence branch (exact)
eje de noveno orden de la inflorescencia (Spanish, exact)
A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a ninth order inflorescence axis (PO:0025110).
eje de décimo orden de la inflorescencia (Spanish, exact)
ninth order inflorescence branch (exact)
Tenth order inflorescence axis (PO:0025111) is the greatest specific inflorescence axis order in the PO; when mapping annotations to inflorescence axes which are of an order greater than ten, or when order is ambiguous or unknown, annotate directly to higher order inflorescence axis (PO:0009081).
A higher order infructescence axis (PO:0025243) which arises from a first order infructescence axis (PO:0025244) and develops from a second order inflorescence axis (PO:0006321).
eje de segundo de la infructescencia (Spanish, exact)
A higher order infructescence axis (PO:0025243) which arises from a second order infructescence axis (PO:0025112) and develops from a third order inflorescence axis (PO:0006322).
eje de tres orden de la infructescencia (Spanish, exact)
second order infructescence branch (exact)
A higher order infructescence axis (PO:0025243) which arises from a third order infructescence axis (PO:0025113) and develops from a fourth order inflorescence axis (PO:0025105).
eje de cuarto orden de la infructescencia (Spanish, exact)
third order infructescence branch (exact)
A higher order infructescence axis (PO:0025243) which arises from a fourth order infructescence axis (PO:0025114) and develops from a fifth order inflorescence axis (PO:0025106).
eje de quinto orden de la infructescencia (Spanish, exact)
fourth order infructescence branch (exact)
A higher order infructescence axis (PO:0025243) which arises from a fifth order infructescence axis (PO:0025115) and develops from a sixth order inflorescence axis (PO:0025107).
eje de sexto orden de la infructescencia (Spanish, exact)
fifth order infructescence branch (exact)
An anatomical space that is part of a plant.
espacio anat&#243mico vegetal (Spanish, exact)
CARO:0000005 'anatomical space' is defined as: An immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes, and is bounded by an anatomical surface.
A plant anatomical space that is a pore at the apex of an anther.
Pollen may be released through the anther pore.
A cardinal organ part that is part of a plant axis and is located behind the elongation zone and contains cells that are differentiating into their final form and function.
zona de diferenciaci&#243n de eje vegetal (Spanish, exact)
A plant sperm cell (PO:0000084) which develops from a spermatogenous cell (PO:0025525) and is located in an antheridium (PO:0025125).
c&#233lula esperm&#225tica del anteridio (Spanish, exact)
Antheridial sperm cells are motile and lack a cell wall.
A plant sperm cell (PO:0000084) that is part of the pollen (PO:0025281).
c&#233lula esperm&#225tica pol&#237nica (Spanish, exact)
Pollen sperm cells are structurally simple, usually non-motile cells that may contain a normal complement of cellular organelles, including heritable cytoplasmic organelles such as mitochondria and, in some plants, plastids, but lack a cell wall. In seed plants, pollen sperm cells are usually two in number. In angiosperms, during double fertilization, one fuses with the plant egg cell (PO:0020094) to produce a plant zygote (PO:0000423) while another fuses with the two polar nuclei of the embryo sac central cell (PO:0020090) to give rise to endosperm (PO:0009089). In angiosperms, the pollen sperm cell arises from the generative cell (PO:0020097). In gymnosperms, the pollen sperm cell arises from the body cell (PO:0025525).
A plant egg cell (PO:0020094) that develops from the archegonium central cell (PO:0025509) and is located in the venter (PO:0030038).
ooc&#233lula del arquegonio (Spanish, exact)
The archegonium egg cell has a common origin with the ventral canal cell.
A plant egg cell (PO:0020094) that is part of an egg apparatus (PO:0020096).
ooc&#233lula del saco embrionario (Spanish, exact)
The egg apparatus is part of an embryo sac (PO:0025074).
A plant organ (PO:0009008) that produces one or more gametes (PO:0025006) and participates in the gametophyte development stage (PO:0028003).
The multicellular plant gametangium; an archegonium (PO:0025126) and/or an antheridium (PO:0025125), occurs in bryophytes, pteridophytes and gymnosperms, but never in angiosperms.
A multicellular plant gametangium (PO:0025124) that produces antheridium sperm cells (PO:0025120) and has as parts an antheridium jacket layer (PO:0030053) and an antheridium stalk (PO:0030035).
The antheridium (PO:0025125) occurs in bryophytes and pteridophytes, but never in gymnosperms or angiosperms, where male gametes are produced in the pollen (PO:0025281), a specialized (reduced) gametangium.
A multicellular plant gametangium (PO:0025124) that develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038) and an archegonium neck (PO:0030039).
At maturity, the archegonium produces an archegonium egg cell (PO:0025122). In mosses, the archegonium also has part an archegonium stalk (PO:0030036). The archegonium (PO:0025126) occurs in bryophytes and pteridophytes, but never in angiosperms, where the female gamete (plant egg cell; PO:0020094) is produced by the embryo sac (PO:0025074), a specialized (reduced) gametangium.
A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.
A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
portion of phyllome primordium tissue (exact)
The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.
A lamina (PO:0025060) that is part of a petiole (PO:0020038).
l&#225mina (ala) del pec&#237olo (Spanish, exact)
The entire petiole may be laminar, or the petiole may be more or less rounded in cross section with laminar extensions.
A leaf near the apex of a stem that is still rolled into a cylinder.
Describes the phenotype of a vascular leaf during a leaf development phase in Musa and other monocots.
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
A plant anatomical space (PO:0025117) that is either a groove on the surface, or a tube in the interior of a plant structure (PO:0009011).
May be cylindrical (PATO:0001203) in shape, with a circular, D-shaped or other irregularly-shaped cross-section.
May occur on the surface or be internal.
A shoot system that forms the basal part of an inflorescence to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.
corona de la ramificaci&#243n de la inflorescencia (Spanish, exact)
A portion of leaf lamina abaxial epidermis PO:0000049) that covers the abaxial surface of a cigar leaf (PO:0025130).
epidermis abaxial de la l&#225mina de la hoja en cigarro (Spanish, exact)
A tepal (PO:0009033) that is part of a collective tepal structure (PO:0025021), along with a fused collective tepal structure (PO:0025138), but is separate from (PATO:0001505) the other tepals.
A free tepal (PO:0025136) only occurs in a perianth (PO:0009058) that contains a fused collective tepal structure (PO:0025138). If you are describing a tepal (PO:0025137) that is part of a perianth (PO:0009058) where none of the tepals (PO:0009033) are fused, you should use tepal.
A tepal (PO:0009033) that is part of a fused collective tepal structure (PO:0025138) in which it is fused to at least one other tepal.
A collective tepal structure (PO:0025021) in which there are at least two fused tepals (PO:0025137).
estrutura colectiva de t&#233palo fusionado (Spanish, exact)
It is not precisely defined how far toward the base from the tip a phyllome apex extends. For the apical most portion of a phyllome, use the term phyllome tip.
The basal part of a phyllome (PO:0006001), where it attaches to a shoot axis (PO:0025029).
The apical most portion of a phyllome apex.
This term is to be used for only the apical most portion of a phyllome. For a larger area, use the term phyllome apex. Use this term when describing the shape of a phyllome tip.
A phyllome tip (PO:0025141) that is part of a leaf apex (PO:0020137).
This term is to be used for only the apical most portion of a leaf. For a larger area, use the term leaf apex. Use this term when describing the shape of a leaf tip. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A phyllome apex PO:0025139) that is part of a tepal (PO:0009033).
&#225pice del t&#233palo (Spanish, exact)
It is not precisely defined how far toward the base from the tip a tepal apex extends. For the apical most portion of a tepal, use the term tepal tip.
A phyllome apex (PO:0025139) that is part of a petal (PO:0009032).
&#225pice del p&#233talo (Spanish, exact)
It is not precisely defined how far toward the base from the tip a petal apex extends. For the apical most portion of a petal, use the term petal tip.
A phyllome apex that is part of a sepal.
&#225pice del s&#233palo (Spanish, exact)
It is not precisely defined how far toward the base from the tip a sepal apex extends. For the apical most portion of a sepal, use the term sepal tip.
A phyllome base (PO:0025140) that is part of a petal (PO:0009032).
A phyllome base that is part of a sepal.
A phyllome base (PO:0025140) that is part of a tepal (PO:0009033).
A phyllome tip that is part of a petal apex.
This term is to be used for only the apical most portion of a petal. For a larger area, use the term petal apex. Use this term when describing the shape of a petal tip.
A phyllome tip that is part of a sepal apex.
This term is to be used for only the apical most portion of a sepal. For a larger area, use the term sepal apex. Use this term when describing the shape of a sepal tip.
A phyllome tip that is part of a tepal apex.
This term is to be used for only the apical most portion of a tepal. For a larger area, use the term tepal apex. Use this term when describing the shape of a tepal tip.
A portion of branch epidermis (PO:0025179) that is part of a peduncle (PO:0009053).
epidermis del ped&#250nculo (Spanish, exact)
A shoot axis trichome that is part of a peduncle epidermis.
tricoma del ped&#250nculo (Spanish, exact)
A phyllome apex (PO:0025139) that is part of a bract (PO:0009055).
&#225pice de la br&#225ctea (Spanish, exact)
It is not precisely defined how far toward the base from the tip a bract apex extends. For the apical most portion of a bract, use the term bract tip.
A phyllome base (PO:0025140) that is part of a bract (PO:0009055).
A phyllome tip that is part of a bract apex.
punta de la br&#225ctea (Spanish, exact)
This term is to be used for only the apical most portion of a bract. For a larger area, use the term bract apex. Use this term when describing the shape of a bract tip.
A portion of shoot system epidermis (PO:0006035) that is part of a phyllome (PO:0006001).
A portion of phyllome epidermis (PO:0025157) that is part of a bract (PO:0009055).
epidermis de la br&#225ctea (Spanish, exact)
A portion of bract epidermis (PO:0025158) that covers the abaxial/lower surface of a bract (PO:0009055).
epidermis abaxial de la br&#225ctea (Spanish, exact)
A portion of bract epidermis (PO:0025158) that covers the adaxial/upper surface of a bract (PO:0009055).
epidermis adaxail de la br&#225ctea (Spanish, exact)
A portion of organism substance that is or was part of a plant.
porci&#243n de sustancia vegetal (Spanish, exact)
Refers to organism substance (CARO:0000004) which is defined as: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome. For plants, the word "body" refers to a whole plant, or part thereof. Includes substances such as latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, and sporopollenin.
A portion of plant tissue (PO:0009007) that forms a non-sclerified outgrowth from the epidermis (PO:0005679).
non-glandular multicelluar trichome (narrow)
non-secretory multicellular trichome (narrow)
A multicellular trichome (PO:0000282) has as parts more than one trichome cell (PO:0008030), may vary in size and complexity, be branched and may contain a secretory gland.
A trichome cell (PO:0008030) that forms a branch of a multicellular trichome (PO:0025162).
c&#233lula ramificada de tricoma multicelular (Spanish, exact)
For branches of a unicellular trichome, see unicellular trichome branch (GO:0090405) in GO.
A plant epidermal cell (PO:0004013) that is part of a root epidermis (PO:0006036).
c&#233lula epid&#233rmica de la ra&#237z (Spanish, exact)
A plant epidermal cell (PO:0004013) that is part of a shoot axis epidermis (PO:0000112).
c&#233lula epid&#233rmica del epiblasto (epiblastema) (Spanish, exact)
An epidermal pavement cell with a short protuberance.
See plant cell papilla (GO:0090395) for the subcellular component papilla.
A papilla cell that is part of a leaf epidermis.
c&#233lula papilosa de la epidermis (Spanish, exact)
See leaf papilla (GO:0090396) for the subcellular component leaf papilla. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
A papilla cell that is part of a stigma epidermis.
c&#233lula papilosa del estigma (Spanish, exact)
See stigma papilla (GO:0090397) for the subcellular component stigma papilla.
A portion of epidermis (PO:0005679) that is a sclerified outgrowth.
A prickle (PO:0025169) that is part of a root (PO:0009005)
espinilla de la ra&#237z (Spanish, exact)
A prickle (PO:0025169) that is part of a shoot axis (PO:0025029).
espinilla del eje del epiblasto (epiblastema) (Spanish, exact)
A branch that is a sclerified, pointed outgrowth.
A thorn is a short, pointed (PATO:0002258) woody structure, may be branched.
A leaf that is a sclerified and pointed and lacks a lamina.
A stipule that is sclerified and pointed.
A prickle (PO:0025169) that is part of a leaf (PO:0025034).
A shoot axis trichome that is part of a stem epidermis.
A shoot axis trichome that is part of a branch epidermis.
tricoma de una ramificaci&#243n (Spanish, exact)
A portion of shoot axis epidermis (PO:0000112) that is part of a stem (PO:0009047).
A portion of shoot axis epidermis (PO:0006035) that is part of a branch (PO:0025073).
epidermis de la ramificaci&#243n (Spanish, exact)
A cardinal organ part (PO:0025001) which is part of a plant axis (PO:0025004), is located proximal to an apical meristem (PO:0020144), and in which plant cells (PO:0009002) are undergoing longitudinal expansion.
zona de elongaci&#243n del eje de la planta (Spanish, exact)
A plant axis elongation zone (PO:0025180) that is part of a root tip (PO:0000025) and located proximal to a root apical meristem (PO:0020147).
zona de elongaci&#243n de la ra&#237z (Spanish, exact)
The root elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissues begin to differentiate in the root elongation zone. This term replaces elongation zone (PO:0020125).
A phyllome trichome that is part of a sepal epidermis.
tricoma de la epidermis del s&#233palo (Spanish, exact)
A phyllome stomatal complex (PO:0025215) that is part of a leaf.
complejo estom&#225tico de la hoja (Spanish, exact)
A portion of phyllome epidermis (PO:0025157) that is part of a tepal (PO:0009033).
epidermis del t&#233palo (Spanish, exact)
A leaf stomatal complex that is part of a leaf lamina.
complejo estom&#225tico de la l&#225mina de la hoja (Spanish, exact)
leaf lamina epidermal stomatal complex (exact)
leaf lamina epidermis stomatal complex (exact)
A trichome that is part of a phyllome epidermis.
A phyllome trichome that is part of a petal epidermis.
A phyllome trichome that is part of a tepal epidermis.
tricoma de la epidermis del t&#233palo (Spanish, exact)
A leaf stomatal complex that is part of a petiole.
complejo estom&#225tico del pec&#237olo (Spanish, exact)
petiole epidermal stomatal complex (exact)
petiole epidermis stomatal complex (exact)
A leaf stomatal complex (PO:0025183) that is part of a leaf abaxial epidermis (PO:0006019).
complejo estom&#225tico de la superficie abaxial de la hoja (Spanish, exact)
leaf abaxial epidermal stomatal complex (exact)
leaf abaxial epidermis stomatal complex (exact)
A leaf stomatal complex that is part of a leaf adaxial epidermis.
complejo estom&#225tico de la superficie adaxial de la hoja (Spanish, exact)
leaf adaxial epidermal stomatal complex (exact)
leaf adaxial epidermis stomatal complex (exact)
A portion of tepal epidermis (PO:0025184) that covers the abaxial/lower surface of a tepal (PO:0009033).
epidermis abaxial del t&#233palo (Spanish, exact)
A portion of tepal epidermis (PO:0025184) that covers the adaxial/upper surface of a tepal (PO:0009033).
epidermis adaxail del t&#233palo (Spanish, exact)
A root meristem (PO:0006085) that gives rise to a root nodule (PO:0003023).
meristema del n&#243dulo de la ra&#237z (Spanish, exact)
A native plant cell (PO:0025606) that develops from a microgametophyte vegetative cell (PO:0020099) and forms a tubular extension of the pollen (PO:0025281).
c&#233lula del tubo pol&#237nico (Spanish, exact)
Carries the male gametes (PO:0025006) into or near the plant ovule (PO:0020003). May be branched in gymnosperms. See GO for pollen tube (GO:0090406) or pollen tube tip (GO:0090404).
A portion of plant tissue (PO:0009007) that is part of an endosperm (PO:0009089) and is composed of basal endosperm transfer cells (PO:0009018).
capa de transferencia del endosperma basal (Spanish, exact)
Involved in transferring nutrients to a plant embryo (PO:0009009).
A cardinal organ part (PO:0025001) that is the central column of a plant axis that consists of the primary vascular tissue and associated ground tissue.
If a pith is present, it is part of the stele, otherwise the stele only includes the primary vascular tissue and the ground tissue that surrounds it.
estela del eje del epiblasto (epiblastema) (Spanish, exact)
A shoot axis stele that is part of a branch.
estela de la ramificaci&#243n (Spanish, exact)
A shoot axis stele that is part of a stem.
A sporangium in which megaspores are produced.
A sporangium (PO:0025094) in which microspores (PO:0020048) are produced.
A vascular bundle (PO:0005020) that is part of a pericarp (PO:0009084).
haz vascular del pericarpo (Spanish, exact)
A shoot axis internode (PO:0005005) that is part of a rhizome (PO:0004542).
A vascular system (PO:0000034) that is part of a shoot system (PO:0009006).
sistema vascular del sistema del epiblasto (epiblastema) (Spanish, exact)
A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a phyllome (PO:0006001).
sistema vascular del filoma (Spanish, exact)
A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a tepal (PO:0009033).
sistema vascular del t&#233palo (Spanish, exact)
A phyllome trichome (PO:0025186) that is part of a carpel epidermis (PO:0025096).
A phyllome trichome that is part of a stamen epidermis.
tricoma vascular del estambre (Spanish, exact)
A leaf trichome that is part of a leaf abaxial epidermis.
tricoma de la superficie abaxial de la hoja (Spanish, exact)
A leaf trichome that is part of a leaf adaxial epidermis.
tricoma de la superficie adaxial de la hoja (Spanish, exact)
An epidermal pavement cell that is part of a leaf epidermis.
c&#233lula de pavimento de la hoja (Spanish, exact)
A leaf pavement cell that is part of a leaf abaxial epidermis.
c&#233lula de pavimento de la superficie abaxial de la hoja (Spanish, exact)
A leaf pavement cell that is part of a leaf adaxial epidermis.
c&#233lula de pavimento de la superficie adaxial de la hoja (Spanish, exact)
A stomatal complex (PO:0002000) that is part of a phyllome (PO:0006001).
complejo estom&#225tico del filoma (Spanish, exact)
phyllome epidermal stomatal complex (exact)
phyllome epidermis stomatal complex (exact)
A phyllome stomatal complex (PO:0025215) that is part of a bract (PO:0009055).
bract epidermal stomatal complex (exact)
bract epidermis stomatal complex (exact)
complejo estom&#225tico de la br&#225ctea (Spanish, exact)
A phyllome stomatal complex that is part of a carpel.
carpel epidermal stomatal complex (exact)
carpel epidermis stomatal complex (exact)
complejo estom&#225tico del carpelo (Spanish, exact)
A phyllome stomatal complex (PO:0025215) that is part of a petal (PO:0009032).
complejo estom&#225tico del p&#233talo (Spanish, exact)
petal epidermal stomatal complex (exact)
petal epidermis stomatal complex (exact)
A phyllome stomatal complex that is part of a sepal.
complejo estom&#225tico del s&#233palo (Spanish, exact)
sepal epidermal stomatal complex (exact)
sepal epidermis stomatal complex (exact)
A phyllome stomatal complex that is part of a stamen.
complejo estom&#225tico del estambre (Spanish, exact)
stamen epidermal stomatal complex (exact)
stamen epidermis stomatal complex (exact)
A phyllome stomatal complex that is part of a tepal (PO:0009033).
complejo estom&#225tico del t&#233palo (Spanish, exact)
tepal epidermal stomatal complex (exact)
tepal epidermis stomatal complex (exact)
A shoot apex that has as part a reproductive shoot apical meristem.
&#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact)
A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016).
&#225pice vegetativo del epiblasto (epiblastema) (Spanish, exact)
A plant anatomical space that is the space between a shoot axis and a leaf, bract, or branch that branches from the shoot axis.
An axil that is the space between a shoot axis and a bract that branches from the shoot axis.
axila de la br&#225ctea (Spanish, exact)
An axil that is the space between a shoot axis and a branch that branches from the shoot axis.
axila de la ramificaci&#243n (Spanish, exact)
A portion of plant tissue consisting of four megaspores that remained joined together shortly after meiosis. One cell will give rise to a female gametophyte.
t&#233trada de megasporas (Spanish, exact)
Usually only one of the four megaspores develops and the other three die.
A cardinal organ part that is a part of a plant structure that splits apart when the structure dehisces.
A valve that is a part of a spore capsule that splits apart when the spore capsule dehisces.
valva de la c&#225psula de musgo (Spanish, exact)
Found in bryophytes. A spore capsule may dehisce ongitudinally, forming evenely sized valves, or it may dehisce at the capsule annulus, forming the operculum, which is a specialized type of valve.
A portion of plant tissue (PO:0009007) that forms the central axis of a plant structure such as a fruit (PO:0009001) or moss capsule (sporangium; PO:0025094).
A columella (PO:0025230) that forms the central axis of a spore capsule.
columela de la c&#225psula de musgo (Spanish, exact)
A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009).
portion of embryonic plant tissue (exact)
tejido embri&#243nico vegetal (Spanish, exact)
This class is for tissues that only occur as part of an embryo.
A stomatal pore that is part of a phyllome stomatal complex.
poro estom&#225tico del filoma (Spanish, exact)
A phyllome stomatal pore that is part of a leaf stomatal complex.
poro estom&#225tico de la hoja (Spanish, exact)
A guard cell that is part of a phyllome stomatal complex.
c&#233lula guardiana del filoma (Spanish, exact)
A phyllome guard cell that is part of a leaf stomatal complex.
c&#233lula guardiana de la hoja (Spanish, exact)
A petiole canal on the abaxial surface of a petiole.
canal abaxial del pec&#237olo (Spanish, exact)
A petiole canal on the adaxial surface of a petiole.
canal adaxial del pec&#237olo (Spanish, exact)
A reproductive shoot system (PO:0025082) that is part of an inflorescence (PO:0009049) and has as parts a second order inflorescence axis (PO:0006321) and any shoot axes (PO:0025029) and flowers (PO:0009046) that arise from it.
inflorescencia de segundo orden (Spanish, exact)
This a sub-inflorescence that arises from the main inflorescence axis.
A reproductive shoot system that is part of an infructescence and has as parts a second order infructescence axis and any infructescence axes and fruits that arise from it.
infructescencia de segundo orden (Spanish, exact)
A shoot axis (PO:0025029) that is part of an infructescence (PO:0006342).
eje de la infructescencia (Spanish, exact)
An infructescence axis (PO:0025242), which is a branch (PO:0025073) in an infructescence (PO:0006342), that develops from a higher order inflorescence axis (PO:0009081).
ejen de la infructescencia (Spanish, exact)
A higher order infructescence axis is named according to its position in an infructescence (PO:0006342). Tenth order infructescence axis (PO:0025112) is the greatest specific infructescence axis (PO:0025242) order in the PO; when mapping annotations to an infructescence axis which is of an order higher than ten, or when order is ambiguous or unknown, annotate directly to higher order infructescence axis (PO:0025243).
An infructescence axis (PO:0025242), which is the primary or main axis of an infructescence (PO:0006342), that develops from a first order inflorescence axis (PO:0025104).
eje de la infructescencia de primer orden (Spanish, exact)
A phyllome that develops from a sepal and remains attached to a fruit at maturity.
A phyllome (PO:0006001) that develops from a tepal (PO:0009033) and remains attached to a fruit (PO:0009001) at maturity.
A phyllome that develops from a stamen and remains attached to a fruit at maturity.
A collective organ part structure that forms a cylindrical false stem composed concentric leaf sheaths.
The peduncle later grows up through the pseudostem. Common in Musa species and some other monocots.
A portion of leaf epidermis (PO:0006016) that is part of a leaf sheath (PO:0020104).
epidermis de la vaina de la hoja (Spanish, exact)
A portion of leaf sheath epidermis (PO:0025249) that covers the abaxial/lower surface of a leaf sheath (PO:0020104).
epidermis abaxial de la vaina de la hoja (Spanish, exact)
A portion of leaf sheath epidermis (PO:0025249) that covers the adaxial/upper surface of a leaf sheath (PO:0020104).
epidermis adaxial de la vaina de la hoja (Spanish, exact)
A higher order infructescence axis (PO:0025243) which arises from a sixth order infructescence axis (PO:0025116) and develops from a seventh order inflorescence axis (PO:0025108).
eje de séptimo orden de la infructescencia (Spanish, exact)
sixth order infructescence branch (exact)
A higher order infructescence axis (PO:0025243) which arises from a seventh order infructescence axis (PO:0025252) and develops from an eighth order inflorescence axis (PO:0025109).
eje de octavo orden de la infructescencia (Spanish, exact)
seventh order infructescence branch (exact)
A higher order infructescence axis (PO:0025243) which arises from an eighth order infructescence axis (PO:0025253) and develops from a ninth order inflorescence axis (PO:0025110).
eighth order infructescence branch (exact)
eje de noveno orden de la infructescencia (Spanish, exact)
A higher order infructescence axis (PO:0025243) which arises from a ninth order infructescence axis (PO:0025254) and develops from a tenth order inflorescence axis (PO:0025111).
eje de decimo orden de la infructescencia (Spanish, exact)
ninth or higher order infructescence branch (exact)
Tenth order infructescence axis (PO:0025112) is the greatest specific infructescence axis (PO:0025242) order in the PO; when mapping annotations to an infructescence axis which is of an order higher than ten, or when order is ambiguous or unknown, annotate directly to higher order infructescence axis (PO:0025243).
A root elongation zone that is part of a lateral root tip.
zona de elongaci&#243n de la ra&#237z lateral (Spanish, exact)
A root elongation zone (PO:0025181) that is part of a primary root tip (PO:0000026).
zona de elongaci&#243n de la ra&#237z primaria (Spanish, exact)
A meristematic cell (PO:0004010) that is part of a portion of procambium (PO:0025275).
c&#233lula del procambio (Spanish, exact)
A portion of shoot procambium (PO:0025276) tissue that is part of a vascular leaf (PO:0009025).
A portion of shoot procambium that is part of a shoot apical meristem and gives rise to the primary vascular tissue of a shoot axis.
procambio del eje del epiblasto (Spanish, exact)
A ground tissue cell that is part of a portion of pericycle.
c&#233lula del periciclo (Spanish, exact)
A septum (PO:0000030) that divides a multilocular plant ovary (PO:0009072).
Found in species with syncarpous gynoecia (fused carpels). A plant ovary septum is derived from the fused walls of two adjacent carpels, while a replum (PO:0005016) develops from early contact of placental tissue from opposite sides of the plant ovary. Annotations for Arabidopsis should go under replum, not under plant ovary septum.
A plant anatomical space (PO:0025117) that is a cavity a reproductive structure.
May be a cavity in a sporophyll, within several fused sporophylls, or within a sporangium. In many instances, the locules are filled with seeds or other plant structures.
A sporangium locule that is part of an anther and is a cavity within a single pollen sac or two or more fused pollen sacs.
l&#243culo del esporangio (Spanish, exact)
A locule (PO:0025263) that is a cavity in a sporangium (PO:0025094) or several fused sporangia.
l&#243culo de la antera (Spanish, exact)
A locule (PO:0025263) that is a cavity in a plant ovary (PO:0009072).
Generally contains at least one ovule. An ovary locule may be part of a single carpel, in the case of unicarpellate flowers. An ovary that is part of a syncarpous gynoecium may have multiple locules, or the anatomical spaces of multiple carpels may be fused to form a single locule.
A portion of fruit placenta tissue (PO:0004535) that divides a fruit (PO:0009001) into two or more chambers and develops from a plant ovary replum (PO:0025272).
A fruit replum develops from the ovary replum and has no suture line in its center, while a fruit septum (PO:0025262) develops from an ovary septum via the fusion of two adjacent ovary walls. Common in Brassicaceae. Annotations for Arabidopsis fruit should go here, and not under fruit septum. If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A septum that divides a cavity or mass of tissue in a fruit and develops from an ovary septum.
Annotations for Arabidopsis should go under fruit replum (PO:0025267), not under fruit septum. The partition between two fruit locules of an orange is a fruit septum. If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) that are part of adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).
&#243rgano colectivo de una parte de la estructura (Spanish, exact)
A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type but may be of different types. Includes plant structures like a septum (PO:0000030) that consists of the walls of two fused carpels (PO:0009030) or a pseudostem (PO:0025248) that consist of multiple, overlapping leaf sheaths (PO:0020104). Unlike a collective plant organ structure (PO:0025007), a collective organ part structure does not contain any complete plant organs.
A locule (PO:0025263) that is a cavity in a fruit (PO:0009001) and develops from a plant ovary locule (PO:0025266).
A portion of ovary placenta tissue (PO:0020001) which divides a plant ovary (PO:0009072) into two or more chambers, and develops from contact of the placental tissue from opposite sides of the plant ovary early in gynoecium development (GO:0048467).
replo (replum) del ovario (Spanish, exact)
An ovary replum develops along with the ovary and has no suture line in its center, while a true ovary septum (PO:0025262) is derived from the fusion two adjacent ovary walls. Common in Brassicaceae. Annotations for Arabidopsis should go here, and not under ovary septum.
A portion of shoot axis procambium gives rise to the primary vascular tissue of a stem.
A portion of shoot axis procambium gives rise to the primary vascular tissue of a branch.
procambio de la ramificaci&#243n (Spanish, exact)
A portion of meristem tissue (PO:0009013) that undergoes differentiation to form the primary vascular tissue (PO:0025408).
May occur in an apical meristem or in a developing phyllome. Gives rise to the primary xylem and primary phloem. This term replaces PO:0006074.
A portion of procambium (PO:0025275) tissue that is part of a shoot system (PO:0009006).
procambio del epiblasto (Spanish, exact)
A microsporangium that is part of a sporophyll and where the pollen grains develop and are located after they develop.
A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
hoja escamosa del rizoma (Spanish, exact)
A whole plant in the gametophyte development stage (PO:0028003) that produces only plant egg cells (PO:0020094).
Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores. In angiosperms, Gnetum, and Weltwischia, the megagametophyte is greatly reduced. The megagametophyte in angiosperms is an embryo sac.
A whole plant (PO:0000003) in the gametophyte development stage (PO:0028003) that produces plant sperm cells (PO:0000084).
The microgametophyte in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In seed plants the male gametophyte is reduced to a pollen grain.
A microgametophyte (PO:0025280) that develops from a microspore (PO:0020048) is located in a pollen sac (PO:0025277).
A megagametophyte (PO:0025279) that has as parts one or more archegonia (PO:0025126).
arquegonio del megagametofito (Spanish, exact)
Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores.
A microgametophyte (PO:0025280) that has as parts one or more antheridia (PO:0025125).
anteridio del microgametofito (Spanish, exact)
Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores.
A sporophyte meristematic apical cell that is part of a plant embryo and is the uppermost cell formed after the first division of a zygote.
c&#233lula apical del embri&#243n (Spanish, exact)
embryonic meristematic apical cell (exact)
A parenchyma cell that is part of a plant callus.
c&#233lula parenquim&#225tica del callo (Spanish, exact)
A coleoptile (PO:0020033) that is part of a plant embryo (PO:0009009).
cole&#243ptile del embri&#243n (Spanish, exact)
A coleoptile (PO:0020033) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
cole&#243ptile de la pl&#225ntula (Spanish, exact)
A seedling coleoptile develops from an embryo coleoptile (PO:0025286).
A coleorhiza (PO:0020034) that is part of a plant embryo (PO:0009009).
coleorriza del embri&#243n (Spanish, exact)
A coleorhiza (PO:0020034) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
coleorriza de la pl&#225ntula (Spanish, exact)
Develops from an embryo coleorhiza (PO:0025288).
A hypocotyl (PO:0020100) that is part of a plant embryo axis (PO:0019018).
hipoc&#243tile del embri&#243n (Spanish, exact)
A hypocotyl (PO:0020100) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
hipoc&#243tile de la pl&#225ntula (Spanish, exact)
Develops from an embryo hypocotyl (PO:0025290). This term should only be used for seed plants.
An epicotyl (PO:0020035) that is part of a plant embryo (PO:0009009).
epic&#243tile del embri&#243n (Spanish, exact)
An epicotyl (PO:0020035) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
epic&#243tile de la pl&#225ntula (Spanish, exact)
Develops from an embryo epicotyl (PO:0025292).
A mesocotyl (PO:0020037) that is part of a plant embryo (PO:0009009).
mesoc&#243tile del embri&#243n (Spanish, exact)
A mesocotyl (PO:0020037) that develops from an embryo mesocotyl (PO:0025294).
mesoc&#243tile de la plantual (Spanish, exact)
A seedling mesocotyl is an elongation of an embryo mesocotyl (PO:0025294) and is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
A radicle (PO:0020031) that is part of a plant embryo (PO:0009009).
rad&#237cula del embri&#243n (Spanish, exact)
May eventually develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive.
A radicle (PO:0020031) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
rad&#237cula de la pl&#225ntula (Spanish, exact)
Develops from an embryo radicle (PO:0025296). May develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive.
A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence.
Develops from the apical portion of a gynoecium, and is commonly found as part of the fruit of species of Myrtaceae, such as Eucalyptus spp. If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.
A hypocotyl-root junction (PO:0004724) that is part of an plant embryo axis (PO:0019018).
conjunci&#243n del hipoc&#243tile-ra&#237z en el embri&#243n (Spanish, exact)
embryonic hypocotyl-root junction (exact)
A hypocotyl-root junction (PO:0004724) that develops from an embryo hypocotyl-root junction (PO:0025300) .
conjunci&#243n del hipoc&#243tile-ra&#237z en la pl&#225ntula (Spanish, exact)
Part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
A plant embryo (PO:0009009) that arises from previously differentiated somatic cells, rather than from fused gametes, i.e. the plant zygote (PO:0000423).
embri&#243n som&#225tico vegetal (Spanish, exact)
Somatic plant embryos may arise where embryos normally would not arise as a product of apomixis. They may occur on the edges of leaves on some species of Kalanchoe or some ferns.
A plant embryo (PO:0009009) that forms as a result of the fusion of gametes.
embri&#243n som&#225tico cigotico (del cigote) (Spanish, exact)
A zygotic plant embryo that is grown or maintained in vitro.
embri&#243n cultivado derivado del cigoto vegetal (Spanish, exact)
A cultured somatic plant embryo that develops from isolated microspores.
microspore-derived cultured embryo (broad)
embri&#243n cultivado derivado de la microspora vegetal (Spanish, exact)
microspore-derived haploid embryo (exact)
microspore-derived cultured plant embryo
A cardinal organ part (PO:0025001) that is composed of the outer layers of a sporangium (PO:0025094) and bounds the archesporium (PO:0030074) or plant spores (PO:0025017).
May have multiple layers such as exothecium, endothecium and tapetum. Early in development, the sporangium wall bounds the archesporium. Later, after spores develop from the archesporium, it bounds the spore or spores.
A sporangium wall (PO:0025306) that is part of a microsporangium (PO:0025202).
pared del microsporangio (Spanish, exact)
A sporangium wall that is part of a megasporangium.
pared del megasporangio (Spanish, exact)
A sporangium wall endothecium (PO:0030049) that is part of a microsporangium wall (PO:0025307).
endotecio del microsporangio (Spanish, exact)
A sporangium wall endothecium (PO:0030049) that is part of a megasporangium wall.
endotecio del megasporangio (Spanish, exact)
A portion of exothecium (PO:0030073) that is part of a microsporangium wall (PO:0025307).
exotecio del microsporangio (Spanish, exact)
A portion of exothecium (PO:0030073) that is part of a megasporangium wall (PO:0025308).
exotecio del megasporangio (Spanish, exact)
A portion of ground tissue (PO:0025059) that is the inner-most layer of a sporangium wall (PO:0025306).
May function in providing nutrition to developing sporocytes or pollen. May have one or more layers of cells. May break down as spores mature. A tapetum does not develop in some plants, such as Psilotum. In angiosperms, the tapetum develops from one of the parietal layers. In non-seed plants, the tapetum may develop from the outer cells of archesporium or from the inner-most layer of the sporangium wall. The tapetum may be one of two types ameboid or secretory/glandular.
An tapetum (PO:0025313) that is part of a microsporangium wall (PO:0025307).
tapeto del microsporangio (Spanish, exact)
A tapetum (PO:0025313) that is part of a megasporangium wall (PO:0025308).
tapeto del megasporangio (Spanish, exact)
A multicellular trichome (PO:0025162) that has as parts a long terminal cell atop a basal stalk and grows in a leaf axil (PO:0009023).
Found in monocots and mosses. The basal stalk may contain one or more cells.
A trichome cell (PO:0008030) that is the long terminal cell of an axillary hair (PO:0008030).
c&#233lula terminal del pelo axilar (Spanish, exact)
A portion of plant tissue (PO:0009007) that is the basal part of an axillary hair (PO:0025316), below the axillary hair terminal cell (PO:0025317).
A trichome cell (PO:0008030) that is part of a base of an axillary hair (PO:0025316).
c&#233lula basal del pelo axilar (Spanish, exact)
An epidermal rhizoid that grows form a cotyledonary node.
rizoide del nodo del cotiled&#243n (Spanish, exact)
A stem node (PO:0020141) from which cotyledons (PO:0020030) may develop.
A plant anatomical space that is an opening in a hydathode.
Similar to a stomatal pore, but lacks the ability to open and close. Involved in the release water or xylem sap through guttation or secretion.
A reproductive shoot system (PO:0025082) that is a second order inflorescence (PO:0025240), or higher, in which the inflorescence branch (PO:0009081) bears two or more flowers (PO:0009046), but is not elongated.
A fascicle appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Fascicles are common in some sections of the Fabaceae, where they are second order inflorescences.
A petal (PO:0009032) that is the top-most petal of a papilionaceous corolla (PO:0009059).
Usually larger than the adjacent wing petals. Found in the flowers of some Fabaceae.
One of two lateral petals (PO:0009032) that is adjacent to the banner petal of a papilionaceous corolla (PO:0009059).
The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.
A petal (PO:0009032) that is one of the two lowest petals of a papilionaceous corolla (PO:0025324).
The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.
A boat-shaped collective phyllome structure (PO:0025023) that consists of the two lowest petals (PO:0009032) of a papilionaceous corolla (PO:0009059).
The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.
A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to absence of the opposite surface on the mature leaf.
hoja unifacial EXACT Spanish [POC:Maria_Alejandra_Gandolfo] (Spanish, exact)
A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia phyllodes). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface. Note that unifacial leaves may have two sides, as in ensiform leaves, but both sides arise from the same surface of the leaf meristem (abaxial or adaxial).
A fused calyx (PO:0025582) that is composed of fused sepals (PO:0025584).
Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused. Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development. Not the same structure as a spore capsule calyptra or fruit operculum. Sometimes erroneously referred to as part of a fruit.
A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583).
Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla). Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development. Not the same structure as a spore capsule calyptra or fruit operculum. Sometimes erroneously referred to as part of a fruit.
A small pistillate flower (PO:0025599) on the margin of a head-type (capitulum) inflorescence (PO:0009049).
Found in the Asteraceae, surrounding the disk flowers (PO:0025332). Usually zygomorphic, and different in form from disk flowers. Usually pistillate but sterile.
A small flower (PO:0009046) in the center of a head-type (capitulum) inflorescence (PO:0009049).
Found in the Asteraceae. May be actinomorphic or bilabiate, often bisexual. Usually surrounded by and different in form from ray flowers (PO:0025331).
A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.
hoja ensiforme EXACT Spanish [POC:Maria_Alejandra_Gandolfo] (Spanish, exact)
Common in many monocots and some dicots. Note that ensiform leaves have two sides, but both sides arise from the same surface of the leaf meristem (abaxial or adaxial). In some leaves, the petiole may twist, giving the appearance that the lamina is ensiform, but it is not.
A unifacial leaf that is round in cross section throughout all of part of the length of the leaf.
hoja cilíndrica EXACT Spanish [POC:Maria_Alejandra_Gandolfo] (Spanish, exact)
The surface of a terete leaf corresponds to either the adaxial or abaxial surface of a normal leaf.
An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane, throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in development.
filodio EXACT Spanish [POC:Maria_Alejandra_Gandolfo] (Spanish, exact)
Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:0025336, transition phyllode leaf). Phyllodes are generally xeromorphic.
A transition vascular leaf in which the basal portion of the leaf has unifacial lamina development in a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.
filodio transicional EXACT Spanish [POC:Maria_Alejandra_Gandolfo] (Spanish, exact)
Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.
A maximal whole plant development stage.
vida de la planta entera (Spanish, exact)
There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083).
collective plant organ structure development stage
A multi-tissue plant structure development stage (PO:0025571) that has as primary participant a plant organ (PO:0009008) .
etapa de desarrollo de un &#243rgano (Spanish, exact)
Includes development stages for leaves and roots.
A gametophyte development stage (PO:0028003) that occurs during the interval between spore germination and the formation of a gametangium.
etapa vegetativa del gemetofito (Spanish, exact)
A gametophyte may begin to senesce or die from other causes before producing gametangia. Some plants, such as the fern Vittaria appalachiana, may never produce gametangia, and remain in the vegetative stage indefinitely. Developmental vegetative growth (GO:0080186) can also occur during the reproductive stage.
A gametophyte development stage (PO:0028003) that occurs during the interval between the initiation of either a multicellular plant gametangium (PO:0025124) or a unicellular plant gametangium (PO:0025521) and the onset of senescence.
etapa reproductiva del gametofito (Spanish, exact)
gametophyte reproductively competent stage (exact)
A whole plant (PO:0000003) may continue developmental vegetative growth (GO:0080186) after it has entered the reproductive stage, and it may revert to a stage in which it is no longer producing gametantia, but once it has initiated a single gametangium, it remains in the reproductive stage until senescence or death by some other cause.
A gametophyte development stage (PO:0028003) during which a gametophyte participates in a dormancy process.
etapa latente del gametofito (Spanish, exact)
A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant (PO:0000003) in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are the moss Polytrichum commune after it has undergone dessication (a type of resurrection plant), the boreal moss Polytrichum alpestre, whose shoot systems have annual growth segments due to a period of dormancy during the winter, the female gametophyte of Ginkgo biloba, which is dormant before fertilization, and dormancy of plant spores.
A gametophyte development stage (PO:0028003) during which a gametophyte participates in multicellular organism senescence.
etapa de senescencia del gametofito (Spanish, exact)
The gametophyte senescent stage is often preceded by the gametophyte reproductive stage, and it ends with death of the gametophyte, either as a result of senescence or some other cause. This stage is distinct from gametophyte dormant stage, in which organs may senesce, but some parts of the plant remain alive. Multicellular organism senescence/aging (GO:0010259) includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.
A gametophyte reproductive stage (PO:0025341) in which a gametophore (PO:0030018) and gametangium is being produced.
etapa de desarrollo del gamet&#243foro reproductivo de la planta entera (Spanish, exact)
gametophore reproductive whole plant development stage
A gametophyte vegetative whole plant development stage during which a gametophore is being produced but no gametangia are being produced.
etapa de desarrollo del gamet&#243foro vegetativo de la planta entera (Spanish, exact)
gametophore vegetative whole plant development stage
A gametophyte reproductive development stage in which a thallus and gametangium is being produced.
etapa de desarrollo del talo reproductivo de la planta entera (Spanish, exact)
thallus reproductive whole plant development stage
A gametophyte vegetative whole plant development stage during which a thallus is being produced but no gametangia are being produced.
etapa de desarrollo del talo vegetativo de la plant entera (Spanish, exact)
May succeed a protonema whole plant development stage or may directly succeed spore germination.
thallus vegetative whole plant development stage
A vascular bundle (PO:0005020) that is part of a phyllome lamina (PO:0025396).
vena del filoma laminar (Spanish, exact)
A cardinal organ part that is a slender, more or less straight and stiff, fine-pointed, terminal or subterminal appendage of a glume, lemma, or palea.
Found in a spikelet of Poaceae. Sometimes the awn is a continuation of the bearing structure's central primary vein.
An enlarged leaf base (PO:0020040) that is fused with adjacent shoot axis (PO:0025029) tissue.
Found in cacti and other succulents. The upper part of a leaf from which a tubercle develops is usually shed early in development. Tubercles are often conical, but they may merge with those directly above and below to form ribs, as in saguaro (Carnegiea), or they may elongate, as in species of pincushion cacti (Mammillaria). In species with tubercles, the areole bud (PO:0025353) is often found at the distal end of the tubercle. The areole bud originates in the leaf axil (PO:0009023) of the leaf that becomes the tubercle, but is displaced to the tip through elongation of the tubercle.
An axillary vegetative bud (PO:0004712) that is not elongated, in which the vascular leaves (PO:0009025) develop as spine leaves (PO:0025173).
Found in Cactaceae. Appears as a cluster of spine leaves (PO:0025173). May be covered in trichomes (PO:0000282). In species with tubercles (PO:0025352), the areole bud is often found at the distal end of the tubercle. The areole bud originates in a leaf axil (PO:0009023) of a leaf that becomes a tubercle but is displaced to the tip of a tubercle through elongation of the tubercle.
A shoot axis that is flattened and expanded.
Has an increased surface area for photosynthesis and may function similar to leaves in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes. Cladodes bear scale leaves (or leaf scars where temporary leaves have fallen off) that subtend axillary buds.
A shoot system (PO:0009006) that has as parts a short, enlarged stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055).
May serve as a storage or perennating organ. Usually underground. A corm differs from a bulb (PO:0025356) in that it does not have fleshy leaves or leaf bases but usually has scale leaves or remnants of dry leaf sheaths that form a protective covering around it. May bear remnants or scars of detached leaves. Adventitious roots may develop from the base of a corm, and these may be contractile, pulling the corm into the soil. Examples include Gladiolus and Crocus. The pseudobulb of an orchid is equivalent to a corm. A corm is very similar to a rhizome (PO:0004542) with very short sympodial units, although not all corms have sympodial growth.
A short, enlarged shoot system (PO:0009006) that has as parts a short stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055) enclosed by fleshy leaves (PO:0009025) or leaf bases (PO:0020040).
May serve as a storage and/or perennating organ. Usually underground. A bulb differs from a corm (PO:0025355) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa. Not the same structure as a bulbil.
A lateral root (PO:0020121) that is erect and protrudes above the surface of the soil or water.
Pneumatophores are found in trees that live in flooded habitats such as mangroves, and often have many lenticels (PO:0000031) which may provide oxygen to below-ground roots growing in flooded soils. Knee roots are a type of pneumatophore in which the lateral root first grows upward, then turns and grows back down into the substrate, forming a knee-like bend. Note that a pneumatophore differs from a prop root (PO:0000044), which is formed at a stem node above the ground, and grows downward into the soil.
A small lateral root that grows from a prop root and has a mealy surface texture.
Found in some palms and other species growing in flooded habitats. Pneumatorhiza appear as small outgrowths on the surface of a prop root. Similar, but distinct from, pneumatophores.
A collective plant organ structure (PO:0025007) on the surface of a vascular leaf (PO:0009025) that has as part a cluster of two or more adjacent sporangia (PO:0025094).
A collective plant organ structure (PO:0025007) on the surface of a vascular leaf that has as parts two or more fused sori (PO:0025359).
融合胞子嚢を有する維管束葉表面の集合構造 (Japanese, exact)
A vascular leaf that is slender and coiling and lacks a lamina.
Aids plant in climbing. A leaf tendril will usually have a bud or shoot axis in its axil. See also leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), stem apex tendril (PO:0025365), leaf rachis tendril (PO:0025366), and prophyll tendril (PO:0025367). Careful observation is required to correctly classify some tendrils.
A leaflet that is slender and coiling and lacks a lamina.
Aids plant in climbing. If the tendril is derived from the terminal leaflet, use this term instead of leaf apex tendril (PO:xxxx). See also leaf tendril (PO:0025361), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), stem apex tendril (PO:0025365), leaf rachis tendril (PO:0025366), and prophyll tendril (PO:0025367). Careful observation is required to correctly classify some tendrils.
A leaf apex of a laminar vascular leaf that is slender and coiling.
&#225pice en zarzillo de la hoja (Spanish, exact)
Aids plant in climbing. Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar or it may be a narrow lamina. If the tendril is derived from the terminal leaflet, use the term leaflet tendril (PO:0025362). See also leaf tendril (PO:0025361), leaflet tendril (PO:0025362), branch tendril (PO:0025364), stem apex tendril (PO:0025365), leaf rachis tendril (PO:0025366), and prophyll tendril (PO:0025367). Careful observation is required to correctly classify some tendrils.
Aids plant in climbing. A branch tendril will usually be subtended by a leaf or leaf scar. May be branched, may have adhesive disks at its distal end, may be woody, and may bear small leaves. See also leaf tendril (PO:0025361), leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), stem apex tendril (PO:0025365), leaf rachis tendril (PO:0025366), and prophyll tendril (PO:0025367). Careful observation is required to correctly classify some tendrils.
A shoot axis that arises from the apical part of a stem and is slender and coiling.
&#225pice en zarzillo del tallo (Spanish, exact)
Aids plant in climbing. May be branched, may have adhesive disks at its distal end, may be woody, and may bear small leaves. A stem apex tendril differs from a branch tendril in that it arises from the shoot apical meristem, rather than in an axil. However, a shoot apex tendril may arise either from the apex itself, in which case it is terminal, or from the side of an apical meristem, in which case it is a lateral structure. In the latter case, the main stem of the plant undergoes sympodial growth. A stem apex tendril is often located on the opposite side of a stem from a leaf at the same node, as in Vitaceae. See also leaf tendril (PO:0025361), leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), leaf rachis tendril (PO:0025366), and prophyll tendril (PO:0025365). Careful observation is required to correctly classify some tendrils.
A leaf rachis (PO:0020055) that is slender and coiling and lacks a lamina.
raquis en zarzillo de la hoja (Spanish, exact)
Aids plant in climbing. Differs from a leaf tendril, in that a leaf rachis tendril bear leaflets. See also leaf tendril (PO:0025361), leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), stem apex tendril (PO:0025365), and prophyll tendril (PO:0025366). Careful observation is required to correctly classify some tendrils.
A prophyll that is slender and coiling and lacks a lamina.
Aids plant in climbing. A prophyll may be difficult to distinguish from a branch tendril, because it may be found in the axil of a leaf, but it develops from a prophyll of the axillary bud, rather than a branch. Found in Curburitaceae. See also leaf tendril (PO:0025361), leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), stem apex tendril (PO:0025365), and leaf rachis tendril (PO:0025366). Careful observation is required to correctly classify some tendrils.
A plant structure development stage (PO:0009012) that has as primary participant a trichome (PO:0000282).
etapa de desarrollo del tricoma (Spanish, exact)
A trichome development stage that has as primary participant a seed trichome.
etapa de desarrollo del tricoma de la semilla (Spanish, exact)
Seed trichome development stage consists of the following sub stages: seed trichome initiation stage (PO:0025370), seed trichome elongation stage (PO:0025371), seed trichome secondary wall biosynthesis stage(PO:0025372) and seed trichome maturation stage (PO:0025373).
A seed trichome development stage which occurs during the interval between the onset of seed trichome initiation and the onset of seed trichome elongation.
etapa de iniciaci&#243n del tricoma de la semilla (Spanish, exact)
Refers to the GO Biological Process terms seed trichome initiation (GO:0090377) and seed trichome elongation (GO:0090378).
A seed trichome development stage which occurs during the interval between the onset of seed trichome elongation and the onset of seed trichome secondary wall biosynthesis.
etapa de elongaci&#243n del tricoma de la semilla (Spanish, exact)
Refers to the GO Biological Process terms: seed trichome elongation (GO:0090378) and secondary cell wall biogenesis involved in seed trichome differentiation (GO:0090379).
A seed trichome development stage which occurs during the interval between the onset of seed trichome secondary wall biosynthesis and the onset of seed trichome maturation.
etapa de bios&#237ntesis de la pared secundaria del tricoma de la semilla (Spanish, exact)
seed hair secondary wall biosynthesis stage (exact)
Refers to the GO Biological Process terms: secondary cell wall biogenesis involved in seed trichome differentiation (GO:0090379) and seed trichome maturation (GO:0090380).
seed trichome secondary wall biosynthesis stage
A seed trichome development stage which encompasses the process of seed trichome maturation.
etapa de maduraci&#n del tricoma de la semilla (Spanish, exact)
Refers to the GO Biological Process term: seed trichome maturation (GO:0090380).
A seed development stage (PO:0001170) during which a seed (PO:0009010) participates in a seed dormancy process (GO:0010162).
etapa latente de la semilla (Spanish, exact)
A seed dormancy process (GO:0010162) is a dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of most physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors. Seed dormancy includes dormancy of the embryo and the seed coat, although these may not begin or end simultaneously. Not all seeds go through a seed dormant stage. Most seeds that go through a dormant stage do so only one time.
A gametophyte development stage (PO:0028003) that occurs during the interval between meiosis and the germination of a spore.
etapa esporof&#237tica de la planta (Spanish, exact)
Includes the stage when a megaspore is present before it develops into a megagametophyte or embryo sac and the stage when a microspore is present before it develops into a microgametophyte or pollen. There may be cell division in a spore before it germinates.
A gametophyte dormant stage during which a spore participates in a dormancy process.
etapa latente esporof&#237tica de la planta (Spanish, exact)
A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
A mature plant embryo stage (PO:0001081) during the interval between when a plant embryo (PO:0009009) begins a dormancy process (GO:0022611) and one of the following: the beginning of the seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
During a plant embryo dormant stage, a plant embryo participates in a dormancy process, but not all plant embryos have a dormant stage. A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. In seed plants, a plant embryo dormant stage may be part of a seed dormant stage.
An arilloid that is an elaborate outgrowth of a seed at the micropylar end.
Generally larger than a caruncle and not hard.
A plant anatomical space that is part of a portion of plant tissue between two or more cells.
Often part of a mesophyll (PO:0006070). This term does not include spaces on the surface of a plant structure, like a stomatal pore (PO:0008032), stomium (PO:0020101), or micropyle (PO:0020025), nor larger cavities or canals that are surrounded by tissue, such as an archegonium neck canal (PO:0030066). May be filled with air or fluid.
An intercellular space that is part of a leaf mesophyll.
espacio intercelular en el mes&#243filo de la hoja (Spanish, exact)
Includes the air spaces in the spongy mesophyll (PO:0005647), the palisade mesophyll (PO:0005648) and substomatal cavity (PO:0025382).
A leaf mesophyll intercellular space that is part of a spongy mesophyll.
espacio intercelular en el mes&#243filo esponjoso de la hoja (Spanish, exact)
An intercellular space that is located directly below and contiguous with a stomatal pore.
cavidad subestom&#225tica (Spanish, exact)
A plant anatomical space that is a phyllome marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate phyllomes.
A phyllome sinus that is a marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate leaves.
A portion of plant substance (PO:0025161) that is the inner layer of a plant cuticle (PO:0000022), and is composed of a polyester matrix of hydroxy- and hydroxy epoxy fatty acid C16 and C18 chains.
Cutin is the insoluble, covalently cross-linked polymer that forms an electron dense layer over the epidermal cells (PO:0004013) of an aerial plant structure.
A portion of plant substance (PO:0025161) comprised predominantly of very long chain aliphatic lipids and is part of a plant cuticle (PO:0000022).
Also includes triterpenoids and minor secondary metabolites, such as sterols and flavonoids. May be embedded within or external to the layer of cutin of the cuticle proper. Phenotypically, wax is distinguished as the glaucous or whitish bloom on a part of a plant shoot system that corresponds to crystalloid epicuticular wax with light scattering capacity.
A portion of plant substance (PO:0025161) that is the inner layer of a plant cuticle (PO:0000022), composed primarily of cutin (PO:0025385), embedded and overlayed with cuticular wax (PO:0025386).
cut&#237cula propia de la planta (Spanish, exact)
A portion of cuticular wax (PO:0025386) that forms crystalloids or a smooth film on the exterior of a plant cuticle (PO:0000022).
Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.
A portion of cuticular wax (PO:0025386) that is an amorphous mixture of lipids embedded in the cutin (PO:0025385) of a plant cuticle proper (PO:0025387).
The intercuticular wax is located adjacent to the cell wall.
A leaf lamina vein (PO:0020138) above the first order that is connected to another vein only at one end.
May be branched or simple. May be found inside a lamina areole. Usually used with third order or higher veins. If vein order is known, an additional annotation should be place on secondary vein (PO:0020140), tertiary vein (PO:0008021), quaternary vein (PO:0008022), or higher order vein (PO:0008023).
A cardinal organ part (PO:0025001) that is part of a phyllome lamina (PO:0025396) and is completely surrounded by phyllome lamina veins (PO:0025348) and cannot be divided into any smaller parts that are completely surrounded by phyllome lamina veins.
areola de la l&#225mina (Spanish, exact)
Any order of phyllome lamina vein can form the sides of a phyllome lamina areole. Taken together, the phyllome lamina areoles form a contiguous field of polygons over the area of a phyllome lamina.
A phyllome lamina areole (PO:0025391) that is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf lamina veins (PO:0020138) and cannot be divided into any smaller parts that are completely surrounded by leaf lamina veins.
areola de la l&#225mina foliar (Spanish, exact)
Any order of leaf lamina vein can form the sides of a leaf lamina areole. Taken together, the leaf lamina areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole.
A collective organ part structure that has a parts one or more pappus elements (scales, awns, or bristles) at the apex of an inferior ovary just beneath or outside the corolla.
Found in flowers and fruits (cypsela) of the Asteraceae. May aid in dispersal by wind or animals. Considered by some to be an evolutionarily modified upper calyx portion, the lower portion having been incorporated into the floral tube casing adnate to the ovary wall; considered by others to be an outgrowth from the ovary wall.
A cardinal organ part that is a segment of a pappus.
A plant organ (PO:0009008) that is part of a flower (PO:0009046).
Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.
A plant organ lamina (PO:0025513) that is part of a phyllome (PO:0006001).
A leaf mesophyll intercellular space that is part of a palisade mesophyll.
espacio intercelular del mes&#243filo en palisada (Spanish, exact)
A substomatal cavity that is part of a phyllome.
cavidad subestom&#225tica del filoma (Spanish, exact)
A phyllome substomatal cavity that is part of a leaf mesophyll.
cavidad subestom&#225tica de la hoja (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is found on the adaxial side of a developing phyllome (PO:0006001).
meristema adaxial del filoma (Spanish, exact)
phyllome adaxial rounding meristem (narrow)
phyllome adaxial unifacial meristem (narrow)
Contributes to the thickness of a phyllome (PO:0006001). There are two types of adaxial meristems. In phyllomes with a petiole (PO:0020038) and lamina (PO:0025060), an adaxial rounding meristem occurs later in development, is separated from the apical meristem (PO:0020144), and contributes to the thickness of the petiole and midrib. In unifacial phyllomes, the an adaxial meristem occurs earlier in development, is close to but separate from the apical meristem, and contributes to the thickness and cross-sectional shape of the entire phyllome. If annotating to a leaf, use the more specific term leaf adaxial meristem (PO:0025401).
A portion of phyllome adaxial meristem (PO:0025400) tissue that is found on the adaxial side of a developing vascular leaf (PO:0009025).
leaf adaxial unifacial meristem (narrow)
Contributes to the thickness of a vascular leaf (PO:0009025). There are two types of adaxial meristems. In leaves with a petiole (PO:0020038) and lamina (PO:0025060), such as Arabidopsis thaliana, an adaxial rounding meristem occurs later in development, is separated from the apical meristem (PO:0020144), and contributes to the thickness of the petiole and midrib. In unifacial leaves, the an adaxial unifacial meristem occurs earlier in development, is close to but separate from the apical meristem, and contributes to the thickness and cross-sectional shape of the entire leaf.
A portion of meristem tissue (PO:0009013) that is found on the abaxial side of a developing phyllome (PO:0006001).
meristema abaxial del filoma (Spanish, exact)
phyllome abaxial rounding meristem (narrow)
phyllome abaxial unifacial meristem (narrow)
Contributes to the thickness of a phyllome (PO:0006001). There are two types of adaxial meristems. In phyllomes with a petiole (PO:0020038) and lamina (PO:0025060), an adaxial rounding meristem occurs later in development, is separated from the apical meristem (PO:0020144), and contributes to the thickness of the petiole and midrib. In unifacial phyllomes, the an adaxial meristem occurs earlier in development, is close to but separate from the apical meristem, and contributes to the thickness and cross-sectional shape of the entire phyllome. If annotating to a leaf, use the more specific term leaf abaxial meristem (PO:0025403).
A portion of phyllome abaxial meristem (PO:0025402) tissue that is found on the abaxial side of a developing vascular leaf (PO:0009025).
leaf abaxial unifacial meristem (narrow)
Contributes to the thickness of a vascular leaf (PO:0009025). There are two types of abaxial meristems. In leaves with a petiole (PO:0020038) and lamina (PO:0025060), such as Arabidopsis thaliana, an abaxial rounding meristem occurs later in development, is separated from the apical meristem (PO:0020144), and contributes to the thickness of the petiole and midrib. In unifacial leaves, the abaxial unifacial meristem occurs earlier in development, is close to but separate from the apical meristem, and contributes to the thickness and cross-sectional shape of the entire leaf.
A portion of meristem (PO:0009013) tissue that is part of a phyllome margin (PO:0025018) of an expanding phyllome (PO:0006001) and has as parts marginal and submarginal initials.
meristema marginal del filoma (Spanish, exact)
Phyllome marginal meristems may develop on the lateral margins of a phyllome after the transition from a phyllome primordium (PO:0025128) and may contribute to expansion of the phyllome lamina (PO:0025396). Marginal growth can occur in a phyllome primordium, but it is not considered part of a phyllome marginal meristem. Phyllome marginal initials may give rise to phyllome epidermis (PO:0025157) while phyllome submarginal initials may give rise to the mesophyll (PO:0006070). May be of limited duration.
A portion of phyllome marginal meristem (PO:0025404) tissue that is part of a leaf margin (PO:0025009) of a vascular leaf (PO:0009025) during a leaf expansion stage (PO:0001052) and has parts marginal and submarginal initials.
Leaf marginal meristems develop on the lateral margins of a vascular leaf after the transition from a vascular leaf primordium (PO:0000017) and may contribute to expansion of the leaf lamina (PO:0020039). Marginal growth can occur in a vascular leaf primordium, but it is not considered part of a leaf marginal meristem. Leaf marginal initials (add) may give rise to leaf epidermis (PO:0006016) while leaf submarginal initials (add) may give rise to the leaf mesophyll (PO:0005645). May be of limited duration.
A native plant cell (PO:0025606) that is part of a portion of phloem tissue (PO:0005417), has sieve areas in its walls, and lacks a nucleus in its mature protoplast.
Sieve elements function mainly in longitudinal conduction of organic solutes. Classified into sieve cells (PO:0025415) and sieve tube elements (PO:0000289) based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial (PO:0000295), a phloem mother cell (PO:0000400), or a cell of the procambium (PO:0025275).
A sclerenchyma cell (PO:0000077) that is elongated and tapering.
c&#233lula fibrosa vegetal (Spanish, exact)
May or may not have lignin in the secondary cell wall (GO:0009531) or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290). Compare with sclerid cells (PO:0025418), which are usually not elongated.
A portion of vascular tissue (PO:0009015) that develops from a procambium (PO:0025275).
tejido vascular primario (Spanish, exact)
Forms as part of primary growth (GO term for primary growth has been requested).
A portion of vascular tissue (PO:0009015) that develops from a vascular cambium (PO:0005598).
tejido vascular secundario (Spanish, exact)
Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system (PO:0025410) and ray system (PO:0025411).
A portion of secondary vascular tissue (PO:0025409) that has as parts cells derived from fusiform initials (PO:0000079) and oriented with their longest diameter parallel to a plant axis (PO:0025004).
Includes portions of secondary xylem (PO:0005848) and axial wood parenchyma (PO:0004533).
A portion of secondary vascular tissue (PO:0025409) that has as part ray wood parenchyma (PO:0004534) and extends radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005848) of a plant axis (PO:0025004).
May include ray tracheids, as in Pinaceae and some Cupressaceae.
A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.
May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.
A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
vena primaria de la hoja (Spanish, exact)
Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms.
A lateral meristem (PO:0020145) that is not contiguous with an apical meristem (PO:0020144) and has a parts multiple layers of meristematic cells (PO:0004010).
meristema de engrosamiento secundario (Spanish, exact)
Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042) and may also be found in the roots (PO:0009005) of some species. May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.
A sieve element (PO:0025406) in which the sieve areas are not aggregated into sieve plates (GO:0097218).
Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants such as ferns. Differ from sieve tube elements, which have sieve plates and more pronounced specialization of sieve areas.
A portion of phloem tissue (PO:0005417) that has as parts a series of sieve tube elements (PO:0000289) arranged end to end and interconnected through sieve plates.
A sieve plate is part of a sieve tube member.
A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.
A sclerenchyma cell (PO:0000077) with many pits in the secondary cell wall.
Usually not very elongated. The lumen of a sclerid cell is occluded by the secondary cell wall.
A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.
fibro-traqueida septada (Spanish, exact)
A septate fiber tracheid septum is composed of the adjacent primary cell walls of two internal cells that arise from mitosis within the septate fiber tracheid after it has formed a secondary cell wall (GO:0009531).
A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.
fibra libriforme septada (Spanish, exact)
A septate libriform fiber cell septum is composed of the adjacent primary cell walls of two internal cells that arise from mitosis within the septate libriform fiber cell after it has formed a secondary cell wall (GO:0009531).
A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.
fibra del floema septada (Spanish, exact)
A septatephloem fiber cell septum is composed of the adjacent primary cell walls of two internal cells that arise from mitosis within the septate phloem fiber cell after it has formed a secondary cell wall (GO:0009531).
A xylem fiber cell (PO:0000274) in which the inner-most layer of the secondary cell wall (GO:0009531) contains abundant cellulose and is poor in lignin.
Often found in reaction wood in dicots and in some phloem fiber cells (PO:0004519), as in Linum usitatissimum. In gelatinous fiber cells, the inner layer of the cell wall is a cellulosic gelatinous-layer or G-layer, which may be relatively porous and less compact than the outer layers of the cell wall and may absorb water and swell.
A plant structure development stage (PO:0009012) that has as primary participant a portion of plant tissue (PO:0009007).
etapa de desarrollo de tejido vegetal (Spanish, exact)
A plant tissue development stage (PO:0025423) that has as primary participant a portion of vascular tissue (PO:0009015).
etapa de desarrollo del tejido vascular (Spanish, exact)
A vascular tissue development stage (PO:0025424) that has as primary participant a portion of xylem (PO:0005352) tissue.
etapa de desarrollo del xilema (Spanish, exact)
A vascular tissue development stage (PO:0025424) that has as primary participant a portion of phloem (PO:0005417) tissue.
etapa de desarrollo del floema (Spanish, exact)
A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem.
etapa de desarrollo del xilema secundario (Spanish, exact)
During a secondary xylem development stage (also called a wood development stage), the cells of secondary xylem (PO:0005848), including tracheary elements (PO:0000290), xylem fiber cells (PO:0000274), and wood parenchyma cells (PO:0004525) undergo cellular developmental processes (GO:0048869) such as cell division (GO:0051301), cell growth (GO:0016049), cell differentiation (GO:0030154), or cell death (GO:0008219). The transition from sapwood to heartwood marks the end of the secondary xylem development stage.
A portion of meristem (PO:0009013) tissue in which the planes of cell division in each layer are anticlinal to the surface of the phyllome (PO:0006001).
meristema en placa del filoma (Spanish, exact)
The activity of a phyllome plate meristem results in increase in the surface area, but not thickness of a phyllome.
A phyllome plate meristem (PO:0025428) in the vascular leaf (PO:0009025).
meristema en placa de la hoja (Spanish, exact)
The activity of a leaf plate meristem results in increase in the surface area, but not thickness of a vascular leaf (PO:0009025).
A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
The phyllome anlagen is only detectable by gene expression, not morphology.
A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148).
This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied).
A phyllome anlagen (PO:0025430) that will give rise to a cotyledon primordium (PO:0000015) and is part of a peripheral zone (PO:000225) of an embryo shoot apical meristem (PO:0006362).
precursor de cotiled&#243n (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).
A vascular bundle (PO:0005020) that is part of a petiole vascular system (PO:0000052).
haz vascular del pec&#237olo (Spanish, exact)
A cork cambium (PO:0005599) that is part of a shoot axis (PO:0025029).
cambium suber&#237geno del &#225pice del epiblasto (Spanish, exact)
A cork cambium (PO:0005599) that is part of a root (PO:0009005).
cambium suber&#237geno de la ra&#237z (Spanish, exact)
A vascular cambium (PO:0005598) that is part of a shoot axis (PO:0025029).
cambium vascular del eje del epiblasto (Spanish, exact)
A vascular cambium (PO:0005598) that is part of a root (PO:0009005).
cambium vascular de la ra&#237z (Spanish, exact)
A cardinal organ part (PO:0025001) that is part of a plant axis (PO:0025004) and has as parts a cambium (PO:0005597) and adjacent cells.
The cambial zone generally consists of the initial cells of the cambium and their immediate derivatives, arranged in radial files. This term is used for the cambium (PO:0005597) and surrounding area, especially when the borders of the cambium are not clear.
A cambial zone that is part of a shoot axis (PO:0025029).
zona cambial del eje del epiblasto (Spanish, exact)
Includes a cambium (PO:0005597) and adjacent cells. This term is used when the borders of the cambium are not clear.
A cambial zone that is part of a root (PO:0009005).
zona cambial de la ra&#237z (Spanish, exact)
A secondary thickening meristem (PO:0025414) that is part of a stem (PO:0009047).
meristema de engrosamiento secundario del tallo (Spanish, exact)
A secondary thickening meristem (PO:0025414) that is part of a root (PO:0009005).
meristema de engrosamiento secundario de la ra&#237z (Spanish, exact)
A tracheary element (PO:0000290) that is part of a primary xylem tissue (PO:0005849).
elemento de tr&#225quea del xilema primario (Spanish, exact)
A tracheary element (PO:0000290) that is part of a portion of secondary xylem tissue (PO:0005848).
elemento de tr&#225quea del xilema secundario (Spanish, exact)
A tracheid (PO:0000301) that is part of a xylem tissue (PO:0005849).
traqueida del xilema primario (Spanish, exact)
A tracheid PO:0000301 that is part of a portion of secondary xylem tissue (PO:0005848).
traqueida del xilema secundario (Spanish, exact)
A xylem vessel member (PO:0002003) that is part of a primary xylem tissue (PO:0005849).
elemento vaso del xilema primario (Spanish, exact)
A xylem vessel member (PO:0002003) that is part of a portion of secondary xylem tissue (PO:0005848).
elemento vaso del xilema secundario (Spanish, exact)
A xylem vessel (PO:0025417) that is part of a primary xylem tissue (PO:0005849).
vaso del xilema primario (Spanish, exact)
A xylem vessel (PO:0025417) that is part of a portion of secondary xylem tissue (PO:0005848).
vaso del xilema secundario (Spanish, exact)
A sieve element (PO:0025406) that is part of a portion of primary phloem (PO:0006075).
elemento criboso del floema primario (Spanish, exact)
A sieve element (PO:0025406) that is part of a portion of secondary phloem (PO:0005043).
elemento criboso del floema secundario (Spanish, exact)
A sieve cell (PO:0025415) that is part of a portion of primary phloem (PO:0006075).
c&#233lula cribosa del floema primario (Spanish, exact)
A sieve tube element (PO:0000289) that is part of a portion of primary phloem (PO:0006075).
elemento de tubo criboso del floema primario (Spanish, exact)
primary phloem sieve tube member (exact)
primary phloem sieve-tube element (exact)
A sieve cell (PO:0025415) that is part of a portion of secondary phloem (PO:0005043).
c&#233lula cribosa del floema secundario (Spanish, exact)
A sieve tube element (PO:0000289) that is part of a portion of secondary phloem (PO:0005043).
elemento de tubo criboso del floema secundario (Spanish, exact)
secondary phloem sieve tube member (exact)
secondary phloem sieve-tube element (exact)
A companion cell (PO:0000400) that is a transfer cell (PO:0000078) with many cell wall invaginations.
c&#233lula de trasnferencia acompa&#241ante (Spanish, exact)
Plasmodesmata between a transfer companion cell and adjacent mesophyll cells may be few in number. Transfer companion cells are found in plants that use apoplastic phloem loading. Unlike sieve tube elements (PO:0000289), transfer companion cells retain their nuclei and other organelles at maturity.
A companion cell (PO:0000400) that lacks cell wall invaginations and has few or no plasmodesmata connecting it to adjacent mesophyll cells.
c&#233lula ordinaria acompa&#241ante (Spanish, exact)
Found in plants that use apoplastic phloem loading. Unlike sieve tube elements (PO:0000289), ordinary companion cells retain their nuclei and other organelles at maturity.
A companion cell (PO:0000400) that has dense cytoplasm, a small vacuole, proplastids rather than chloroplasts, and abundant and highly branched plasmodesmata linking it to adjacent mesophyll cells.
c&#233lula intermediaria acompa&#241ante (Spanish, exact)
Intermediary companion cells translocate high concentrations of raffinose-family oligosaccharides and are found in plants that use symplastic phloem loading. Unlike sieve tube elements (PO:0000289), intermediary companion cells retain their nuclei and other organelles at maturity.
A secondary xylem tracheary element (PO:0025445) that is part of a portion of early wood (PO:0004515).
Early wood tracheary elements generally have larger cell lumens than late wood tracheary elements (PO:0025462) of the same growth ring (PO:0004514).
A secondary xylem tracheary element (PO:0025445) that is part of a portion of late wood (PO:0004516).
elemento de tr&#225quea de madera temprana (Spanish, exact)
Late wood tracheary elements generally have smaller cell lumens than early wood tracheary elements (PO:0025461) of the same growth ring (PO:0004514).
A secondary xylem development stage (PO:0025427) that occurs during the interval between the first and last cell division in a portion of secondary xylem tissue (PO:0005848), during which cells are produced by divisions of cambial initials (PO:0000295) or xylem mother cells.
elemento de tr&#225quea de madera tard&#237a (Spanish, exact)
This stage includes production of xylem mother cells by cambial initials and production of tracheary elements (PO:0000290) or other xylem cells by xylem mother cells. Precedes a cell differentiation stage of secondary xylem (PO:0025469), although cell differentiation may begin before a cell division stage of secondary xylem ends.
A cell differentiation stage of secondary xylem (PO:0025469) that occurs during the interval between the end of a cell division stage of secondary xylem (PO:0025463) and the onset of a secondary cell wall formation stage of secondary xylem (PO:0025465), during which the cells undergo cell growth (GO:0016049).
etapa de expansi&#243n celular del xilema secundario (Spanish, exact)
This stage succeeds a cell division stage of secondary xylem (PO:0025463) and precedes secondary cell wall formation stage of secondary xylem (PO:0025465). At least part of this stage can be easily observed in woody species containing xylem vessels (PO:0025417).
A cell differentiation stage of secondary xylem (PO:0025469) that occurs during the interval between the onset of secondary wall biogenesis (GO:0009834) of the cells in a portion of secondary xylem (PO:0005848) and the beginning of a cell death stage of secondary xylem (PO:0025466).
estapa de formaci&#243n de la pared secundaria celular del xilema secundario (Spanish, exact)
During this stage, secondary cell walls (GO:0009531) are being formed in a portion of secondary xylem tissue, preventing further expansion of the cells. This stage succeeds a cell expansion stage of secondary xylem (PO:0025464) and precedes a cell death stage of secondary xylem.
secondary cell wall formation stage of secondary xylem
A cell differentiation stage of secondary xylem (PO:0025469) that occurs during the interval between the first cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274) and the death of the last secondary xylem parenchyma cell (PO:0004525) or septate fiber cell (PO:0004521) in a portion of secondary xylem (PO:0005848).
etapa de muerte celular del xilema secundario (Spanish, exact)
During this stage, the cells of a portion of secondary xylem are undergoing cell death (GO:0008219), sometimes called apoptosis. Death of the tracheary elements and non-septate xylem fiber cells generally precedes the death of secondary parenchyma cells and septate fiber cells. Once all cells in portion of secondary xylem are dead, it transitions from sapwood (PO:0004513) to heartwood (PO:0004512), and secondary xylem development ends.
A cell death stage of secondary xylem (PO:0025466) that occurs during the interval between the first and last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274).
etapa de muerte del elemento de tr&#225a del xilema secundario (Spanish, exact)
During this stage, the tracheary elements and non-septate xylem fiber cells of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219), but most of the secondary xylem parenchyma cells (PO:0004525) and septate xylem fiber cells (septate fiber tracheid, PO:0025419, and septate libriform fiber cell, PO:0025420) remain alive. Precedes a secondary xylem parenchyma cell death stage of secondary xylem (PO:0025468).
tracheary element death stage of secondary xylem
A cell death stage of secondary xylem (PO:0025466) that occurs during the interval between the last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274) and the last cell death in a portion of secondary xylem (PO:0005848).
etapa de muerte de las c&#233lulas parenquim&#225ticas del xilema secundario (Spanish, exact)
During this stage, the secondary xylem parenchyma cells (PO:0004525) and septate xylem fiber cells (septate fiber tracheid, PO:0025419, and septate libriform fiber cell, PO:0025420) of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219). Succeeds a tracheary element death stage of secondary xylem (PO:0025467). Once all cells in portion of secondary xylem are dead, it transitions from sapwood (PO:0004513) to heartwood (PO:0004512), and secondary xylem development ends.
secondary xylem parenchyma cell death stage of secondary xylem
A secondary xylem development stage (PO:0025427) that occurs during the interval between the end of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem.
etapa de diferenciaci&#243 celular del xilema secundario (Spanish, exact)
During a this stage, cells of secondary xylem undergo cell differentiation (GO:0030154), including cell growth (GO:0016049), cell morphogenisis (GO:0000902), or cell death (GO:0008219). Cell death is considered part of differentiation in secondary xylem, because it is an essential part of wood development. This stage succeeds the last cell division in a cell division stage of secondary xylem, even though cell differentiation may begin before all cell division finishes.
cell differentiation stage of secondary xylem
A cotyledon (PO:0020030) that is part of a plant embryo (PO:0009009).
A cotyledon (PO:0020030) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131).
Develops from an embryo cotyledon (PO:0025470).
A portion of secondary xylem (PO:0005848) found on either the upper or lower side of a shoot axis (PO:0025029) that is or was angled away from vertical, with anatomical characteristics that depend on whether it is compression wood (PO:0025473) or tension wood (PO:0025474).
Develops as a response to gravity (either tension or compression) and may function in restoring a stem (PO:0009047) or branch (PO:0025073) that is leaning to its original position. May be either compression wood, found on the lower side of a gymnosperm shoot axis, or tension wood, found on the upper side of an angiosperm shoot axis.
A portion of reaction wood (PO:0025472) found on the lower side of a shoot axis (PO:0025029) that is or was angled away from vertical and that has as parts heavily lignified tracheids (PO:0000301) with a specialized S2 layer that contains more lignin and has a larger (more horizontal) microfibril angle.
Develops as a response to gravity (compression) and may function in restoring a stem (PO:0009047) or branch (PO:0025073) that is leaning to its original position. Found in gymnosperms.
A portion of reaction wood (PO:0025472) found on the upper side of a shoot axis (PO:0025029) that is or was angled away from vertical and that has as parts gelatinous fiber cells (PO:0025422).
Develops as a response to gravity (tension) and may function in restoring a stem (PO:0009047) or branch (PO:0025073) that is leaning to its original position. Found in angiosperms. Secondary xylem tracheary elements (PO:0025445) in tension wood are often longer than the tracheary elements in non-tension wood of the same plant. The gelatinous fiber cells found in reaction wood have a cell wall inner layer (G layer) that contains abundant cellulose and is poor in lignin.
A root development stage (PO:0007520) during which a coleorhiza (PO:0020034) emerges from the seed coat (PO:0009088).
A root (PO:0009005) that develops from a tuberous root (PO:0025523) and is further radially enlarged for storage.
Functions in storage. This term should be used for tubers derived from roots (PO:0009005), as found in Cassava or sweet potato (Ipomoea batatas), not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term shoot axis tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root tuber may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch. A tuberous root tuber usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).
A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
floral structure primordia (exact, plural)
portion of floral structure primordium tissue (exact)
primordio de organo floral (Spanish, exact)
If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).
A floral structure primordium (PO:0025477) that is committed to the development of an androecium (PO:0009061).
portion of androecium primordium tissue (exact)
primordium del androecio (Spanish, exact)
Use stamen primordium (PO:0004705) for the primordium (PO:0025127) of an individual stamen (PO:0009029).
A root primordium (PO:0005029) that is committed to the development of a basal root (PO:0025002).
portion of basal root primordium tissue (exact)
primordio basal de la ra&#237z (Spanish, exact)
下胚軸由来の根の原基(可視的）、不定根原基(可視的） (Japanese, exact)
Transition from basal root primordium to basal root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
A root primordium (PO:0005029) that is committed to the development of a shoot-borne root (PO:0000042).
portion of shoot-borne root primordium tissue (exact)
primordio del eje del epiblasto de la ra&#237z (Spanish, exact)
Transition from shoot-borne root primordium to shoot-borne root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
A primordium (PO:0025127) that develops as part of a leaf primordium (PO:0000017) of a compound leaf (PO:0020043) and is committed to the development of a leaflet (PO:0020049).
portion of leaflet primordium tissue (exact)
primordio del fol&#237olo (Spanish, exact)
Leaflets of palms does not develop from leaflet primordia but by separation of segments of a leaf lamina (PO:0020039).
A phyllome anlagen (PO:0025430) that will give rise to a bract primordium (PO:0025487) and is part of a peripheral zone (PO:000225) of a reproductive shoot apical meristem (PO:0008028).
A phyllome anlagen (PO:0025430) that will give rise to a lodicule primordium (PO:0008040) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
anlagen del lod&#237culo (Spanish, exact)
A phyllome anlagen (PO:0025430) that will give rise to a petal primordium (PO:0000021) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
A phyllome anlagen (PO:0025430) that will give rise to a sepal primordium (PO:0004704) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
A phyllome anlagen (PO:0025430) that will give rise to a stamen primordium (PO:0004705) and is part of a peripheral zone (PO:000225) of a flower meristem (PO:0000229).
A phyllome primordium (PO:0025487) that is committed to the development of a flower bract (PO:0009055).
portion of bract primordium tissue (exact)
primordio de la br&#225ctea (Spanish, exact)
A bract primordium (PO:0025128) is committed to the development of a flower bract (PO:0009034).
portion of flower bract primordium tissue (exact)
primordio de la br&#225ctea floral (Spanish, exact)
A bract primordium (PO:0025128) is committed to the development of an inflorescence bract (PO:0009054).
inflorescence bract primordia (exact, plural)
primordio de la br&#225ctea de la inflorescencia (Spanish, exact)
portion of inflorescence bract primordium tissue (related)
A plant ovule (PO:0020006) that is part of a plant ovary (PO:0009072).
A plant ovule (PO:0020006) that is part of an ovuliferous scale (add).
&#243vulo de la escama ovul&#237fera (Spanish, exact)
A lateral root primordium (PO:0000016) that develops from a portion of pericycle tissue (PO:0006203) and is committed to the development of a pericyclic lateral root (PO:0025494).
primordio de ra&#237z lateral peric�clica (Spanish, exact)
A lateral root primordium (PO:0000016) that develops from a portion of plant tissue (PO:0009007) other than a pericycle (PO:0006203) and is committed to the development of a non-pericyclic lateral root (PO:0025495).
primordio de ra&#237z lateral no peric�clica (Spanish, exact)
内鞘以外の組織から発生する分枝根始原体 (Japanese, exact)
A non-pericyclic lateral root primordium may develop from cells of an endodermis (PO:0000252) in ferns and some seed plants.
A lateral root (PO:0025495) that develops from a pericyclic lateral root primordium (PO:0025492).
ra&#237z lateral peric&#237clica (Spanish, exact)
A pericyclic lateral root primordium develops from cells that are part of a pericycle (PO:0006203). This is the most common type of lateral root in seed plants.
A lateral root (PO:0025495) that develops from a non-pericyclic lateral root primordium (PO:0025493).
ra&#237z lateral no peric�clica (Spanish, exact)
A non-pericyclic lateral root primordium develops from cells that are not part of a pericycle (PO:0006203). Develops from cells in an endodermis (PO:0000252) in ferns and some seed plants.
A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types.
A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva (Spanish, exact)
This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006).
A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.
parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact)
Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049).
cardinal part of multi-tissue plant structure
An shoot epidermal pavement cell (PO:0000332) that is part of sepal epidermis (PO:0006040) and is approximately one fifth the length of a sepal (PO:0009031).
Compare to other epidermal pavement cells that are approximately one hundredth of the length of a sepal (PO:0009031). In Arabidopsis, sepal giant epidermal cells arise by DNA endoreplication (GO:0042023) and have high DNA content (up to 16C).
A sporophyte reproductive stage that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) that is not currently participating in a whole plant fruit development stage begins a fruit initiation stage (PO:0025503), and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
A whole plant fruit development stage begins with the beginning of whole plant fruit formation stage (PO:0007042) and ends with the end of a whole plant fruit ripening stage (PO:0007010). A whole plant fruit development stage can be thought of as a fruiting cycle for a whole plant that begins when the plant starts to produce fruit and ends when all of the fruit on the plant are ripe, unless the plant enters a sporophyte senescent stage or sporophyte dormant stage before all the fruit is ripe. An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage. Some plants retain their fruit after ripening and through dormancy, and thus may begin a new whole fruit development stage while fruits from the previous whole plant fruit development stage are still present.
A fruit development stage (PO:0001002) that begins with the formation of a plant zygote (PO:0000423) that is contained in the fruit (PO:0009001) being studied and ends when that fruit's fruit ripening stage (PO:0025502) begins.
A fruit formation stage may begin without fertilization or formation of a plant zygote (PO:0000423) in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage applies to an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).
A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).
Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. Fruit ripening (GO:0009835) is defined as: an aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).
A fruit formation stage (PO:0025501) that begins with the formation of a plant zygote (PO:0000423) that is contained in the fruit (PO:0009001) being studied and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand.
The fruit initiation stage may begin without fertilization or formation of a plant zygote (PO:0000423) in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand and may be very brief. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).
A fruit formation stage (PO:0025501) that begins when the plant cells (PO:0009002) in a fruit (PO:0009001) begin to divide or expand, and ends when the fruit has reached 10% of its final size.
Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).
A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.
Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).
A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.
Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).
A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.
Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).
A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.
Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).
A native plant cell (PO:0025606) that is the larger, distal cell arising from the first division of an archegonium initial cell (PO:0025510).
The archegonium central cell divides asymmetrically to form a smaller ventral canal cell (PO:0025524) and a larger archegonium egg cell (PO:0025122). It is larger than the archegonium neck canal cell (PO:0030065), which also develops from the archegonium initial cell (PO:0025510). The archegonium central cell only occurs in gymnosperms.
An initial cell (PO:0004011) that divides asymmetrically to form an archegonium central cell (PO:0025509) and a smaller archegonium neck canal cell (PO:0030035).
A cardinal organ part (PO:0025001) that is a slender, hollow extension of a petal (PO:0009032).
Often contains nectar. Use this term if the spur is part of a single petal. If the spur is part two or more fused petals, use corolla spur (PO:0025512).
A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.
Often contains nectar. Use this term if the spur is part of two or more fused petals (PO:0009032). If the spur is part of a single petal, use petal spur (PO:0025511).
A lamina (PO:0025060) that is part of a plant organ (PO:0009008).
A cardinal organ part (PO:0025001) that is a projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends one quarter or more of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
A phyllome lobe may be either rounded or angular at the tip, and may have phyllome teeth (PO:0025515) or phyllome crenae (PO:0025516) on its margin. The corresponding phyllome sinus may be rounded or angular.
A cardinal organ part (PO:0025001) that is an angular projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
See phyllome lamina crena (PO:0025516) for a small rounded projection. The corresponding phyllome sinus may be rounded or angular.
A cardinal organ part (PO:0025001) that is a rounded projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
See phyllome lamina tooth (PO:0025515) for a small angular projection. The corresponding phyllome sinus may be rounded or angular.
A phyllome lobe (PO:0025514) that is a projection on a leaf lamina margin (PO:0025009) for which the corresponding leaf sinus (PO:0025384) extends one quarter or more of the distance to the center of the long axis of the leaf lamina (PO:0020039).
lóbulo de la lámina de la hoja (Spanish, exact)
A leaf lobe may be either rounded or angular at the tip, and may have leaf teeth (PO:0025518) or leaf crenae (PO:0025519) on its margin. The corresponding leaf sinus may be rounded or angular.
A phyllome lamina tooth (PO:0025515) that is an angular projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).
diente de la lámina de la hoja (Spanish, exact)
See leaf lamina crena (PO:0025519) for a small rounded projection. The corresponding leaf sinus may be rounded or angular.
A phyllome lamina crena (PO:0025516) that is a rounded projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).
crena de la lámina de la hoja (Spanish, exact)
See leaf lamina tooth (PO:0025518) for a small angular projection. The corresponding leaf sinus may be rounded or angular.
A leaf lamina vein (PO:0020138) that is just inside the leaf lamina margin (PO:0025009) and extends from the leaf lamina base (PO:0008019) to the leaf apex (PO:0020137).
vena intramarginal de la lámina de la hoja (Spanish, exact)
The leaf lamina intramarginal vein is much thinner than the leaf midvein (PO:0020139; syn: midrib), and is of constant thickness.
A native plant cell (PO:0025606) that produces one or more gametes (PO:0025006) and participates in the gametophyte development stage (PO:0028003).
Occurs in some green alga, such as Ulva. Participates in the gametophyte development stage (PO:0028003).
A plant axis (PO:0025004) that is radially enlarged.
Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
A root (PO:0009005) that is radially enlarged relative to other lateral roots (PO:0020121) or shoot-borne roots (PO:0000042) on the same plant, but not as enlarged as a tuberous root tuber (PO:0025476).
A native plant cell (PO:0025606) that develops from the archegonium central cell (PO:0025509), and lies at the base of the archegonium neck (PO:0030039), above the archegonium egg cell (PO:0025122) in the venter (PO:0030038).
The ventral canal cell is smaller than the archegonium egg cell (PO:0025122), which also develops from the asymmetric division of the archegonium central cell (PO:0025509). It lack a plant-type cell wall (GO:0009505) (ref? ). When the archegonium (PO:0025126) is mature, the ventral canal cell (along with the archegonium neck canal cells; PO:0030065), contributes to the formation of the archegonium neck canal (PO:0030066) by distintegrating and becoming mucilaginous. The canal cells and may produce chemicals to attract the male gamete, the antheridium sperm cells (PO:0025120).
A native plant cell (PO:0025606) that gives rise to one or more plant sperm cells (PO:0000084).
In liverworts, hornworts and mosses the spermatogenous cell gives rise to a single, biflagellated, antheridium sperm cell (PO:0025120). In angiosperms please use the generative cell (PO:0020097) and in gymnosperms use the body cell (PO:0025526).
A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) that divides to produce a vegetative cell (PO:0020099) and the pollen sperm cell (PO:0025121).
A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003).
A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).
A bud development stage (PO:0025528) during which a bud (PO:0009006) participates in a bud dormancy process (GO:0097207).
A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
reproductive shoot system development stage
A bud development stage (PO:0025528) during which a bud (PO:0009006) enlarges due to growth of the shoot system (PO:0009006).
A shoot system development stage (PO:0025527) during which a shoot system (PO:0009006) emerges from the bud (PO:0009006).
A native plant cell (PO:0025606) which is vegetative and develops from the division of the microspore (PO:0020048) of vascular plants other than angiosperms.
The prothallial cell (PO:0025533) is part of the microgametophyte (PO:0025280) and is believed to be the remnant of the vegetative tissue of the male gametophyte.
A shoot axis (PO:00025029) that develops in an unusual place.
eje adventicio del epiblasto (Spanish, exact) (related)
A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome apex (PO:0025551).
punta multicelular del tricoma (Spanish, exact)
This term describes the apex region of a tip of a multicellular trichome (PO:0000282). The tip may be various shapes. A tip of a unicellular trichome is a GO cellular component term; unicellular trichome tip (GO:0090553).
A portion of plant cuticle (PO:000022) that forms a ridge, may be overlayed with epicuticular wax (PO:0025388).
cresta de la cuticula vegetal (Spanish, exact)
A trichome (PO:0000282) that is a single plant cell (PO:0009002).
non-glandular unicellular trichome (narrow)
non-secretory unicellular trichome (narrow)
This should not be confused with a trichome cell (PO:0008030), which is a plant cell (PO:0009002) that is part of a multicellular trichome (PO:0000282). For parts of the unicellular trichome (such as branch, tip, apex), please see the GO cellular component terms; unicellular trichome apex (GO:0090552), unicellular trichome tip (GO:0090553), and unicellular trichome branch (GO:0090405).
A portion of plant substance (PO:0025161) that is an aqueous solution that can be transported through the apoplast (GO:0048046) or symplast (GO:0055044).
Plant sap should not be confused with latex, resins or plant cell cytoplasm.
A plant sap (PO:0025538) that is an aqueous solution which may contain mineral elements, nutrients, and plant hormones, and is transported from the root system (PO:0025025) toward the leaves through the tracheary elements (PO:0000290) of the xylem.
A plant sap (PO:0025538) that is an aqueous solution which may contain sugars, mineral elements, and plant hormones, and is transported through the phloem sieve elements (PO:0025406).
A ground tissue cell (PO:0000076) that is part of a bundle sheath (PO:0006023).
celula de la vaina del haz vascular (Spanish, exact)
A chlorenchyma cell (PO:0000076) that is part of a bundle sheath (PO:0006023).
celula clorenquimatica de la vaina del haz vascular (Spanish, exact) (exact)
A native plant cell (PO:0025606) that is part of the tapetum (PO:0025313).
The tapetum is the inner-most layer of a sporangium wall (PO:0025306).
A tapetum cell (PO:0025543) that is part of a microsporangium tapetum (PO:0025314).
c&#233lula del tapete del microsporangio (Spanish, exact)
A microsporangium tapetum cell (PO:0025544) that is part of the anther wall tapetum (PO:0009071).
célula de la pared del tapete de la antera (Spanish, exact)
A second order inflorescence axis (PO:0006321) borne in the same axil (PO:0025224) as an existing second order inflorescence axis.
accessory second order inflorescence axis (exact)
A second order inflorescence axis (PO:0006321) borne on an elongated first order inflorescence axis (PO:0025104).
A second order inflorescence axis (PO:0006321) borne on a compacted first order inflorescence axis (PO:0025104), forming the rosette.
paraclado en roseta (Spanish, exact) (related)
A plant structure (PO:0009011) that is the apical most portion of a trichome apex (PO:0025550).
This term is the parent to the tip of a multicellular trichome (PO:0025162) or the tip of a unicellular trichome (PO:0025537), specifically, a multicellular trichome tip (PO:0025535) and a unicellular trichome tip (GO:0090553), which is a GO cellular component term.
A plant structure (PO:0009011) that is the apical most portion of a trichome (PO:0000282).
This term is the parent to the apex of a multicellular trichome (PO:0025162) or a unicellular trichome (PO:0025537), specifically, a multicellular trichome apex (PO:0025551) and an unicellular trichome apex (GO:0090552) which is a GO cellular component term.
A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162).
apex of a multicellular trichome (exact)
This term describes the apex region of a multicellular trichome (PO:0000282). The apex of a unicellular trichome is a GO cellular component: unicellular trichome apex (GO:0090552).
A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem of the shoot system progresses centrifugally with the oldest elements (protoxylem) in the center of the axis.
This pattern was common in early land plants.
A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses both centripetally and centrifugally from the center.
Mesarch protoxylem is found in ferns and cycads stems.
A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the plant axis (PO:0025004).
A portion of exarch protoxylem (PO:002554) tissue in which the maturation of primary xylem (PO:0005849) of the root system (PO:0025025) progresses centripedally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
protoxilema exarco de la raiz (Spanish, exact) (exact)
A portion of exarch protoxylem (PO:002554) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
protoxilema exarco del sistema del epiblasto (Spanish, exact)
A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses centrifugally, with the oldest elements (protoxylem) towards the center of the plant axis (PO:0025004).
Endarch protoxylem is typically found in stems of seed plants, and also in leaves in which the protoxylem is on the adaxial side.
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has only one protoxylem strand or pole, and differentiation progresses centripetally, with the oldest element (protoxylem) farthest from the center of the plant axis (PO:0025004).
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has two protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has three protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has four protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has more than five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the plant axis (PO:0025004).
A tapetum cell (PO:0025543) that is part of a megasporangium tapetum (PO:0025315).
c&#233lula del tapete de megasporangio (Spanish, exact)
A xylem sap (PO:0025539) that is located in the shoot system (PO:0009006).
savia del floema del epiblasto (Spanish, exact) (exact)
A phloem sap (PO:0025540) that is located in the shoot system (PO:0009006).
savia del floema del sistema del epiblasto (Spanish, exact)
A phloem sap (PO:0025540) that is located in the root system (PO:0025025).
savia del floema del sistema de la raiz (Spanish, exact)
A xylem sap (PO:0025539) that is located in the root system (PO:0025025).
savia del xilema del sistema de la raiz (Spanish, exact)
A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
A free petal (PO:0025569) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583). If you are describing a petal (PO:0009032) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use petal.
A leaf development stage (PO:0001050) that occurs during the interval between the onset of the vascular leaf initiation stage (PO:0001051) and the termination of the vascular leaf senescent stage (PO:0001054).
In some plants, the leaf developmental stages may occur in the same leaf simultaneously. For example, leaves maize (or other grasses) have various zones where stages are occurring along the length of the lamina.
A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure (PO:0025496).
multi-tissue plant structure development stage
A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).
The vascular leaf primordium adaxial side (PO:0004726) is the side proximal to the axis of the vegetative shoot apical meristem (PO:0020148), while abaxial side (PO:0004725) is the distal side.
vascular leaf primordium polarity determination stage
A leaf development stage (PO:0001050) that has as a primary participant a non-vascular leaf (PO:0025075).
A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
vascular leaf morphogenesis stage (exact)
A primary xylem tracheary element (PO:0025444) with predominately annular or helical secondary wall thickening that are the first formed tracheary elements (PO:0000290) at a particular location.
elemento de traqueida del protoxilema (Spanish, exact)
In a given portion of primary xylem (PO:0005849), protoxylem tracheary elements are generally smaller in size, fewer in number, un-pitted and have less secondary wall material than metaxylem tracheary elements (PO:0025576).
A primary xylem tracheary element (PO:0025444) that may have helical, scalariform, reticulate and/or pitted secondary wall thickening.
elemento de traqueida del metaxilema (Spanish, exact)
In a given portion of primary xylem (PO:0005849), metaxylem tracheary elements are generally larger in size, greater in number, are pitted and have more secondary wall material than protoxylem tracheary elements (PO:0025575).
A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063).
A collective plant organ stucture development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).
estado de desarrollo de la estructura colectiva del filoma (Spanish, exact)
collective phyllome structure development stage
A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023).
estado de desarrollo del filoma (Spanish, exact)
A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused (PATO:0000642).
The petals (PO:0009032), sepals (PO:0009031) and tepals (PO:0009033) may be fused anywhere along the phyllome margin (PO:0025018). In some cases where the calyx (PO:0009060) and corolla (PO:0009060) are fused at the base it is referred to as a perianth tube.
A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
A calyx (PO:0009060) that is composed of fused sepals (PO:0025584).
A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).
In fused perianth (PO:0025580), the fused petal (PO:0025583) may be joined to a fused sepal (PO:002569) or another fused petal.
A sepal (PO:0009031) that is part of the fused calyx (PO:0025582) or a fused perianth (PO:0025580).
A flower development stage (PO:0007615) that occurs in an individual flower (PO:000904) during the interval between the onset of a floral organ meristem development stage (PO:0007601) and the onset of a flowering stage (PO:0007616).
During this stage, the process of floral organ development (GO:0048437) occurs. Floral organ development is defined as the process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.
A native plant cell (PO:0025606) that is part of the phyllome anlagen (PO:0025430).
As a group, the phyllome founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a phyllome anlagen (PO:0025430). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.
A sepal (PO:0009031) that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
A free sepal (PO:0025587) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583). If you are describing a sepal (PO:0009031) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use sepal.
A flower development stage (PO:0007615) which begins with the transition of a portion of meristem tissue (PO:0009013) to a flower meristem (PO:0000229) and ends with the onset of the floral organ formation stage (PO:0025585).
During this stage, a process occurs involving a vegetative to reproductive phase transition of meristem (GO:0010228), defined as the process involved in transforming a meristem that produces vegetative structures, such as leaves, into a meristem that produces reproductive structures, such as a flower or an inflorescence.
A leaf tip (PO:0025142) that is the distal portion of the leaf lamina (PO:0020039).
This is the portion of the leaf lamina (PO:0020039) that is furthest away from the stem (PO:0009047).
A portion of pith (PO:0006109) that is part of a receptacle (PO:0009064).
A portion of cortex (PO:0005708) that is part of a receptacle (PO:0009064).
A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).
As a group, the vascular leaf founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a vascular leaf anlagen (PO:0025431). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria. The analagen may consist of one or more founder cells.
A shoot-borne root (PO:0000042) that arises from a shoot axis internode (PO:0005005).
A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the shoot system (PO:0009006).
The meristem L2 layer (PO:0009021) and meristem L3 layer (PO:0009021) of the are part of the shoot system ground meristem (PO:0025595).
A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the root system (PO:0025025).
An infructescence (PO:0006342) in Zea species that bears kernels (i.e. caryopsis fruit; PO:0030104) on a compact ear infructescence axis (PO:0025623) and develops from the ear inflorescence (PO:0020136).
An inflorescence (PO:0009049) that includes as part only pistillate flowers (PO:0025599).
A flower (PO:0009046) that includes as part a single carpel (PO:0009030) or a gynoecium (PO:0009062), but the androecium (PO:0009061) is absent or has aborted during development.
A flower (PO:0009046) that includes as part an androecium (PO:0009061), and the gynoecium (PO:0009062) is absent or has aborted during development.
An inflorescence (PO:0009049) that includes as part only staminate flowers (PO:0025600).
A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
A portion of plant substance (PO:0025161) that consists of a complex mixture of organic aromatic compounds such as mono-, sesqui-, and diterpenoids.
Plant resins are often produced by Gymnosperms but not restricted to those plants. In the conifers, plant resins are constitutively and inducibly produced through the secretory activity of resin cells (PO:0025604), and can be exuded through a resin canal (PO:0005665) to a site of injury or predator attack.
A plant epidermal cell (PO:0004013) that secretes plant resin (PO:0025603), and may line resin canals (PO:0005665) and/or be associated with resin blisters (or cysts).
An abscission zone (PO:0000146) that forms as a swelling or joint on a fruit pedicel (PO:0030114).
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
A shoot system (PO:0009006) that has as parts only vegetative tissues and organs.
An abscission zone (PO:0000146) that forms as a swelling or joint on a flower pedicel (PO:0030113).
A portion of plant tissue (PO:0009007) that forms a tough, protective outer layer on a shoot axis and includes as parts a shoot axis hypodermis (PO:0005057) and a shoot axis epidermis (PO:0000112).
A portion of hypodermis (PO:0005051) that is part of a stem cortex (PO:0025612).
A portion of shoot axis tegument layer (PO:0025609) that a tough, protective outer layer on a stem (PO:0009047) and includes as parts a stem hypodermis (PO:0025610) and a stem epidermis (PO:0025178).
A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047).
A petiole (PO:0020038) that is sclerified and persistent.
The petiole (PO:0020038) abcisses longitudinally and the leaf lamina (PO:0020039) withers.
A portion of plant tissue (PO:0009007) which is a small ball of cells born on a thallus (PO:0030027) and is involved in asexual reproduction.
A collective leaf structure (PO:0025022) consisting of a group of rosette leaves (PO:0000014), generally borne at the base of the plant, that are separated by very short stem internodes (PO:0020142).
A cardinal organ part (PO:0025001) which is a short, abrupt, flexible point at the apex of the lemma (PO:0009037).
A portion of carpel epidermis (PO:0025096) that covers the abaxial surface of a carpel (PO:0009030).
The abaxial surface is the one which is furthest from the plant axis.
A portion of carpel epidermis (PO:0025096) that covers the adaxial surface of a carpel (PO:0009030).
The adaxial surface is the one which is closest to the plant axis.
A cardinal organ part (PO:0025001) that is the edge of a laminar portion of a leaf sheath (PO:0020104) and the area immediately internally adjacent to it.
A primary xylem vessel (PO:0025450) which is part of the metaxylem (PO:0000372).
Metaxylem vessels are composed of metaxylem vessel members (elements; PO:0025622).
A primary xylem tracheid (PO:0025446) that is part of the metaxylem (PO:0000372).
A primary xylem vessel member (PO:0025448) that is part of the metaxylem (PO:0000372).
A first order infructescence axis (PO:0025244) in an ear infructescence (PO:0025597) that bears kernels (i.e. caryopsis fruit; PO:0030104).
A ground tissue cell (PO:0025030) that is part of a portion of endodermis (PO:0000252).
An initial cell (PO:0004011) that produces cortex (PO:0005708) and endodermis (PO:0000252).
A portion of plant tissue (PO:0009007) that develops in response an organism for the benefit of that organism.
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis.
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and the time that the whole plant ceases to exist.
In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophyte development stage but bears the chromosome complement that would normally be found in the sporophyte development stage (PO:0028002). A whole plant in the gametophyte development stage usually has half the chromosome complement of a plant in the sporophyte development stage, but not in the case of apospory. A whole plant in the gametophyte development stage may cease to exist by death at any point in its development. In seed plants, the whole plant in the gametophyte development stage may cease to exists through transformation, such as when pollen (PO:0025281) releases its pollen sperm cells (PO:0025121) or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperm. During the gametophytic phase, a plant may produce gametes (PO:0025006) by mitosis.
A shoot axis apex (PO:0000037) that is part of a branch (PO:0025073).
A collective plant organ structure (PO:0025007) which is a cluster of gametophore branches (PO:0030021) or non-vascular leaves (PO:0025075) at the top of the gametophore axis (PO:0030020), forming a tuft.
In the moss genus Sphagnum, the gametophore coma is always composed of gametophore branches, but in all other mosses, it is composed of non-vascular leaves.
A chlorenchyma cell that is part of a chloronema and has cross walls of adjacent cells that are perpendicular to the protonema axis.
c&#233lula del cloronema (Spanish, exact)
A chloronema cell contains many well-developed chloroplasts.
A chlorenchyma cell that is part of a caulonema and has cross walls of adjacent cells that are oblique to the protonema axis.
c&#233lula del caulonema (Spanish, exact)
A caulonema cell contains fewer, less well-developed chloroplasts than a chloronema cell.
A portion of chlorenchyma tissue that develops directly from a spore and grows by division of an apical cell to form filaments that are one cell wide and dichotomously branching.
The protonema is the first structure that develops in the gametophytic phase of mosses, some other bryophytes, and leptosporangiate ferns. The term protonema is also used to refer to the phase of development in which protonemal tissue is produced (see PO:0030006 protonema phase). In some species of moss, the protonema is perennial. A protonema may develop from sporophytic tissue during apospory.
A portion of protonema tissue that consists of only chloronema cells.
Generally, the development of chloronema precedes the development of caulonema. Only the caulonema, and not the chloronema, initiates gametophore buds.
A portion of protonema tissue that consists of only caulonema cells.
Generally, the development of caulonema follows the development of chloronema. Only the caulonema, and not the chloronema, initiates gametophore buds.
A gametophyte development stage during which a gametophyte undergoes filamentous growth and that succeeds spore germination and precedes a thalloid development stage (planar growth) or gametophore development stage.
The protonema phase ends with the development of gametophores in mosses, some other bryophytes, and leptosporangiate ferns and with the development of a thallus in other bryophytes, although protonema tissue may persist of continue to develop after this.
A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs.
Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later.
A sporophyte meristematic apical cell that is part of a root tip.
c&#233lula apical de la ra&#237z (Spanish, exact)
Occurs in the sporophytic phase of pteridophytes.
A meristematic apical cell that is part of a shoot system.
c&#233lula apical del epiblasto (Spanish, exact)
May occur in shoot axes or leaves of bryophytes or ferns.
A shoot meristematic apical cell that is part of a shoot apex.
c&#233lula apical del eje del epiblasto (Spanish, exact)
Divides to produces leaf initial cells (if leaves are present) and other stem or branch tissues.
A shoot meristematic apical cell that is part of a leaf apex.
c&#233lula apical de la hoja (Spanish, exact)
Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.
A leaf meristematic apical cell that is part of the leaf apex of a vascular leaf.
c&#233lula apical de la hoja vascular (Spanish, exact)
Occurs in vascular leaves of some ferns in their sporophytic phase.
A leaf meristematic apical cell (PO:0030011) that is part of a leaf apex of a non-vascular leaf.
c&#233lula apical de la hoja no vascular (Spanish, exact)
non-vascular leaf apical initial (exact)
維管束を持たない葉の分裂組織の頂端細胞 (Japanese, exact)
Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
non-vascular leaf meristematic apical cell
An apical cell that is part of a whole plant in the gametophytic phase.
c&#233lula apical gametof&#237tica (Spanish, exact)
gametophytic meristematic apical cell (exact)
A meristematic apical cell that is part of a whole plant in the sporophytic phase.
c&#233lula apical esporof&#237tica (Spanish, exact)
sporophytic meristematic apical cell (exact)
Occurs in pteridophytes and the sporophyte of bryophytes.
A shoot axis meristematic apical cell at the tip of a seta.
c&#233lula apical de la seta (Spanish, exact)
Ceases being an apical cell when the sporangium begins to develop.
A plant anatomical space that is the opening on the apical end of a spore capsule.
boca de la c&#225psula productora de esporas (Spanish, exact)
A shoot system (PO:0009006) that consists of the shoot axes (PO:0025029) and non-vascular leaves (PO:0025075) of a plant in the gametophyte development stage (PO:0028003) .
A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.
A shoot meristematic apical cell that is part of a gametophore.
c&#233lula apical del gamet&#243foro (Spanish, exact)
Occurs in the non-vascular shoot system of the gametophyte of mosses and leafy liverworts.
A shoot axis (PO:0025029) that is part of a gametophore (PO:0030018).
Found in mosses and leafy liverworts. A stem or branch of the leafy part of a bryophyte.
rama del gamet&#243foro (Spanish, exact)
A branch of the leafy part of a bryophyte shoot system.
tallo del gamet&#243foro (Spanish, exact)
A stem (the primary axis) of the leafy part of a bryophyte shoot system.
A shoot axis meristematic apical cell at the tip of a gametophore axis.
c&#233lula apical del eje del gamet&#243foro (Spanish, exact)
non-vascular shoot axis apical cell (exact)
Occurs at the tips of the stems and branches of bryophytes.
gametophore axis meristematic apical cell
A shoot axis meristematic apical cell at the tip of a shoot apex in a shoot system that has as part vascular tissue.
c&#233lula apical del eje del epiblasto vascualr (Spanish, exact)
vascular shoot axis apical initial (exact)
維管束を持つシュート軸分裂組織の頂端細胞 (Japanese, exact)
Occurs in some ferns in their sporophytic phase.
vascular shoot axis meristematic apical cell
A gametophyte apical cell that is part of a thallus.
c&#233lula apical del talo (Spanish, exact)
A vegetative bud that develops into a gametophore.
yema del gamet&#243foro (Spanish, exact)
Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
A bract (PO:0009055) that subtends an antheridium (PO:0025125).
br&#225ctea del perigonio (Spanish, exact)
When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.
A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore.
Found in bryophytes and some pteridophytes. In mosses, the foot is located below the seta. In ferns, the foot is formed from the upper hypobasal quandrant of the embryo. The sporophyte foot serves for both attachment and absorption. The outer portion of the foot is composed of absorptive transfer cells.
A bract (PO:0009055) that subtends an archegonium (PO:0025126).
When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually perichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.
A collective phyllome structure that consists of two or more of the most distal perichaetal bracts on a gametophore axis and surround a capsule.
perianto del grametofito (Spanish, exact)
The perichaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
A stalk (PO:0025066) that supports a spore capsule, the sporangium (PO:0025094).
Found in some bryophytes, especially mosses and liverworts.
A stalk (PO:0025066) that supports an antheridium head (PO:0030075).
Found in mosses and other bryophytes such as the liverwort Marchantiales.
A stalk (PO:0025066) that supports an archegonium head (PO:0030034).
A stalk (PO:0025066) that is the basal part of an antheridium (PO:0025125).
ped&#250nculo del anteridio (Spanish, exact)
The antheridium stalk raises the antheridium (PO:0025125) from the antheridium head (PO:0030075).
A stalk (PO:0025066) that the basal part of an archegonium (PO:0025126).
ped&#250nculo del arquegonio (Spanish, exact)
Raises the venter above the rest of the gametophyte.
A cardinal organ part (PO:0025001) that develops from an archegonium (PO:0025126) and is a cap or hood enclosing the sporangium (syn: spore capsule; PO:0025094).
caliptra de la c&#225psula productora de esporas (Spanish, exact)
Found in bryophytes. The spore capsule calyptra is a membranous or hairy cap or hood, composed of gametophytic tissue (venter; PO:0030038) that protects the embryonic sporophyte within the archegonium (PO:0025126). In some species, it may persist after the sporophyte develops and gets carried upward as the seta (PO:0030032) elongates. The spore capsule calyptra is usually lost before the spores are released, and its shape can be used for identification purposes.
A cardinal organ part (PO:0025001) that is the enlarged basal part of an archegonium (PO:0025126) and has an archegonium egg cell (PO:0025122) located in it.
After fertilization, the venter develops into the spore capsule calyptra (PO:0030037), which protects the sporangium (syn: spore capsule; PO:0025094) containing the developing sporophyte.
A cardinal organ part (PO:0025001) that is the elongated, apical part of an archegonium (PO:0025126).
Early in development, the archegonium neck is occluded by a single row of neck canal cells (PO:0030065). At maturity, the neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal (PO:0030066) for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).
A cardinal organ part that is the basal (distal) part of a sporangium.
Term used for bryophytes and pteridophytes. The sporangium base is the sterile part of the sporangium below the sporangium theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis.
A cardinal organ part that is the main body of a sporangium and has spores located in it.
Term used for bryophytes and pteridophytes.
A single or double circle of peristome teeth inside a sporangium mouth.
The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.
A cardinal organ part that is a single lobe of a peristome.
Generally triangular. Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
op&#233rculo de la c&#225psula productora de esporas (Spanish, exact)
Found in mosses. May remain partly attached to the rest of the capsule.
A ground tissue cell with thickened cell walls.
Found only in bryophytes in gametophore axes, setae, or leaves. Functions in support rather than conduction. May or may not retain a living protoplast at maturity.
A gametophyte meristematic apical cell that is part of a protonema.
c&#233lula meristem&#225tica apical del protonema (Spanish, exact)
A portion of plant tissue (PO:0009007) that has as parts hydroid (PO:0025032) cells and cells of no other types.
A hydrome is composed of only hydroids. Found in bryophytes, in the center of a non-vascular shoot axis (PO:0025029) such as a gametophore (PO:0030018) or seta (PO:0030032). Often surrounded by the leptome (PO:0030048). May function in water conduction and may provide support.
A portion of plant tissue (PO:0009007) that has as parts leptoid (PO:0025033) cells and cells of no other types.
A leptome is composed of only leptoids (PO:0025033). Found in bryophytes, in non-vascular shoot axes such as a gametophore axis or seta (PO:0030032) or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.
A portion of ground tissue (PO:0025059) that is the sub-epidermal layer of a sporangium wall (PO:0025306).
endotecio de la pared del esporangio (Spanish, exact)
Term used for vascular plants to describe the outermost layer of a sporangium wall that is internal to the exothecium.
A portion of ground tissue (PO:0025059) that has as parts stereid cells (PO:0030045) and no other cell types.
A stereome is composed of only stereids. Found only in bryophytes in gametophore axes or non-vascular leaves. May function in support.
A portion of plant tissue (PO:0009007) that is an axial strand in the center of a gametophore axis (PO:0030020) or seta (PO:0030032) and has as part a hydrome (PO:0030047) or a leptome (PO:0030048).
Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a protostele in vascular plants, but this ontology class should only be used for non-vascular plants. Analogous to a vein or vascular bundle in vascular plants.
A native plant cell (PO:0025606) that is part of an antheridium jacket layer (PO:0030053).
capa c&#233lular de la cubierta del anteridio (Spanish, exact)
A portion of plant tissue (PO:0009007) that is a single layer of cells on the outside of an antheridium (PO:0025125).
capa de la cubierta del anteridio (Spanish, exact)
Cells in the antheridium jacket layer surround the spermatogenous cells (PO:0025525) and do not give rise to antheridium sperm cells (PO:0025120).
A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule columella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
Present in some moss species of the family Polytrichaceae.
A gametophore axis that is a leafless extension of a gametophore stem or branch on which a sporophyte is borne.
Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
A native plant cell (PO:0025606) that divides to gives rise to a sporocyte (PO:0006204) and is part of a sporangium (PO:0025094).
c&#233lula arquesporial (Spanish, exact)
May also give rise to sterile cells such as elators (in liverworts) or tapetal cells. In most species outside seed plants, multiple archesporial cells are part of an archesporium or sporogenous tissue.
A native plant cell (PO:0025606) located at the base of a non-vascular leaf (PO:0025075) adjacent to where the leaf attaches to the stem (PO:0009047).
Found in mosses. Alar cells occur in an area at the base of a leaf that may be triangular, ovate or rectangular and is sometimes called the alar region. They are different in size, shape, color, thickness, or ornamentation from other cells in the leaf.
A native plant cell (PO:0025606) that develops from a cell in a protonema (PO:0030003) and has a thick cell wall.
原糸体細胞の細胞壁を厚くした細胞、耐性細胞(brood cell?) (Japanese, exact)
Found in mosses. A brachycyte is a drought tolerant cell that can act as a gemma (PO:0025614) and may give rise to a new plant. Cells of a protonema (PO:0030003) may develop into brachycytes under stress. May form a chain or be separated by tmema cells (PO:0030059).
A native plant cell (PO:0025606) at the base of a gemma (PO:0025614) or adjacent to a brachycyte (PO:0030058) that breaks down to allow abscission of the gemma or brachycyte.
May be a single cell adjacent to a brachycyte (PO:0030058) or part of a portion of tmema tissue.
An axillary hair that grows in a leaf axil of a non-vascular leaf.
pelo axilar del gamet&#243foro (Spanish, exact)
Found in pleurocarpous mosses. Form in the axils of leaf primordia and may disappear when the gametophore is mature.
A portion of plant tissue (PO:0009007) that has as parts tmema cells (PO:0030059).
Found in bryophytes at the base of a gemma (PO:0025614). Participates in abscission of the gemma.
An axillary hair terminal cell that is the long terminal cell of a gametophore axillary hair.
c&#233lula terminal de pelo axilar del gamet&#243foro (Spanish, exact)
A axillary hair base that is the basal part of a gametophore axillary hair, below the gametophore axillary hair terminal cell.
base del pelo axilar del gamet&#243foro (Spanish, exact)
An axillary hair basal cell that is part of a gametophore axillary hair base.
c&#233lula basal del pelo axilar del gamet&#243foro (Spanish, exact)
gametophore axillary hair base cell (exact)
A native plant cell (PO:0025606) that is one of the axial row of cells in an immature archegonium neck (PO:0030039).
c&#233lula del canal del cuello del arquegonio (Spanish, exact)
During archegonium development, the archegonium neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).
A canal (PO:0025132) in the center of an archegonium neck (PO:0030039).
canal del cuello del arquegonio (Spanish, exact)
An protonema sub-apical initial that gives rise to a branch of a protonema.
protonemal side branch initial cell (exact)
rama lateral inicial del protonema (Spanish, exact)
May give rise to a chloronema, caulonema, protonema rhizoid, tmema cell, or brachycyte.
A plant epidermal initial cell (PO:0000349) that gives rise to an epidermal rhizoid (PO:0030071).
rizoide inicial epid&#233rmico (Spanish, exact)
Part of the epidermis of a thallus or gametophore of a bryophyte or pteridophyte in the gametophytic phase or the stem of a monocot in the sporophytic phase.
A portion of plant epidermis (PO:0005679) tissue that is an outgrowth from the epidermis between the leaves of a gametophore axis (PO:0030020).
Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.
A slender, usually uniseriate multicellular trichome (PO:0025162) that grows intermixed with the gametangia.
Found in bryophytes and pteridophytes, especially in mosses.
A rhizoid (PO:0030078) that develops from an epidermal rhizoid initial cell (PO:0030068).
Found in bryophytes and pteridophytes growing from the epidermis of a gametophore or the lower surface of a thallus and in some monocots growing from the stem at the cotyledonary node. May be considered a type of trichome.
A portion of plant tissue (PO:0009007) that is a single or double strand in the center of a non-vascular leaf (PO:0025075) and has as part hydrome (PO:0030047) or leptome (PO:0030048).
Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this ontology class should only be used for non-vascular leaves.
A portion of plant epidermis (PO:0005679) that is the outermost layer of a sporangium wall (PO:0025306).
Develops from the outermost layer of an amphithecium in bryophytes.
A portion of plant tissue (PO:0009007) that is the internal part of a sporangium (PO:0025094), bounded by the sporangium wall (PO:0025306), and has as parts archesporial cells (PO:0030056).
Gives rise to sporocytes and may give rise to other sterile cells such as elators.
A disk-shaped cardinal organ part (PO:0025001) that is the apical portion of an antheridiophore (PO:0030033) and bears antheridia (PO:0025125).
An umbrella-shaped cardinal organ part that is the apical portion of an archegoniophore and bears archegonia.
A protonema side branch initial that gives rise to a protonemal rhizoid.
protonema side branch rhizoid initial (exact)
protonemal side branch rhizoid initial (exact)
rama lateral inicial del rizoide proton&#233mico (Spanish, exact)
protonemal side branch rhizoid initial cell
A plant structure (PO:0009011) that is a uniseriate filament with positive geotropism that grows from an epidermis (PO:0005679) or protonema (PO:0030003).
May be unicellular or multicellular. Serves to anchor the plant to the substrate, and may function in nutrient and water uptake. Usually lacks chlorophyll. Includes epidermal rhizoids that grow from the epidermis of bryophytes and pteridophytes in the gametophytic phase or from the stems of some monocots, protonemal rhizoids that branch from a protonema, and rhizoids that develop from a basal cell of a gametophore bud.
A rhizoid that is part of a protonema and develops from a protonemal side branch rhizoid initial.
rizoide proton&#233mico (Spanish, exact)
A gametophyte meristematic apical cell that is part of a rhizoid.
c&#233lula apical meristem&#225tica del rizoide (Spanish, exact)
A protonema meristematic apical cell that is part of a caulonema.
c&#233lula apical meristem&#225tica del caulonema (Spanish, exact)
A protonema meristematic apical cell that is part of a chloronema.
c&#233lula apical meristem&#225tica del cloronema (Spanish, exact)
A protonema sub-apical initial hat gives rise to a gametophore bud.
In Physcomitrella patens, a gametophore bud initial typically is more bulbous than a protonema side branch initial, and its plane of first cell division is oblique, rather than perpendicular, to the plane of growth.
A portion of plant tissue (PO:0009007) that is the outer layer or layers of a sporangium (PO:0025094) early in sporangium development (GO:0043582).
Term used for bryophytes. May have one or more layers. An amphithecium may give rise to an exothecium and other layers of a sporangium wall (jacket layer or layers). In true mosses, the amphithecium gives rise to the sporangium wall and the peristome. In hornworts and peat mosses, it gives rise to the sporangium wall and sporogenous tissue.
A portion of ground tissue (PO:0025059) that is the tissue internal to an amphithecium early in sporangium development.
endotecio del protoesporangio (Spanish, exact)
Term used for bryophytes. In liverworts an early sporangium endothecium produces sporogenous tissue. In Sphagnum, Andreaea, and hornworts, it produces columella and sporogenous tissue.
An initial cell that is produced by longitudinal division of a sub-apical cell of a protonema.
c&#233lula subapical inicial del protonema (Spanish, exact)
protonemal sub-apical initial cell (related)
May give rise to a branch of the protonema (including a protonema rhizoid, tmema cell or brachycyte), a gametophore bud, or may not divide further.
An initial cell (PO:0004011) that is part of a gametophore (PO:0030018) and gives rise to a non-vascular leaf (PO:0025075).
c&#233lula inicial de la hoja no vascular (Spanish, exact)
In Physcomitrella patens, non-vascular leaf initials arise from the daughter cells of a gametophore axis apical cell. Subsequent division of a non-vascular leaf initial establishes a non-vascular leaf apical cell.
A lateral root (PO:0020121) that is sclerified and pointed.
Lateral root spines cannot grow indeterminately or supply the plant with water and solutes. See JSTOR:43235457 for documentation of lateral root spines in Dioscorea prehensilis (Dioscoreaceae) and Moraea sp. (Iridaceae).
A shoot-borne root (PO:0000042) that is sclerified and pointed.
Shoot-borne root spines cannot grow indeterminately or supply the plant with water and solutes. See PO_REF:00015 for documentation of shoot-borne root spines in Acanthorhiza aculeata (Arecaceae).
A portion of root periderm (PO:0005047) formed in response to a disruption of the root epidermis (PO:0006036).
Root periderm scars are lenticel-like structures on the tuberous roots (PO:0025523), primary roots (PO:0020127), and/or tuberous root tubers (PO:0025476) of plants such as sweet potato, cassava, parsnips, and carrots. Disruption of the epidermis by the emergence of a lateral root initiates a wound response which results in the production of a root periderm scar. Gas exchange does not occur through a root periderm scar.
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that usually dehisce.
Capsule fruits (PO:0030091) are divided into subcategories depending upon the location of sutures in the pericarp (PO:0009084) that the seeds (PO:0009010) are released through.
A capsule fruit (PO:0030091) which at maturity dehisces through fruit locules (PO:0025270).
When annotating to a capsule fruit (PO:0030091) which dehisces through both the fruit septa (PO:0025268) and fruit locules (PO:0025270), annotate to coccarium capsule fruit (PO:0030094). When annotating to a capsule fruit which only dehisces through the fruit septa, annotate to septicidal capsule fruit (PO:0030093). Examples: cotton (Gossypium raimondii) and rose mallow (Hibiscus syriacus).
A capsule fruit (PO:0030091) which dehisces through a fruit septa (PO:0025268).
When annotating to a capsule fruit (PO:0030091) which dehisces through both the fruit septa (PO:0025268) and fruit locules (PO:0025270), annotate to coccarium capsule fruit (PO:0030094). When annotating to a capsule fruit which only dehisces through the fruit locules, annotate to loculicidal capsule fruit (PO:0030092). Examples: dutchman's pipe (Aristolochia elegans) and black cottonwood (Populus trichocarpa).
A capsule fruit (PO:0030091) which at maturity dehisces through both the fruit septa (PO:0025268) and the fruit locules (PO:0025270).
lokulizide-septifrage kapsule (exact, German)
When annotating to a capsule fruit (PO:0030091) which only dehisces through the fruit septa (PO:0025268), annotate to septicidal capsule fruit (PO:0030093). When annotating to a capsule fruit which only dehisces through the fruit locules (PO:0025270), annotate to loculicidal capsule fruit (PO:0030092). Examples: physic nut (Jatropha curcas) and Manihot brachyloba.
A capsule fruit (PO:0030091) which at maturity dehisces through pores on a pericarp (PO:0009084).
A capsule fruit (PO:0030091) which at maturity dehisces through the release of a fruit operculum (PO:0025298).
A circumscissile capsule fruit (PO:0030096) which at maturity contains one seed (PO:0009010) that is not attached to a pericarp (PO:0009084).
Example: common amaranth (Amaranthus retroflexus).
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that separate into mericarps (PO:0020075).
Each individual carpellate unit of a schizocarp fruit (PO:0030098) is a mericarp (PO:0020075). Example: maple (Acer spp.).
A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that are elongated into a wing-like structure.
The pericarp (PO:0009084) can be expanded laterally or radially. The wing-shaped fruits of maples (Acer spp.) are often mistakenly identified as samara fruits (PO:0030099), but are instead schizocarp fruits (PO:0030098) with samaroid mericarps (PO:0020075). Examples: green ash (Fraxinus pennsylvanicum) and tree-of-heaven (Ailanthus altissima).
A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that dehisce along two fruit valves (PO:0000033).
Legume fruit (PO:0030100) is characteristic of the plant family Fabaceae. Examples: pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), peanut (Arachis hypogaea), soybean (Glycine max), and lentil (Lens culinaris subsp. culinaris).
A legume fruit (PO:0030100) which at maturity separates into indehiscent, one-seeded segments.
The pericarp (PO:0009084) of some legume fruit (PO:0030100), such as peanuts, is constricted between each seed, but these constrictions are due to a lack of support of the pericarp (PO:0009084) in the space between the seeds (PO:0009010). Contrastingly, the constrictions in the pericarp of loment fruits (PO:0030101) are sclerified and contain regions where cell death leads to disarticulation of the fruit (PO:0009001). Examples: some members of Fabaceae, including Mimosa and Desmodium spp.
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that are not fused to a seed coat (PO:0009088).
The common names of some species do not accurately reflect their fruit type. For example, the fruit (PO:0009001) of the peanut plant is a legume fruit (PO:0030100) rather than a nut fruit (PO:0030102). Example: pecan (Carya illinoinensis), walnut (Juglans regia), pistachio (Pistacia vera), lotus (Nelumbo nucifera), and acorn (Quercus spp.).
A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and a stony endocarp (PO:0009086).
May develop from an inferior or superior carpel (PO:0009030) and may contain one or more seeds (PO:0009010). Examples: Amborella trichopoda (basal angiosperm), coffee (Coffea canephora), Cornaceae (Davidia spp.), cashew (Anacardium occidentale), coconut (Cocos nucifera), and almond, peach and plum (Prunus spp.).
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that are fused to a seed coat (PO:0009088).
Caryopsis fruit (PO:0030104) is characteristic of the Poaceae (the grass family). Caryopsis fruits develop from a pseudomonomerous gyneocium (PO:0009062), and contain only a single seed due to the abortion of two of the three carpels (PO:0009030). The pericarp of caryopsis fruits of some bamboo species is somewhat fleshy at maturity and is fused to the seed coat; these fruits are referred to in the literature as bacoid caryopses. Examples: barley (Hordeum vulgare), rice (Oryza spp.), wheat (Triticum spp.), corn (Zea mays), sorghum (Sorghum bicolor), oat (Avena spp.), zebra grass (Miscanthus spp.), Tausch’s goatgrass (Aegilops tauschii), stiff brome (Brachypodium distachyon), cutgrass (Leersia perrieri), and foxtail millet (Setaria italica).
A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that dehisce along a single fruit valve (PO:0000033).
Examples: milkweed (Asclepias syriaca) and carolina larkspur (Delphinium carolinianum).
A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086), that dehisce along two fruit valves (PO:0000033) and separate from a persistent fruit replum (PO:0025267).
In contrast to legume fruit (PO:0030100), silique fruit develop from a syncarpous (multicarpellate) gynoecium (PO:0009062) separated by a false septum (replum, PO:0025267), which persists through fruit maturity. Examples: members of Brassicaceae, lyrate rockcress (Arabidopsis lyrata), mouse-ear cress (Arabidopsis thaliana), wild cabbage (Brassica oleracea), field mustard (Brassica rapa), and pink shepherd's purse (Capsella rubella).
A fruit (PO:0009001) which develops from a carpel (PO:0009030) or gyneocium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), a dry mesocarp (PO:0009087), and a dry endocarp (PO:0009086) that are connected to a seed coat (PO:0009088) by a funicle (PO:0020006).
Plant structures commonly referred to as ‘accessory’ (such as strawberry) or multiple fruits (such as figs..) which are comprised of accrescent receptacle (PO:0009064) or infructescence (PO:0006342) tissue, contain as parts achene fruits (PO:0030107). For example, when annotating for a gene involved in strawberry development, any gene of interest that is involved in the development of the receptacle tissue would be mapped to receptacle (PO:0009064); genes involved in sepal (PO:0009031) persistence or accrescence would map to sepal (PO:0009031), and those involved in fruit characteristics would be mapped to achene (PO:0030107). Examples: sunflower (Helianthus annuus), strawberry (Fragaria spp.), fig (Ficus sp.), and marijuana (Cannabis sativa).
A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085).
Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera).
A berry fruit (PO:0030108) which develops from a superior gynoecium (PO:0009062) and at maturity comprises a thickened exocarp (PO:0009085), thickened mesocarp (PO:0009087), and endocarp (PO:0009086), and has as parts juice sacs (PO:0006013) on a carpel adaxial epidermis (PO:0025618).
A hesperidium fruit (PO:0030109) develops from a superior gynoecium (PO:0009062), and therefore is not surrounded by receptacle (PO:0009064) tissue. Examples: orange, grapefruit, lemon, and lime (Citrus spp.).
A berry fruit (PO:0030108) which develops from an inferior gynoecium (PO:0009062) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and hardened endocarp (PO:0009086) and has as a part a fleshy hypanthium (PO:0009065) which is indistinct from the exocarp (PO:0009085).
A pome fruit (PO:0030110) is a specialized type of berry fruit (PO:0030108) which is encapsuled in persistent, accrescent receptacle (PO:0009064) and/or hypanthium (PO:0009065) tissue. Examples: Apple, crab apple, and pear (Malus spp. and Pyrus spp.)
A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085).
A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptical tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084). Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus) and banana (Musa acuminata).
A shoot axis (PO:0025029) that bears only a flower (PO:0009046) or a fruit (PO:0009001).
A pedicel has a single internode, determinate growth, and is the ultimate shoot axis (PO:0025029) in a plant. When annotating to this term, use the most specific subclass of pedicel: flower pedicel (PO:0030113), inflorescence flower pedicel (PO:0009052), fruit pedicel (PO:0030114), or infructescence fruit pedicel (PO:0004536).
A pedicel (PO:0030112) that bears a flower (PO:0009046).
A pedicel (PO:0030112) that bears a fruit (PO:0009001).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of pedicellate flowers (PO:0009046) on an indeterminate, first order inflorescence axis (PO:0025104).
Examples include mouse-ear cress (Arabidopsis thaliana, Brassicaceae), wild black cherry (Prunus serotina, Rosaceae), and pokeweeds (Phytolacca spp., Phytolaccaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of an indeterminate, first order inflorescence axis (PO:0025104) and pedicellate flowers (PO:0009046) on indeterminate higher order inflorescence axes (PO:0009081).
Examples include many species Brassicaceae, such as pepperweeds (Lepidium spp.), and Fabaceae, such as melilot (Melilotus officinialis) and hop trefoil (Trifolium campestre) species, as well as bananas (Musa spp.; Musaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of sessile flowers (PO:0009046) on an indeterminate, first order inflorescence axis (PO:0025104).
The basal-most flowers of some spike inflorescences have short inflorescence flower pedicels (PO:0009052), such as in ladies'-tresses orchids (Spiranthes; Orchidaceae). Examples include black pepper (Piper nigrum; Piperaceae).
An inflorescence (PO:0009049), with a monopodial growth habit, which at anthesis is composed of an indeterminate first order inflorescence axis (PO:0025104) and sessile (PATO:0001436) flowers (PO:0009046), or spikelets (PO:0009051), on indeterminate higher order inflorescence axes (PO:0009081).
Examples include some amaranth species (Amaranthus spp., Amaranthaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of indeterminate, first order inflorescence axes (PO:0025104) and sessile, unisexual flowers (PO:0009046) that are each subtended by conspicuous inflorescence bracts (PO:0009054).
Examples include poplars (including Populus trichocarpa, Salicaceae) and birches (Betula spp., Betulaceae). Catkin inflorescences are often pendulate.
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of sessile flowers (PO:0009046) on a radially-enlarged, indeterminate, first order inflorescence axis (PO:0025104), and a basal, enveloping inflorescence bract (PO:0009054).
Examples include aroids (Araceae), palms (Arecaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of a radially-enlarged, determinate, first order inflorescence axis (PO:0025104) with sessile flowers (PO:0009046).
Many capitulum inflorescences have basal involucral bracts (PO:0009045) and are often discoid or globose in shape. Examples include sunflowers (Helianthus spp.; Asteraceae) and teasels (Dipsacus spp.; Dipsacaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of a radially-enlarged inflorescence axis (PO:0020122), and sessile flowers (PO:0009046) on determinate higher order inflorescence axes (PO:0009081) with basal involucral bracts (PO:0009045).
heterothetic compound capitulum (narrow)
Examples include many species of daisy family (Asteraceae). The second order inflorescences (PO:0025240) of compound capitulum inflorescences are often called glomerules.
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of pedicellate flowers (PO:0009046) or spikelets (PO:0009051) on determinate inflorescence axes (PO:0020122).,
Examples include the majority of species in the grass family Poaceae including oats (Avena spp.), brome (Brachypodium spp.), barley (Hordeum vulgare), cutgrass (Leersia perrieri), rice (Oryza spp.), foxgrass (Setaria spp.), wheat (Triticum aestivum), wild rice (Zizania palustris), and the staminate inflorescence of cultivated corn (Zea mays), as well as grapes (Vitis spp.; Vitaceae), and Polemonium caeruleum (Polemoniaceae). Panicle inflorescences are most often conical in shape.
An inflorescence (PO:0009049) with both monopodial and sympodial growth habits, which at flowering stage (PO:0007616), is composed of a determinate, first order inflorescence axis (PO:0025104), and determinate higher order inflorescence axes (PO:0020122) with pedicellate flowers (PO:0009046) that collectively form a convex plane of flowers.
Examples include highbush blueberry (Vaccinium corymbosum; Ericaceae).
An inflorescence (PO:0009049) with both monopodial and sympodial growth habits, which at flowering stage (PO:0007616), is composed of a determinate, first order inflorescence axis (PO:0025104) and determinate, higher order inflorescence axes (PO:0020122) with pedicellate flowers (PO:0009046) that collectively form a concave plane of flowers.
Examples include species of Filipendula (Rosaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of a determinate, first order inflorescence axis (PO:0025104) and pedicellate flowers (PO:0009046) on paired, determinate higher order inflorescence axes (PO:0009081).
Cyme inflorescence is used here to treat inflorescences that are commonly referred to as dichasial, pleiochasial, or polychasial cymes; each of which are named according to the number of higher order inflorescence axes at a single axis. Cyme is not used here to treat monochasial cymose inflorescences, which contain at least one repeating sympodial unit, such as cincinnus inflorescence (PO:0030132), compound cincinnus inflorescence (PO:0030133), bostryx (PO:0030134), rhipidium inflorescence (PO:0030131), drepanium inflorescence (PO:0030135), and compound drepanium inflorescence (PO:0030136). Examples include many species of the Figwort family (Scrophulariaceae, including green figwort Scrophularia umbrosa) and the Verbena family (Verbenaceae).
An inflorescence (PO:0009049) which at flowering stage (PO:0007616), is composed of an indeterminate, first order inflorescence axis (PO:0025104) and dichasial second order inflorescences (PO:0025240) with pedicellate flowers (PO:0009046), and determinate higher order inflorescence axes (PO:0009081).
The higher order inflorescence axes (PO:0009081) of an indeterminate thyrse inflorescence may have either a monopodial or sympodial growth habit depending on whether single or paired inflorescence axillary meristems (PO:0009105) develop at each axis. Examples include beardtongues (Penstemon spp.; Plantaginaceae).
An inflorescence (PO:0009049) which at flowering stage (PO:0007616) is composed of a determinate, first order inflorescence axis (PO:0025104) and dichasial second order inflorescences with pedicellate flowers (PO:0009046) and determinate, higher order inflorescence axes (PO:0009081).
The higher order inflorescence axes (PO:0009081) of an determinate thyrse inflorescence may have either a monopodial or sympodial growth habit depending on whether single or paired inflorescence axillary meristems (PO:0009105) develop at each axis. Examples include lilacs (Syringia spp.; Oleaceae), buckeyes (Aesculus spp.; Hippocastanaceae) and hydrangea (Hydrangea paniculata; Hydrangeaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of pedicellate flowers (PO:0009046) on a first order inflorescence axis (PO:0025104) with compressed inflorescence axis internodes (PO:0006326).
The flowers (PO:0009046) of an umbel inflorescence appear as clusters originating from a single point, due to compression of the inflorescence axis internodes (PO:0006326) of the first order inflorescence axis (PO:0025104). Umbel inflorescences are characteristic of the the Ivy family (Apiaceae or Umbelliferae), including english ivy (Hedera helix), ginseng (Panax ginseng), and the onion family (Alliaceae).
An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616), is composed of a first order inflorescence axis (PO:0025104) with compressed inflorescence axis internodes (PO:0006326), and pedicellate flowers (PO:0009046) on higher order inflorescence axes, with compressed inflorescence axis internodes (PO:0006326).
The flowers (PO:0009046) of a compound umbel inflorescence appear as clusters originating from a single point, due to compression of inflorescence axis internodes (PO:0006326) of the higher order inflorescence axes (PO:0009081). Examples include species of the Ivy family (Apiaceae or Umbelliferae), including dill (Anethum graveolens), fennel (Foeniculum vulgare, Apiaceae) and poison hemlock (Conium maculatum, Apiaceae).
An inflorescence (PO:0009049) with a sympodial growth habit, which at flowering stage (PO:0007616), is composed of determinate inflorescence axes (PO:0020122) that bear pedicellate flowers (PO:0009046) in a single plane, with the latest-developing flowers on the highest order inflorescence axis, found at the center of the inflorescence.
Examples include species of the Iris family (Iridaceae).
An inflorescence (PO:0009049) with a sympodial growth habit, which at flowering stage (PO:0007616), is composed of determinate inflorescence axes (PO:0020122) with pedicellate flowers (PO:0009046), with the latest-developing flowers on the highest order inflorescence axis.
Examples include species of the Dayflower family (Commelinaceae).
An inflorescence (PO:0009049) with sympodial and monopodial growth habits, which at flowering stage (PO:0007616), is composed of determinate inflorescence axes (PO:0020122) with pedicellate flowers (PO:0009046), with the latest-developing flowers on the highest order inflorescence axes of the second order inflorescences (PO:0025240).
Examples include some species of the Forget-me-not family (Boraginaceae).
An inflorescence (PO:0009049) with a sympodial growth habit, which at flowering stage (PO:0007616), is composed of pedicellate flowers (PO:0009046) on determinate inflorescence axes (PO:0020122), each of which develop at a branch angle of approximately 90 degrees from each higher inflorescence axis (PO:0009081).
An inflorescence (PO:0009049) with a sympodial growth habit, which at flowering stage (PO:0007616), is composed of pedicellate flowers (PO:0009046) on determinate inflorescence axes (PO:0020122), each of which develops at progressively more acute angles from each higher inflorescence axis (PO:0009081).
Examples include tomato (Lycopersicum esculentum; Solanaceae).
An inflorescence (PO:0009049) with both sympodial and monopodial growth habits, which at flowering stage (PO:0007616) is composed of pedicellate flowers (PO:0009046) on determinate inflorescence axes (PO:0020122), each of which develops at progressively more acute angles from each higher inflorescence axis (PO:0009081).
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
hematopoietic progenitor cell antigen CD34
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage.
An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
cell surface glycoprotein MAC-1 subunit alpha
A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
T-cell surface antigen T3/Leu-4 epsilon chain
A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain.
A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration.
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
T-lymphocyte differentiation antigen T8/Leu-2
T-cell surface glycoprotein CD8 alpha chain
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
membrane-spanning 4-domains subfamily A member 1
A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues.
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
myeloid cell-specific leucine-rich glycoprotein
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain.
vascular endothelial growth factor receptor
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
vascular endothelial growth factor receptor 2
A protein that is the translation product of any of the LY6 genes (LY6A-LY6I).
An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Ly76 gene in mouse.
Category=organism-gene. Requested by=CL.
A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof.
An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
class A basic helix-loop-helix protein 17
T-cell acute lymphocytic leukemia protein 1
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif.
Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575].
A protein that is encoded in the genome of Mus musculus.
A protein that is encoded in the genome of Homo sapiens.
A protein that is encoded in the genome of some Eukaryota.
A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide.
A material entity that minimally consists of a protein.
Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).
An insulin gene translation product that is encoded in the genome of human.
insulin gene translation product (human)
A CD4 molecule that is encoded in the genome of human.
A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse.
T-cell surface glycoprotein Lyt-2 (mouse)
T-cell surface glycoprotein CD8 alpha chain (mouse)
A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human.
T-lymphocyte differentiation antigen T8/Leu-2 (human)
T-cell surface glycoprotein CD8 alpha chain (human)
A transferrin receptor protein 1 that is encoded in the genome of human.
An integrin alpha-M that is encoded in the genome of mouse.
CD11 antigen-like family member B (mouse)
cell surface glycoprotein MAC-1 subunit alpha (mouse)
A T-cell surface glycoprotein CD5 that is encoded in the genome of human.
A CD4 molecule that is encoded in the genome of mouse.
T-cell differentiation antigen L3T4 (mouse)
A CD2 molecule that is encoded in the genome of human.
T-cell surface antigen T11/Leu-5 (human)
A CD3 epsilon that is encoded in the genome of human.
T-cell surface antigen T3/Leu-4 epsilon chain (human)
T-cell surface glycoprotein CD3 epsilon chain (human)
A CD14 molecule that is encoded in the genome of human.
myeloid cell-specific leucine-rich glycoprotein (human)
monocyte differentiation antigen CD14 (human)
A CD2 molecule that is encoded in the genome of mouse.
T-cell surface antigen T11/Leu-5 (mouse)
A CD14 molecule that is encoded in the genome of mouse.
myeloid cell-specific leucine-rich glycoprotein (mouse)
monocyte differentiation antigen CD14 (mouse)
An integrin alpha-M that is encoded in the genome of human.
CD11 antigen-like family member B (human)
cell surface glycoprotein MAC-1 subunit alpha (human)
A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human.
leukocyte surface antigen Leu-16 (human)
membrane-spanning 4-domains subfamily A member 1 (human)
A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse.
A neural cell adhesion molecule 1 that is encoded in the genome of human.
A neural cell adhesion molecule 1 that is encoded in the genome of mouse.
A CD19 molecule that is encoded in the genome of human.
An interleukin-7 receptor subunit alpha that is encoded in the genome of human.
interleukin-7 receptor subunit alpha (human)
An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse.
interleukin-7 receptor subunit alpha (mouse)
A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human.
T-cell leukemia/lymphoma protein 5 (human)
class A basic helix-loop-helix protein 17 (human)
T-cell acute lymphocytic leukemia protein 1 (human)
A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse.
B-cell differentiation antigen Ly-44 (mouse)
membrane-spanning 4-domains subfamily A member 1 (mouse)
A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse.
T-cell acute lymphocytic leukemia protein 1 homolog (mouse)
A CD3 epsilon that is encoded in the genome of mouse.
T-cell surface antigen T3/Leu-4 epsilon chain (mouse)
T-cell surface glycoprotein CD3 epsilon chain (mouse)
A CD19 molecule that is encoded in the genome of mouse.
A CD34 molecule that is encoded in the genome of human.
hematopoietic progenitor cell antigen CD34 (human)
A cadherin-5 that is encoded in the genome of human.
A lymphocyte antigen 6G that is encoded in the genome of mouse.
A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse.
protein-tyrosine kinase receptor flk-1 (mouse)
vascular endothelial growth factor receptor 2 (mouse)
A vascular endothelial growth factor receptor 2 that is encoded in the genome of human.
protein-tyrosine kinase receptor flk-1 (human)
vascular endothelial growth factor receptor 2 (human)
A fibroblast growth factor 8 that is encoded in the genome of mouse.
A fibroblast growth factor 8 that is encoded in the genome of human.
A cadherin-5 that is encoded in the genome of mouse.
A sonic hedgehog protein that is encoded in the genome of human.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human)
A sonic hedgehog protein that is encoded in the genome of mouse.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse)
A transferrin receptor protein 1 that is encoded in the genome of mouse.
A CD34 molecule that is encoded in the genome of mouse.
hematopoietic progenitor cell antigen CD34 (mouse)
Any entity that is ordered in discrete units along a linear axis.
Any individual unit of a collection of like units arranged in a linear order
An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
Any entity that can be divided into parts such that each part is an atomical unit of a sequence
Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
The clusters of hormone-producing cells that are scattered throughout the pancreas.
Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]
A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)
PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
pars sympathica divisionis autonomici systematis nervosi
sympathetic part of autonomic division of nervous system
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
create a separate class for distributed pancreas, eg cyclostomes?
The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]
The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
A light sensing organ composed of ommatidia.
The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
camera-type eye plus associated structures
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
An organ that is capable of transducing sensory stimulus to the nervous system.
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
One of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
A lamina propria that is part of a respiratory airway.
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Uberon includes clade-specific subclasses, e.g. nematod larva
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
proximo-distal subdivision of respiratory tract
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
mixed ectoderm/mesoderm/endoderm-derived structure
A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159
A mass of cells that develop into the body of the embryo and some extraembryonic tissues.
A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]
embryoblastus; massa cellularis interna; pluriblastus senior
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144
The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta.
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta
Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast]
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
Stage succeeding embryo, including mature structure.
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
A lung lobe is one of the rounded projections that compose the lung[GO].
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
Structure derived from foregut that becomes a lung[GO].
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
we limit this structure by definition to chordate and vertebrate nervous systems
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
requires alignment with EHDAA2 and complete developmental relationships
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
hindgut endoderm and proctodeal ectoderm.
most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572
Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
A section dividing a colon along a proximal-distal axis.
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex.
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
Pleural effusion is a bodily fluid that is produced in exess and accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Excessive amounts of such fluid can impair breathing by limiting the expansion of the lungs during inhalation.
A bodily fluid secreted from the body via the mouth or nose.
Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
The bone forming the forehead and roof of the eye orbit.
fused in humans, paired in other animals
In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).
vertebral foramen of cervical vertebra 1
The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital.
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath.
TODO - add layer relations. 'tendon sheath' GAT in FMA.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
A mucosa that is part of a cecum [Automatically generated definition].
intestinum crassum caecum mucosa of organ
intestinum crassum caecum mucous membrane
mucosa of organ of intestinum crassum caecum
mucous membrane of intestinum crassum caecum
organ mucosa of intestinum crassum caecum
Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
A mucosa that is part of a duodenum [Automatically generated definition].
An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
Bone marrow in which the fat cells predominate in the meshes of the reticular network.
A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
Note that some sources treat 'intestinal gland' as synonymous with crypts
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex].
Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
A mucosa that is part of a pharynx [Automatically generated definition].
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated).
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
Medial ramus (sensory) of the trigeminal nerve.[AAO]
relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
maxillary division of fifth cranial nerve
maxillary division of trigeminal nerve (Vb; V2)
A mucosa that is part of a respiratory airway.
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
The core of the crystalline lens, surrounded by the cortex.
An epithelium that is part of a colon [Automatically generated definition].
Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
An anatomical wall that is part of an artery [Automatically generated definition].
A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
this relationship may be too strong and may be weakened in future
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Multi-tissue structure that is part of a compound organ.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
The organs and associated structures associated with bearing offspring in a female animal.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Anatomical group whose component anatomical structures lie in close proximity to each other.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA].
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
A semifluid mass of partly digested food expelled by the stomach into the duodenum.
Chyle is a bodily fluid consisting of a milky fluid consisting of lymph and emulsified fats; formed in the small intestine during digestion of ingested fats.
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]
this term should be ceded to the arthropod anatomy ontology
The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina.
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
This class excludes compound eye corneal lenses.
The lens is avascular and nourished by diffusion from the aqueous and vitreous humors.
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The gonad of a female organism which contains germ cells.
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406
Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
WBbt coelomocyte currently classified as circulating cell
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A portion of tissue which is a fasiculated group of axons.[TAO]
A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Consider generalizing to deuterostome pharynx
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
in FMA this represents an embryonic region.
The caudalmost subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
the caudal portion of the primitive digestive tube of the embryo
in FMA this class has no children. In MA it has a single child hindgut epithelium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The terminal portion of the intestinal tube, terminating with the anus.
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)
A zone of skin that is part of a back [Automatically generated definition].
EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
superficial branch of transverse cervical artery
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455
A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice.
A potential space between the visceral and parietal layers of the pericardium.
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
Endocardium that is part of the cardiac ventricle.
An epicardial layer that lines a cardiac ventricle.
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
A zone of skin that is part of a head [Automatically generated definition].
A zone of skin that is part of a trunk [Automatically generated definition].
Transudate contained in the pleural cavity.
Excretion that is the output of a kidney.
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
The first vertebral bone in the vertebral column.
First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]
Vertebra that is posteriorly adjacent to the neurocranium.[TAO]
The second vertebral bone in the vertebral column.
Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).
Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]
we deliberately merge the MA classes as we believe them equivalent
Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae
An anatomical wall that is part of a esophagus [Automatically generated definition].
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]
The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus
originate from the cervical somites, likely C3-C5[PMID:23586979]
ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278
Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
Portion of the liver which develops on the fish's left side.[TAO]
Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton
Anatomical cluster that consists of all the vertebra in the body.[VSAO]
The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]
Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53
A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch.
Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
Vein that carries blood away from the liver[ZFA].
todo - add developmental relationships for other taxa
A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
gonad of female reproductive system vein
gonada of female reproductive system vein
vein of female reproductive system gonad
vein of female reproductive system gonada
vein of gonad of female reproductive system
vein of gonada of female reproductive system
The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct.
Duct that connects the gall bladder and the common bile duct.[TAO]
The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong]
A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
Some references do not consider the caecum to be part of the colon.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
we include this as zone of stomach even though it is not distinguished by gland type
The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum.
We follow Kardong in defining stomach regions by glands
The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between.
An anatomical wall that is part of a small intestine [Automatically generated definition].
An anatomical wall that is part of a large intestine [Automatically generated definition].
The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP].
The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]
The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct.
Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]
The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP].
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part
The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct.
The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct.
The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space.
Anatomical cavity bounded by visceral and parietal peritoneum.
The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted].
In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].
Artery that supplies blood to the liver.[TAO]
The mucosal layer that lines the stomach.
The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].
The fibrous connective tissue layer beneath the stomach mucosa.
The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum.
anatomical wall of stomach serous membrane
anatomical wall of ventriculus serous membrane
serosa of anatomical wall of ventriculus
serous membrane of anatomical wall of stomach
serous membrane of anatomical wall of ventriculus
serous membrane of stomach anatomical wall
serous membrane of ventriculus anatomical wall
ventriculus anatomical wall serous membrane
A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].
(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]
A mucosa that is part of a small intestine [Automatically generated definition].
Submucosal tissue in the small intestines.
A serous membrane that is part of a small intestine [Automatically generated definition].
duodenum, 1st part serosa, 2nd - 4th adventitia
A mucosa that is part of a large intestine [Automatically generated definition].
A submucosa that is part of a large intestine [Automatically generated definition].
A serous membrane that is part of a large intestine [Automatically generated definition].
A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP].
currently defined as equivalent to any submucosal gland in the duodenum.
Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds
The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold.
in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]
the BTO class refers to a generic villous
A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted].
Lamina propria that is part_of the small intestine.
lamina propria mucosa of small intestine
lamina propria mucosae of small intestine
lamina propria of mucosa of small intestine
A serous membrane that is part of a wall of intestine [Automatically generated definition].
anatomical wall of bowel serous membrane
anatomical wall of intestine serous membrane
intestine anatomical wall serous membrane
serous membrane of anatomical wall of bowel
serous membrane of anatomical wall of intestine
serous membrane of bowel anatomical wall
serous membrane of intestine anatomical wall
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
opening of terminal part of digestive tract
The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
An anatomical wall that is part of a intestine [Automatically generated definition].
we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct.
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
Transudate contained in the peritoneal cavity.
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
Epithelial layer that lines the intestine.
Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]
An epithelium that is part of a large intestine [Automatically generated definition].
A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver.
The functional units of the liver including the lobules.
the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]
DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)
Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers.
(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]
DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)
The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule.
Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)
The anus and surrounding regions. Encompasses both internal and external regions, where present.
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
The outer layer of peritoneum that is attached to the abdominal and pelvic walls.
Peritoneum attached to the abdominal wall.[AAO]
A zone of skin that is part of an abdomen [Automatically generated definition].
A zone of skin that is part of a neck [Automatically generated definition].
A zone of skin that is part of a thorax [Automatically generated definition].
An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
A lymphatic vessel that is part of a face [Automatically generated definition].
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
A zone of skin that is part of a lip [Automatically generated definition].
A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO].
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery.
The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]
The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]
birds have right aortic arch, mammals left.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
results from fusion of left and right dorsal aortae
The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery.
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta.
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]
In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]
The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]
The subclavian artery that supplies the right pectoral appendage.
in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery
proximal part arises from right 4th aortic arch in humans
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
The subclavian artery that supplies the left pectoral appendage.
in humans, branches off the arch of aorta
arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans
A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
A sphincter muscle that is part of the iris.
In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]
WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure
A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted].
It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
A portal vein that transports nutrients from the digestive tract to the liver[Kardong].
Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]
In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265
The first major branch of the abdominal aorta.
Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).
Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625
The pulmonary artery that supplies the right lung.
TODO - add class 'pulmonary artery tree organ'
The pulmonary artery that supplies the left lung.
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
The cranial ganglion that is associated with and extends fibers into the trigeminal nerve.
consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]
In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.
The bone at the lower, posterior part of the skull.
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
basi paired exo and supra occipital bones
An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended.
part of viscerocranium (facial skeleton) in FMA
A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP].
A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]
The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]
todo - homology e.g. mesethmoid of teleost
Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259
Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball.
Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]
in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
See notes for jaw w.r.t skeletal element vs subdivision of head.
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
The groups of nerve cell bodies associated with the twelve cranial nerves.
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
An anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye.
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes.
Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
MP treats posterior uvea and optic choroid as distinct
The lamellated connective tissue of the cornea between the Bowman and Descemet membranes.
Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]
A double layer covering the ciliary body that produces aqueous humor.
The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae.
The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified].
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified].
The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified].
The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells.
Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).
Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
The elastic, clear, membrane-like structure, that is outer most layer of the lens.
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia.
ganglion of sympathetic part of autonomic division of nervous system
sympathetic part of autonomic division of nervous system ganglion
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
Lip that covers the upper portion of the mouth.[TAO].
Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]
Lip that covers the lower portion of the mouth.[TAO].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]
A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces.
The most anterior region of the brain including both the telencephalon and diencephalon.
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.
The division of the forebrain that develops from the foremost primary cerebral vesicle.
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia].
An epithelium that is part of a small intestine [Automatically generated definition].
Intestinal epithelium which lines the lumen of the mid intestine.[TAO]
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
An endothelium that is part of a venule [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
A multi-tissue structure that is part of a spinal cord.
The liquid component of blood, in which erythrocytes are suspended.
Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
aids the process of digestion of lipids in the small intestine
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
major excretory route for potentially harmful exogenous lipophilic substances
many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
A submucosa that is part of a esophagus [Automatically generated definition].
A lamina propria that is part of a esophagus [Automatically generated definition].
A serous membrane that is part of a esophagus [Automatically generated definition].
The epithelial layer that lines the luminal space of the esophagus.
TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins.
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Excretion in semisolid state processed by the intestine.[FMA]
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
The simple columnar epithelial lining of the gall bladder.
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
A systemic artery that supplies the lung with with oxygenated blood.
rami bronchiales partis thoracicae aortae
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Respiration organ that develops as an outpocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
In humans this includes the superior and inferior phrenic arteries
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]
relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]
(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]
GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3
The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.
Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]
Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]
In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]
A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.
Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]
The chamber of the heart that receives blood from the lungs[XAO:EJS].
A cardiac ventricle that is in the right side of the heart.
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
In mammals continuous with the pulmonary arteries
Cardiac chamber in which blood enters the heart.
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)
A cardiac septum that divides the left and right atria of the heart.
The partition separating the right and left atria of the heart. [TFD][VHOG]
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
Cardiac septum which separates the right ventricle from the left ventricle.[FMA].
The partition separating the right and left ventricles of the heart. [TFD][VHOG]
The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]
involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430
Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon.
in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery.
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
The organ that functions to filter blood and to store red corpuscles and platelets.
An organ involved in red blood cell filtration and immune response.[AAO]
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
multiple sources - true spleen appear in jawed vertebrates
ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
An organ that aids digestion and stores bile produced by the liver[WP].
Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition].
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
superior olivary nucleus (Barr & Kiernan)
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
TODO - check ZFA/pons. also GO says part of dorsorostral pons
Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
Lung which consists of the left upper lobe and left lower lobe.[FMA].
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA].
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA].
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
covers the brain dorsally in chondrichthyans
The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO].
The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord].
columna grisea anterior medullae spinalis
periventricular zone of the hypothalamus
A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure
A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere.
Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).
The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA].
The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]
The yellow or brown waxy secretions produced by vestigial apocrine sweat glands in the external ear canal[MESH].
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
The atrial part of middle layer of the heart, comprised of involuntary muscle.
Part of choroid plexus contained in the lateral ventricle.
chorioid plexus of cerebral hemisphere of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere
A neural nucleus that is part of the brain.
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct
Any muscle organ that is part of a back [Automatically generated definition].
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells
pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
distinction between abdomen muscle and abdomen musculature
The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
A thoracic vertebra endochondral element that is composed primarily of a bone tissue.
Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs
A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO].
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)
The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA].
WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node.
An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles.
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]
The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
Serous membrane which is divided into parietal and visceral serous pericardium.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
An epithelium that lines the peritoneal cavity.[TAO]
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA].
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
The soft tissue that fills the cavities of bones.
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
consider placement of NCIT:C53466 medullary bone
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
Any skeletal muscle that is part of the head region.
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Any muscle that is part of the cervical (neck) region.
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.
A duct that carries bile from the liver to the intestine.
Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]
we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA
The triangular flat bone of the nasal septum.
Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]
Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]
relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]
relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]
In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]
The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]
The outer serous membrane of the pulmonary pleural.
the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax
The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs.
Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura].
The fluid-filled cavity that lies between the visceral and parietal pleurae.
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning
the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)
A double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity
this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
Transudate contained in the pericardial cavity.[FMA].
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)
The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
Consider changing name to make distinction from inferred superclass 'vertebral element' clear
we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones
Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]
Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]
A vertebra that is located in the cervical region of the vertebral column.
In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
The part of the digestive system that contains the liver and the biliary system.
System responsible for the production and movement of bile[ZFIN:curator].
The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
A blood vessel that is part of a choroid [Automatically generated definition].
cannot find singular in FMA, using Set class
The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries.
Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061].
Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine.
A mucosa that is part of a esophagus [Automatically generated definition].
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
An epithelium that is part of a iris [Automatically generated definition].
The supporting bundles of muscular fibers lining the walls of the ventricles of the heart.
The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented
Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea.
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof.
The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816]
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
May be composed of smooth muscle and elastic tissue
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
An organ that functions as a secretory or excretory organ.
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node.
See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest
Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]
Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt].
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
TODO discriminate between stages and organisms
Whole organism that is premetamorphic or a very immature individual.[TAO]
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube.
cavity of ventricular system of neuraxis
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
A spinal cord segment that adjacent_to a cervical region.
segmenta cervicalia medullae spinalis [1-8
A nucleus of brain that is part of a trigeminal nuclear complex.
massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.
nucleus tractus mesencephali nervi trigeminalis
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
A wall, dividing a cavity or structure into smaller ones[WP].
The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted].
segmenta thoracica medullae spinalis [1-12]
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue.
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.
In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion.
The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]
The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]
The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]
These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]
Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively
in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)
TODO - add grouping class for the anterior end of the neural tube at all stages
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
Extension of the dorsal aorta in the tail.
Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]
The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
Gonochoristic organism that can produce female gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ.
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]
Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus.
The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
in XAO, called branchial arch 2 and df VP4
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles.
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
The vessels formed within the first pair of branchial arches in embryogenesis.
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
The vessels formed within the fourth pair of branchial arches in embryogenesis.
Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]
The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
The vessels formed within the sixth pair of branchial arches in embryogenesis.
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
GO uses genitalia for the singular organ
A female organ involved in reproduction.
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
Septum that divides the internal chambers (camerae) of the shell of a cephalopod, namely nautiloids or ammonoids.
An epithelium that is part of a upper jaw [Automatically generated definition].
epithelial tissue of palatoquadrate arch
An epithelium that is part of a lower jaw [Automatically generated definition].
epithelial tissue of ventral mandibular arch
ventral mandibular arch epithelial tissue
The portion of the yolk sac that is derived from endoderm and lines the yolk sac.
An endoderm that is part of a foregut [Automatically generated definition].
An endoderm that is part of a midgut [Automatically generated definition].
An endoderm that is part of a hindgut [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones.
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum.
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]
A mesentery that is part of a esophagus [Automatically generated definition].
A mesentery that is part of a midgut [Automatically generated definition].
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
A gland that is part of a integumental system [Automatically generated definition].
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
Mesenchyme that is part of a developing ovary [Automatically generated definition].
female reproductive system gonad mesenchyme
female reproductive system gonada mesenchyme
gonad of female reproductive system mesenchyme
gonada of female reproductive system mesenchyme
mesenchyme of female reproductive system gonad
mesenchyme of female reproductive system gonada
mesenchyme of gonad of female reproductive system
mesenchyme of gonada of female reproductive system
The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme.
Mesenchyme that is part of a developing upper jaw [Automatically generated definition].
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
A submucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically submucosa
submucosa of anal canal viewed anatomically
The submucous layer of the wall of the rectum.
A submucosa that is part of a colon [Automatically generated definition].
A submucosa that is part of a duodenum [Automatically generated definition].
A serous membrane that is part of a rectum [Automatically generated definition].
A serous membrane that is part of a colon [Automatically generated definition].
A serous membrane that is part of a duodenum [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
A ganglion that is part of a central nervous system [Automatically generated definition].
this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia
A mucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically mucosa of organ
anal canal viewed anatomically mucous membrane
anal canal viewed anatomically organ mucosa
mucosa of anal canal viewed anatomically
mucosa of organ of anal canal viewed anatomically
mucosa of organ of anatomical anal canal
mucous membrane of anal canal viewed anatomically
mucous membrane of anatomical anal canal
organ mucosa of anal canal viewed anatomically
A mucosa that is part of a oral opening [Automatically generated definition].
A mucosa that is part of a rectum [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
An epithelium that is part of a hindgut [Automatically generated definition].
An epithelium that is part of a rectum [Automatically generated definition].
An epithelium that is part of a right lung [Automatically generated definition].
An epithelium that is part of a left lung [Automatically generated definition].
An unilaminar epithelium that surrounds a pectoral appendage bud.
A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition].
cardiac muscle tissue of heart right atrium
cardiac muscle tissue of right atrium of heart
textus muscularis of myocardium of right atrium
textus muscularis of myocardium of right atrium of heart
textus muscularis of myocardium of right cardiac atrium
A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition].
cardiac left atrium cardiac muscle tissue
textus muscularis of myocardium of cardiac left atrium
textus muscularis of myocardium of heart left atrium
textus muscularis of myocardium of left atrium
textus muscularis of myocardium of left atrium of heart
textus muscularis of myocardium of left cardiac atrium
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of right ventricle
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
cardiac muscle of interventricular septum
cardiac muscle tissue of interventricular septum
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi.
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
A mesothelium that is part of a pericardium [Automatically generated definition].
cavity of pericardial sac meso-epithelium
meso-epithelium of cavity of pericardial sac
mesothelium of cavity of pericardial sac
A mesothelium that is part of a diaphragm [Automatically generated definition].
A mesothelium that is part of a pleural cavity [Automatically generated definition].
A mesentery that is part of a urinary system [Automatically generated definition].
A mesentery that is part of a hindgut [Automatically generated definition].
A mesentery that is part of a rectum [Automatically generated definition].
A mesentery that is part of a colon [Automatically generated definition].
A mesentery that is part of a duodenum [Automatically generated definition].
A cartilage element that is part of a respiratory system [Automatically generated definition].
A gland that is part of a digestive tract [Automatically generated definition].
Mesenchyme that is part of a pectoral appendage bud.
Mesoderm that is part of the pectoral fin bud.[TAO]
An adipose tissue that is part of a dermis [Automatically generated definition].
A nerve that is part of an abdomen [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
A nerve that is located in a thoracic cavity [Automatically generated definition].
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition].
cardiac muscle muscle tissue of trabecula carnea
cardiac muscle textus muscularis of trabecula carnea
cardiac muscle tissue of trabecula carnea
heart muscle muscle tissue of trabecula carnea
heart muscle textus muscularis of trabecula carnea
heart myocardium muscle tissue of trabecula carnea
heart myocardium textus muscularis of trabecula carnea
muscle of heart muscle tissue of trabecula carnea
muscle of heart textus muscularis of trabecula carnea
muscle tissue of cardiac muscle of trabecula carnea
muscle tissue of heart muscle of trabecula carnea
muscle tissue of heart myocardium of trabecula carnea
muscle tissue of muscle of heart of trabecula carnea
muscle tissue of myocardium of trabecula carnea
myocardium muscle tissue of trabecula carnea
myocardium textus muscularis of trabecula carnea
textus muscularis of cardiac muscle of trabecula carnea
textus muscularis of heart muscle of trabecula carnea
textus muscularis of heart myocardium of trabecula carnea
textus muscularis of muscle of heart of trabecula carnea
textus muscularis of myocardium of trabecula carnea
trabecula carnea cardiac muscle muscle tissue
trabecula carnea cardiac muscle textus muscularis
trabecula carnea heart muscle muscle tissue
trabecula carnea heart muscle textus muscularis
trabecula carnea heart myocardium muscle tissue
trabecula carnea heart myocardium textus muscularis
trabecula carnea muscle of heart muscle tissue
trabecula carnea muscle of heart textus muscularis
trabecula carnea muscle tissue of cardiac muscle
trabecula carnea muscle tissue of heart muscle
trabecula carnea muscle tissue of heart myocardium
trabecula carnea muscle tissue of muscle of heart
trabecula carnea muscle tissue of myocardium
trabecula carnea myocardium muscle tissue
trabecula carnea myocardium textus muscularis
trabecula carnea textus muscularis of cardiac muscle
trabecula carnea textus muscularis of heart muscle
trabecula carnea textus muscularis of heart myocardium
trabecula carnea textus muscularis of muscle of heart
trabecula carnea textus muscularis of myocardium
A lymphatic vessel that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lymphatic vessel
lymphatic vessel of apparatus respiratorius
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a neck [Automatically generated definition].
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
A bone that is part of a trunk [Automatically generated definition].
An artery that is part of a respiratory system [Automatically generated definition].
The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose.
ramus labialis superior arteriae facialis
The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
A vein that is part of a respiratory system [Automatically generated definition].
The inferior labial vein is the vein receiving blood from the upper lip.
The inferior labial vein is the vein receiving blood from the lower lip.
A vein that is part of a thoracic cavity [Automatically generated definition].
A vein that is part of a tail [Automatically generated definition].
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
respiratory system capillary endothelium
A venule that is part of a respiratory system [Automatically generated definition].
An arteriole that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a brain [Automatically generated definition].
A blood vessel that is part of a cornea [Automatically generated definition].
A blood vessel that is part of a retina [Automatically generated definition].
blood vessel of tunica interna of eyeball
A blood vessel that is part of a neck [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a iris [Automatically generated definition].
A blood vessel that is part of a lung [Automatically generated definition].
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A blood vessel that is part of a tail [Automatically generated definition].
A capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
capillary vessel of apparatus respiratorius
A gray matter that is part of a brain [Automatically generated definition].
A zone of skin that is part of a tail [Automatically generated definition].
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
neck (volume) portion of connective tissue
portion of connective tissue of neck (volume)
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
lower respiratory tract connective tissue
A portion of connective tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a trunk [Automatically generated definition].
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
cavity of chest portion of connective tissue
cavity of thorax portion of connective tissue
chest cavity portion of connective tissue
pectoral cavity portion of connective tissue
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
thoracic cavity portion of connective tissue
A portion of connective tissue that is part of a tail [Automatically generated definition].
portion of connective tissue of post-vent region
post-vent region portion of connective tissue
A cartilage that is part of a neck [Automatically generated definition].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
A skin gland that is part of a camera-type eye [Automatically generated definition].
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
adult aorta textus connectivus elasticus
dorsal aorta textus connectivus elasticus
elastic connective tissue of adult aorta
elastic connective tissue of dorsal aorta
elastic connective tissue of trunk of aortic tree
textus connectivus elasticus of adult aorta
textus connectivus elasticus of dorsal aorta
textus connectivus elasticus of trunk of aortic tree
trunk of aortic tree elastic connective tissue
trunk of aortic tree textus connectivus elasticus
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An elastic tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius elastic connective tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
An elastic tissue that is part of a circulatory system [Automatically generated definition].
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
Elastic tissue layer that lines a blood vessel layer.
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
textus connectivus elasticus of blood vessel
Elastic tissue that is part of a lung [Automatically generated definition].
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
A muscle organ that attaches to a tail vertebra [Automatically generated definition].
the BTO class may possibly refer to an invertebrate structure
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
Design pattern notes: check whether this fits the foramen design pattern
The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas.
The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles.
Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct
Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts
Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]
The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava.
A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.
All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers
The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls.
The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted].
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of a thorax [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
bone organ of abdominal segment of trunk
Any muscle organ that is part of a thorax [Automatically generated definition].
Any muscle organ that is part of a respiratory system [Automatically generated definition].
Any muscle organ that is part of a esophagus [Automatically generated definition].
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
muscle organ of abdominal segment of trunk
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of a thorax [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
abdominal segment of trunk connective tissue
abdominal segment of trunk portion of connective tissue
abdominal segment of trunk textus connectivus
connective tissue of abdominal segment of trunk
portion of connective tissue of abdominal segment of trunk
textus connectivus of abdominal segment of trunk
An anatomical space that surrounded_by a neural tube.
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
Mesenchyme that is part of a developing gonad [Automatically generated definition].
A presumptive structure that has the potential to develop into a ganglion.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ
One of the skeletal muscles of the head and neck, spine, and ribs.
A portion of skeletal muscle tissue in the trunk.
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP].
Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]
some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).
endothelium of irregular blood filled space
The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue.
epithelial tissue of chorioid plexus of cerebral hemisphere
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
A blood vessel that carries blood from the capillaries toward the heart.
Embryonic structure that develops into pancreatic bud.
in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds
revisit after standardizing terms 'primordium', 'anlagen', 'bud'
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID].
Pancreatic bud that gives rise to the accessory pancreatic duct.
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]
DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)
Pancreatic bud that gives rise to the major pancreatic duct.
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship.
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
The sensory system for the sense of touch and pain.
The neural tissue involved in the transmission of sensory signals
MP defines this in a may more appropriate to somatosensory cortex
The brain ventricles or their associated choroid plexuses.
The anterior segment of the lamellated connective tissue layer of the cornea.
The posterior segment of the lamellated connective tissue layer of the cornea.
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity.
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
The connection between the embryo proper and extraembryonic tissues.
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP].
In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout.
The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it.
Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.
One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid.
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
The middle of the face including the nose and its associated bony structures[MW].
this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
A vasculature that is part of a iris [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633
Any of the layers of the myocardium. Example: compact layer, trabecular layer.
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA].
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]
A myocardium trabecular layer that is part of a cardiac ventricle.
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
Missing definition for term UBERON:0004133. Please replace it using linked reference.
The first recognizable structure derived from the heart field.
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract septum is a partition in the outflow tract.
The outflow tract is the portion of the heart through which blood flows into the arteries.
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles.
Vein of heart that drains the myocardium.
A cardiac chamber surrounds an enclosed cavity within the heart.
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium.
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
The nonstriated, involuntary muscle tissue located in the wall of the aorta.
A portions of the gut that is derived from endoderm.
A nerve that is part of a back [Automatically generated definition].
A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition].
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
smooth muscle tissue of gastrointestinal system
A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum involuntary muscle
anal part of perineum non-striated muscle
anal part of perineum smooth muscle tissue
involuntary muscle of anal part of perineum
non-striated muscle of anal part of perineum
smooth muscle tissue of anal part of perineum
A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition].
smooth muscle tissue of lymphatic vessel
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
Smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition].
A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
A blood vessel that is part of a back [Automatically generated definition].
A myocardium that is part of a outflow tract [Automatically generated definition].
(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]
PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)
A portion of connective tissue that is part of a back [Automatically generated definition].
A pericardium that is part of a outflow tract [Automatically generated definition].
A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle
chorioid plexus of cerebral hemisphere epithelium of lateral ventricle
choroid plexus epithelial tissue of lateral ventricle
choroid plexus epithelium of lateral ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelial tissue of choroid plexus of lateral ventricle
epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelium of choroid plexus of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue
lateral ventricle chorioid plexus of cerebral hemisphere epithelium
lateral ventricle choroid plexus epithelial tissue
lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
lateral ventricle epithelial tissue of choroid plexus
lateral ventricle epithelium of chorioid plexus of cerebral hemisphere
lateral ventricle epithelium of choroid plexus
lateral ventricle choroid plexus epithelium
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]
A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle of lymph vessel of respiratory system
respiratory system lymphatic vessel smooth muscle
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle tissue of blood vessel of respiratory system
respiratory system blood vessel smooth muscle
Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition.
distinction between trophectoderm and trophoblast unclear/inconsistent in many sources
The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]
(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]
BTO has this has part of the trophoblast
ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106
The embryonic structure that gives rise to the corneal ectoderm.
Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries.
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP].
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta.
derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast.
Blood vessel that is connected to the yolk sac.
A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].
Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]
The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Vascular network that is connected to the yolk sac.
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra.
In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)
it's not clear if the XAO class belongs here or below
Sum of all sensory systems in an organism.
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a back [Automatically generated definition].
A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles.
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
Any collection of muscles that is part of a trunk [Automatically generated definition].
currently defined by location rather than attachment
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition].
interatrial septum cardiac muscle tissue
cardiac muscle tissue of interatrial septum
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition].
A muscle that is attached to a vertebra of the vertebral column.
A vasculature that is part of a muscle organ [Automatically generated definition].
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of right ventricle
A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of left ventricle
A projection or outgrowth of tissue from a larger body or organ.
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.
A vascular network consisting of blood vessels.
An eye that is part of a left side of organism [Automatically generated definition].
An eye that is part of a right side of organism [Automatically generated definition].
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the venous system that drains the general body tissues[Kardong].
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart.
The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein.
should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]
An anatomical wall that is part of an aorta, enclosing the luminal space.
The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers.
The membranous portion of the wall between the two lower chambers of the heart.
The membranous septum is the upper part of ventricular septum[GO:0003149].
membranous part of interventricular septum
membranous portion of interventricular septum
pars membranacea (septi interventricularis)
pars membranacea septi interventricularis
The muscular portion of the wall between the two lower chambers of the heart.
The muscular septum is the lower part of the ventricular septum[GO]
muscular part of interventricular septum
pars muscularis (septi interventricularis)
pars muscularis septi interventricularis
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
An endothelium that is part of a vena cava [Automatically generated definition].
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)
An endothelium that is part of an arterial system [Automatically generated definition].
An endothelium that is part of a venous system [Automatically generated definition].
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
respiratory system blood vessel endothelium
A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches.
TODO - check relationship to bulbus arteriosus
A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]
An appendage that is part of an appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.
While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]
DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
taken from version of VSAO used in TAO and used directly in Uberon
Dermis-derived entity that is made of skeletal tissue.
A gland that is part of an anal canal [Automatically generated definition].
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
cartiligionous skeletal structure of skull
Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
Do not manually classify under here - bones are automatically classified
Anatomical system that consists of all the joints of the body.
A submucosa that is part of a respiratory system [Automatically generated definition].
A lamina propria that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lamina propria mucosa
lamina propria mucosa of apparatus respiratorius
lamina propria mucosa of respiratory system
lamina propria of apparatus respiratorius
respiratory system lamina propria mucosa
A lamina propria that is part of a gastrointestinal system.
A lamina propria that is part of a gallbladder [Automatically generated definition].
A serous membrane that is part of a digestive system [Automatically generated definition].
serous membrane of gastrointestinal system
A serous membrane that is part of a gallbladder [Automatically generated definition].
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
anatomical wall of lower chamber of heart
The mucous membrane lining the respiratory tract.
TODO - split respiratory tract mucosa from respiratory system mucosa
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
A mucosa that is part of a gastrointestinal system.
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
A mucous gland that is part of the skin.
A secretion that is part of a endocrine pancreas [Automatically generated definition].
A secretion that is part of a exocrine pancreas [Automatically generated definition].
A secretion that is part of a esophagus [Automatically generated definition].
A secretion that is part of a pancreas [Automatically generated definition].
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi.
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
Any epithelium that lines one of the bile ducts.
The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium.
An epithelium that is part of a extrahepatic bile duct [Automatically generated definition].
epithelial tissue of extrahepatic bile duct
extrahepatic bile duct epithelial tissue
An epithelium that is part of a intrahepatic bile duct [Automatically generated definition].
epithelial tissue of intrahepatic bile duct
intrahepatic bile duct epithelial tissue
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition].
Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum skeletal muscle tissue
skeletal muscle of anal part of perineum
skeletal muscle tissue of anal part of perineum
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips
Smooth muscle tissue in all or part of a hepatic duct.
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system endothelium of artery
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
vein endothelium of apparatus respiratorius
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall.
endothelium of trunk of systemic arterial tree
trunk of systemic arterial tree endothelium
An endothelium that is part of the cardiovascular system.
A mesentery that is part of a digestive system [Automatically generated definition].
A connective tissue that surrounds a skeletal muscle tissue.
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle tissue
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
A vasculature that is part of a retina [Automatically generated definition].
Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye.
note that the AAO and ZFA class is a cavity
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
The central region of trunk mesoderm. This tissue forms the notochord.
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
The mass of tissue made up of mesenchymal cells in the lung.
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra.
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila.
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct.
Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]
One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct.
Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP].
musculus sphincter ampullae hepatopancreatica
A sphincter muscle that is part of a anal region.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
A submucosa that is part of a cystic duct [Automatically generated definition].
A submucosa that is part of a cecum [Automatically generated definition].
A submucosa that is part of an ascending colon [Automatically generated definition].
A submucosa that is part of a transverse colon [Automatically generated definition].
A submucosa that is part of a descending colon [Automatically generated definition].
A submucosa that is part of a sigmoid colon [Automatically generated definition].
A submucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) submucosa
submucosa of corpus gastricum (ventriculare)
A submucosa that is part of a pyloric antrum [Automatically generated definition].
A submucosa that is part of a pylorus [Automatically generated definition].
A submucosa that is part of a biliary tree [Automatically generated definition].
A submucosa that is part of a common bile duct [Automatically generated definition].
submucosa of ductus choledochus (biliaris)
A submucosa that is part of a common hepatic duct [Automatically generated definition].
A submucosa that is part of a right hepatic duct [Automatically generated definition].
A submucosa that is part of a left hepatic duct [Automatically generated definition].
A mucosa that is part of a cystic duct [Automatically generated definition].
A mucosa that is part of an ascending colon [Automatically generated definition].
A mucosa that is part of a transverse colon [Automatically generated definition].
A mucosa that is part of a descending colon [Automatically generated definition].
A mucosa that is part of a sigmoid colon [Automatically generated definition].
A mucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) mucosa of organ
corpus gastricum (ventriculare) mucous membrane
corpus gastricum (ventriculare) organ mucosa
mucosa of corpus gastricum (ventriculare)
mucosa of organ of corpus gastricum (ventriculare)
mucous membrane of corpus gastricum (ventriculare)
organ mucosa of corpus gastricum (ventriculare)
A mucosa that is part of a pyloric antrum [Automatically generated definition].
mucosa of organ of stomach pyloric antrum
mucous membrane of stomach pyloric antrum
A mucosa that is part of a pylorus [Automatically generated definition].
mucosa of organ of pyloric part of stomach
mucosa of organ of stomach pyloric region
mucous membrane of pyloric part of stomach
mucous membrane of stomach pyloric region
A mucosa that is part of a biliary tree [Automatically generated definition].
A mucosa that is part of a common bile duct [Automatically generated definition].
ductus choledochus (biliaris) mucosa of organ
ductus choledochus (biliaris) mucous membrane
ductus choledochus (biliaris) organ mucosa
mucosa of organ of ductus choledochus (biliaris)
mucous membrane of ductus choledochus (biliaris)
organ mucosa of ductus choledochus (biliaris)
A mucosa that is part of a common hepatic duct [Automatically generated definition].
A mucosa that is part of a right hepatic duct [Automatically generated definition].
A mucosa that is part of a left hepatic duct [Automatically generated definition].
A mucosa that is part of a upper lip [Automatically generated definition].
A mucosa that is part of a lower lip [Automatically generated definition].
A mucosa that is part of a gallbladder [Automatically generated definition].
An external genitalia that is part of a female reproductive system [Automatically generated definition].
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
external genitalia of female reproductive system
An organ that is part of a immune system [Automatically generated definition].
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
Missing definition for term UBERON:0005064. Please replace it using linked reference.
Missing definition for term UBERON:0005066. Please replace it using linked reference.
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003
A bud is a protrusion that forms from an epithelial sheet by localized folding.
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
The functional tissue of the central nervous system consisting of neurons and glial cells.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion).
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same
A duct that carries bile from the liver to the small intestine.[TAO]
The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]
The hepatic duct is the duct that leads from the liver to the bile duct[GO].
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A vein that is part of a thorax [Automatically generated definition].
A parenchyma that is part of a right lobe of liver [Automatically generated definition].
A parenchyma that is part of a left lobe of liver [Automatically generated definition].
An ectoderm that is part of a medial nasal prominence [Automatically generated definition].
An ectoderm that is part of a optic eminence [Automatically generated definition].
The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
An endocardium that is part of a interventricular septum [Automatically generated definition].
interventricular septum endocardial tissue
A myocardium that is part of a bulbus cordis [Automatically generated definition].
An anatomical cavity that is part of a yolk sac [Automatically generated definition].
In mammals, the yolk sac cavity contains fluid rather than platelets
in EHDAA2, there are separate primary and secondary yolk sac cavities
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Mesenchyme that is part of a developing trunk.
A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP].
ventricular system of central nervous system
A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm].
Tela chorioidea that lines the telencephalic ventricle.
tela chorioidea of telencephalic ventricle
tela choroidea of telencephalic ventricle
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The endothelial lining of the endocardium.
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
A lamina propria that is part of a mucosa of oral region.
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord.
region of wall of ventricular system of neuraxis
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
directing or focusing light onto light receptors
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
A sex gland that is part of a female reproductive system.
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3
A limb bud that develops into a forelimb or pectoral fin.
Fin bud that develops into the pectoral fin.[TAO]
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]
apical ectodermal ridge pectoral fin bud
pectoral appendage apical ectodermal ridge
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:.
The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.
A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG]
It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]
PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)
A vitelline vein that is in the left side of a multicellular organism.
A vitelline vein that is in the right side of a multicellular organism.
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
neural tube lateral wall sulcus limitans
The paired veins that carry blood from the yolk sac back to the embryo.
One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]
Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]
check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460
Portion of tissue on the side of the lumen of the neural tube.
todo - epidermis? todo - track down EHDAA2 class in new release
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A neural tube lateral wall that is part of a rhombomere.
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Somite located in the head region, caudal to the otic vesicle.
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum.
The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans
ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
Arteries which arise from the abdominal aorta and distribute to most of the intestines.
includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries
A vein that returns blood from the intestines.
In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein
A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part.
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]
An epithelium that is part of a pylorus.
An epithelium that is part of a anterior chamber of eyeball.
An epithelium that is part of a lens vesicle.
An ectoderm that is part of a pharyngeal arch 4.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
An endoderm that is part of a pharyngeal arch 4.
A mesothelium that is part of a peritoneal cavity.
we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood
An endothelium that is part of a right lung.
An endothelium that is part of a left lung.
A dorsal mesentery that is part of a midgut.
A dorsal mesentery that is part of a caecum.
An anatomical cavity that is part of a lens vesicle.
Mesenchyme that is part of a pharyngeal arch 4.
Mesenchyme that is part of a optic eminence.
A mesentery of duodenum that is part of a foregut.
A mesentery of duodenum that is part of a midgut.
A venous system that is part of a hindbrain.
A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme.
Embryonic region that develops into the pectoral fin bud.[TAO]
pectoral appendage field of lateral plate mesoderm
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
limb/fin field of lateral plate mesoderm
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
A tunica intima that is part of a artery.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term
A spinal cord segment that adjacent_to a caudal region.
segmenta coccygea medullae spinalis [1-3]
for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip.
The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA].
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA].
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
An outflow tract that is part of a cardiac atrium.
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk.
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA].
An outflow tract of atrium that is part of a left atrium.
The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium.
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation.
The supporting bundles of muscular fibers lining the walls of the atrial myocardium.
The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.
The paired arteries that carry blood to the yolk sac from the dorsal aorta.
Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664]
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
A bone that is part of a post-anal tail.
MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future.
Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this.
This region is reduced in humans and corresponds to the coccyx
We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud
That portion of the spine comprising the cervical vertebrae. The neck area of the spine.
Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]
That part of the spine comprising the thoracic vertebrae.
Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae.
Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]
in AAO, this is posterior to the caudal-sacral region
A collection of all skeletal elements in some subdivision of the vertebral column.
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
The foremost region of the future forebrain that develops into the diencephalon.
consider obsoleting, the ethmoid is endochondral?
An anatomical junctions that overlaps the foregut and midgut.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A tendon that has the potential to develop into a central tendon.
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.
cranial derivative of septum transversum
A presumptive structure that has the potential to develop into a forebrain.
A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops.
An anatomical junctions that overlaps the mouth and foregut.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Either of two openings transmitting nerves and blood vessels to or from the orbit.
Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.
Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle.
A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP].
check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
A segment of the eyeball that is filled with refractive media.
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A nucleus of brain that is part of a brainstem.
An artery that connects two larger arteries.
A lobe of lung that is part of a right lung.
4 in mice, divided into 3 in human by two interlobal fissures
A portion of organism substance that secreted_by a zone of skin.
A portion of organism substance that is secreted by a female reproductive gland.
female reproductive system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
A tube that is part of a excretory system.
An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA].
A myocardium that is part of a left ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of aorta.
A myocardium that is part of a right ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.
A nucleus of brain that is part of a hypothalamus.
A nucleus of brain that is part of a diencephalon.
A trabecula carnea that is part of a heart right ventricle.
A trabecula carnea that is part of a heart left ventricle.
trabeculae carneae (ventriculus sinister)
The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:.
FMA also has FMA:29321 but it's not clear how this differs
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
A rigid covering that envelops an object.
A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis.
currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)
An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO].
typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.
The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.
In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]
An anatomical boundary that adjacent_to a epithelium.
A vein that is part of a vertebral column.
A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes.
TODO - check neural vs vertebral canal; embryonic vs adult?
Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO]
The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm.
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
An epithelium that is composed primarily of secretory cells.
consider splitting epithelium from epithelial tissue
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
The supporting bundles of muscular fibers lining the walls of the atria[MP].
Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only'
A subdivision of a the reproductive tract in a female organism that is the site of embryo development.
Vein that is central to a lobule in the liver.
Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
the EHDAA2 term and the FMA term may not be exact equivalents - check
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
Mesenchyme that is part of a mandibular prominence.
An anatomical space that surrounded_by a digestive tract.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA].
A squamous epithelium that is part of a esophagus.
MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass
A squamous epithelium that is part of a stomach.
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
Any gland that is part of the digestive system.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA].
Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A capillary that is part of the coronary system.
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
Cranial neural crest that migrates into the mandibular arch.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
GO uses blood circulation generically to include the haemolymphatic fluid of arthropods
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail.
By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx).
An anatomical cavity that surrounded_by a midgut.
An anatomical cavity that surrounded_by a hindgut.
An anatomical cavity that surrounded_by a anal canal.
An anatomical cavity that surrounded_by a colon.
A lamina propria that is part of a colonic mucosa.
lamina propria of colonic mucous membrane
A mesothelium that is part of a serous pericardium.
The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis.
The vasculature consisting of brachiocephalic arteries and veins.
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
Mesenchyme that develops_from a trunk neural crest.
mesenchyme derived from trunk neural crest
relationship to Meckel's cartilage to be added
relationship to palatoquadrate to be added
A tunica media that is part of a artery.
A tunica adventitia that is part of a artery.
A tunica adventitia that is part of a vein.
Gray matter of the central nervous system which is a collection of clustered nuclei.
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
Portion of tissue that is part of the heart tube and will become the sinus venosus.
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A blood vessel that is part of a pectoral appendage.
A blood vessel that is part of a limb/fin.
A vasculature that is part of a pectoral appendage.
A vasculature that is part of a chordate pharynx.
A vasculature that is part of a limb/fin.
A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans.
In mice many lobules lack islets, in contrast to other mammals including humans
A duct that collects and carries secretions of the exocrine pancreas to the intestine.
this class groups together accessory (dorsal) and main (ventral) pancreatic ducts
Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms
A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones.
check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
A cartilage tissue that is part of a paired limb or fin.
Cartilage which is part of one of the paired fins.[TAO]
A cartilage tissue that is part of a pectoral appendage.
Cartilage which is part of the pectoral fin.[TAO]
A nucleus of brain that spans a midbrain tegmentum.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
A ring of smooth muscle cells whose contraction closes the opening of the ring.
A ring of striated muscle cells whose contraction closes the opening of the ring.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
Epithelium bearing vibratile cilia on the free surface.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
A neural nucleus that is part of a medulla oblongata.
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].
in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
An anatomical structure that connects two structures.
A sphincter that is part of an esophagus.
check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
A bone that is part of a reproductive organ.
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces.
characteristically low in protein and cellular content (unless there has been secondary concentration)
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton.
Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]
Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]
present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
Mesentery that is located in the peritoneum.
A bone that is part of a appendage girdle region.
A bone that is part of a pectoral girdle region.
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
A bone that is part of a craniocervical region.
The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
A skeletal joint that is part of a appendage girdle region.
An anatomical surface that is part of a cartilage element.
A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
subclasses of this should be checked for taxonomic consistency
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
Any muscle organ that is part of a pectoral girdle region.
EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
A muscle of back that is part of a dorsal thoracic segment of trunk.
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
An epithelium that is part of a duodenum.
A vertebral foramen that is part of a cervical vertebra.
A vertebral foramen that is part of a thoracic vertebra.
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers.
The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals.
The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines.
the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two
The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter.
The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
Any skeletal muscle organ in the hypodermis / superficial fascia.
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
Subdivision of endoskeleton derived from pharyngeal arches.
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
A lobe of lung that is part of a left lung.
1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure
One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed.
System pertaining to blood vessels in the brain.
A zone of skin that is part of a dorsal thoracic segment of trunk.
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
A gonad prior to differentiating into a definitive testis or ovary.
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
Cranial ganglion which develops from an epibranchial placode.
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
Endocardium that is part of the right atrium.
A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.
A vein that is part of a craniocervical region.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid bone pre-cartilage condensation
A sphenoid endochondral element that is composed primarily of cartilage tissue.
Mesenchyme that is part of a medial nasal prominence.
medial or lateral; in EHDAA2 also frontonasal or intermaxillary
The axilla is the area directly under the joint where the forelimb connects to the shoulder.
An ectoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a buccopharyngeal membrane.
Mesenchyme that is part of a foregut-midgut junction.
associated mesenchyme of foregut-midgut junction
A mesentery that is part of a foregut-midgut junction.
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
An epithelium that is part of a foregut-midgut junction.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head.
Mesenchyme that is part of a developing hindgut.
An endoderm that is part of a anal region.
Mesenchyme that is part of a maxillary prominence.
A hepatic sinusoid that is part of a left lobe of liver.
hepatic sinusoid of left of lobe of liver
A hepatic sinusoid that is part of a right lobe of liver.
hepatic sinusoid of right of lobe of liver
An endoderm that is part of a foregut-midgut junction.
A submucosa that is part of a intestine.
Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions.
thoracolumbar region of vertebral column
A sulcus limitans of neural tube that is part of a future spinal cord.
spinal cord lateral wall sulcus limitans
A sulcus limitans of neural tube that is part of a future medulla oblongata.
A sulcus limitans of neural tube that is part of a future metencephalon.
A sulcus limitans of neural tube that is part of a future myelencephalon.
Mesenchyme that is part of a 1st arch mandibular component.
mesenchymal region of mandibular component of first pharyngeal arch
Mesenchyme that is part of a developing left lung.
Mesenchyme that is part of a developing right lung.
A neural plate that develops_from a future forebrain.
A neural plate that develops_from a presumptive midbrain.
A neural plate that develops_from a presumptive hindbrain.
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
A nucleus of brain that is part of a telencephalon.
An anatomical space that surrounded_by a embryonic cloaca.
An anatomical space that surrounded_by a rectum.
Any endocardium that is part of the right ventricle of the heart.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
Any endocardium that is part of the left ventricle of the heart.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
An anatomical cavity that surrounded_by a stomodeum.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures.
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas.
A ganglion that is part of a abdominal segment of trunk.
A serous sac that has the pleura and the pleural cavity as parts.
despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
An epithelium that is part of a embryonic cloaca.
A multicellular organism that existence_starts_and_ends_during a nematode larval stage.
Branch or outpocketing of the digestive tract.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).
extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].
In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested
in mouse has left ventricular identity[PMID:22855565]
Mesenchyme that is part of a developing face.
todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)
A portion of an organ, such as the liver, lung, breast, or brain.
A multicellular organism that existence_starts_with a post-embryonic stage.
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
An epithelium that is part of a pancreatic duct.
in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this
An anatomical structure that has more than one cell as a part.
A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF].
Mesenchyme that is part of a pharyngeal arch 6.
An organ of the digestive tract that is capable of retaining and storing food.
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Mesenchyme that is part of a pharyngeal arch 1.
Mesenchyme that is part of a 1st arch maxillary component.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
entire pharyngeal arch associated mesenchyme
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
An anatomical space with at least one opening to another space or the exterior.
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
An extrahepatic bile duct that has the potential to develop into a common hepatic duct.
Mesenchyme that has the potential to develop into a dermis.
A structure that will develop into a diaphragm.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
A gray matter that has the potential to develop into a superior salivatory nucleus.
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
A mucous secretion that is produced by glands in the epidermis.
An anatomical cavity that surrounded_by a blood vessel.
The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation.
One of the laterally paired arteries that supply the gonads.
A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver.
Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
A vasculature that is part of a post-anal tail.
A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified].
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
The core globe-shaped component of the camera-type eye.
An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
4th pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from neural crest
branchial arch 4 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
pharyngeal arch 6 mesenchyme from neural crest
branchial arch 6 mesenchyme from neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
mesenchyme derived from neural crest of mesenchyme of 1st arch
pharyngeal arch 1 mesenchyme from neural crest
branchial arch 1 mesenchyme from neural crest
Any anatomical space that is part of a vertebral column.
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
An endothelium that is part of a sclera.
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
An epithelium that is part of a extraembryonic structure.
Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus.
epithelium stratificatum squamosum noncornificatum
nonkeratinizing stratified squamous epithelium
stratified squamous non-keratinized epithelium
stratified squamous nonkeratinizing epithelium
non-keratinized stratified squamous epithelium
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
A skeletal element that is part of a orbital region.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
Mesenchyme that is part of a limb/fin bud.
Mesenchyme that is part of a extraembryonic membrane.
Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme.
head mesenchyme derived arch 4 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from head mesenchyme
branchial arch 4 mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
branchial arch 6 mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from neural crest
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from head mesenchyme
pharyngeal arch mesenchyme from head mesenchyme
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')
Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a splanchnopleure.
One of the branches of the splenic artery[MP].
When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]
One of the veins that feed the splenic vein.
The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
An organ that is capable of detecting electrical stimulus.
Skeletal element that forms as a replacement or substitution of another element or tissue.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
An organ cavity that surrounded_by a bone.
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.
considering adding pectoral and pelvic complex skeleton classes
note that the MA class includes girdle parts so it belongs here;
bone of forelimb or pectoral fin or pectoral girdle
A muscle of a pectoral girdle, pectoral fin or anterior limb.
the MA class belongs here, based on its current child classes
Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Skeletal element that forms around the notochord and is part of the vertebral column.
we include a distinct subclass for bony vertebra
In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]
Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage
DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)
Any muscle organ that is part of either the head or the neck.
A cartilage element that is part of a splanchnocranium.
The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG].
The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups
vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist
The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
A synovial joint that is part of a pectoral girdle region.
in FMA, these are part of the bony pectoral girdle
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue.
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton.
primary subdivision of cranial skeletal system
A bone that is part of a neurocranium [Automatically generated definition].
Synovial joint that articulates bones of upper and lower jaw.
Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
A sphincter muscle that is part of the gastrointestinal system.
A lamina propria that is part of a large intestine.
lamina propria of mucosa of large intestine
A muscle layer that is part of a large intestine.
A muscle layer that is part of a small intestine.
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Muscles within the eye (bulbus oculi).[AAO]
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
The most anterior region of the braincase. Provides structural support for peripheral olfactory organ.
currently this is not restricted to skeletal elements, unlike UBERONREF:0000007
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
A portion of gray matter that is part of a telencephalon.
predominantly gray regional part of telencephalon
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
A lymph vasculature that is part of a head.
An anatomical cavity that is part of a esophagus.
The collection of all skeletal elements in an individual limb or fin.
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly.
A cardiovascular system that is part of a conceptus.
An anatomical space that is part of a bone of lower jaw.
An anatomical space that is part of a bone of upper jaw.
A neural nucleus that is part of the spinal cord.
Ectodermal placode that does not develop into a component of the nervous system.
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets.
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity.
A muscle layer that is part of a wall of esophagus.
In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
Masses of developing blood cells attached to endothelium in the yolk sac.
A region of the stomach that is lined with glandular epithelium.
as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus
A hepatic vein that is part of a left lobe of liver.
A hepatic vein that is part of a right lobe of liver.
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6
this is distinct (but not disjoint) from palatine bone
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
A substance that is consumed by the organism for food.
A primordium that has the potential to develop into a stomach.
A zone of skin that is part of a craniocervical region.
The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.
An artery that originates from the abdominal aorta.
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].
Epithelium that derives from the mesoderm. [Automatically generated definition].
One of five swellings formed during the development of the face.
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery.
Unclear if MA class belongs here or in parent
descending branch of the transverse cervical
A bone element that is part of a jaw region.
A muscle layer that is part of an intestine.
A layer of tissue between the muscularis and serosa.
Contains nerves, blood vessels, lymphatics and lymph nodes
respiratory system arterial smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified].
a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction
increases the surface area of a cell lining whilst minimizing increase in volume
FMA class represents an individual microvillus.
A microvillus layer that is striated and found in the intestine.
Blood-forming tissue, consisting of reticular fibers and cells.
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
An anatomical space that is enclosed by a cloaca.
the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/
The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives.
An anatomical space that is enclosed by a terminal part of digestive tract.
includes the cloacal lumen, in species where this is present
lumen of terminal part of digestive tract
An anatomical space with no opening to another space or to the exterior.
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The posterior region of the neck, including the suboccipital region.
A mucosa that is part of a cloaca [Automatically generated definition].
cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium.
A submucosa that is part of a cloaca [Automatically generated definition].
A serous membrane that is part of a cloaca [Automatically generated definition].
A muscular coat that is part of a cloaca.
A muscular coat that is part of a duodenum.
A muscular coat that is part of a colon.
A muscular coat that is part of a anal canal.
An adventitia that is part of a esophagus.
An anatomical junction that connects a stomach and connects a duodenum.
A mucosa that is part of a gastroduodenal junction.
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
The part of the venous system that drains the lungs[Kardong].
Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung.
Any vein within the general circulation that transports blood back to the right atrium of the heart.
A gland that is part of a foregut-midgut junction.
A bodily secretion that is produced by a gland of anal sac.
the anal gland secretions of species such as civet and beavers are used perfumery
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
Anatomical cavity that is the lumen of the skull and contains the brain.
A blood vessel endothelium that is part of a lung [Automatically generated definition].
A sphincter muscle that is part of a cloaca.
the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938).
A caudal vertebra endochondral element that is composed primarily of cartilage tissue.
coccygeal vertebral cartilage condensation group
A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
coccygeal vertebra pre-cartilage condensation
tail vertebral pre-cartilage condensation
caudal vertebra pre-cartilage condensation
A cervical vertebra endochondral element that is composed primarily of cartilage tissue.
cervical vertebral cartilage condensation group
A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
cervical vertebra pre-cartilage condensation
A thoracic vertebra endochondral element that is composed primarily of cartilage tissue.
thoracic vertebral cartilage condensation group
A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
thoracic vertebra pre-cartilage condensation
The anatomical space that is enclosed by a stomach.
Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].
An epithelium that is part of a intestinal villus.
Anatomical space that is an opening in a bone of the skull.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
Vascular endothelium found in colon blood vessels.
Epithelium lining the exocrine pancreas.
Musculature of the head and neck, spine, and ribs.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
Anatomical projection that is part of the integumentl system.
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
Fluid contained within the notochordal canal.
An organ component layer that is part of a integumental system.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
Embryonic structure that gives rise to the telencephalon.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
Muscle that is part of the respiratory system.
this class may be merged with 'respiratory system muscle'; check intercostals
An anatomical space that is enclosed by a sinusoid.
A sinusoidal space that is part of a hepatic sinusoid.
A part of the body present only in a specific gender.
A part of the body present only in females.
Subcutaneous adipose tissue that is located in the peritoneal cavity.
Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041].
Subcutaneous adipose tissue that is located in the abdominal region.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A ventral horn of spinal cord that is part of a thoracic spinal cord.
A gray matter of spinal cord that is part of a cervical spinal cord.
A ventral horn of spinal cord that is part of a cervical spinal cord.
A gray matter of spinal cord that is part of a thoracic spinal cord.
An epithelium that is part of a frontonasal prominence.
A unilaminar epithelium that develops_from a ectoderm and is part of a anal region.
An anatomical space that is enclosed by a pleuroperitoneal canal.
A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells.
A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular.
A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory.
A neuromere that is part of the presumptive forebrain.
A neuromere that is part of the presumptive midbrain.
A neuromere that is part of the presumptive spinal cord.
Any muscle organ that is part of a cloaca.
Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin.
Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin).
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A portion of tissue that will develop into vasculature.
One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites.
Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4].
A vertebral endochondral element in the cervical region of the vertebral column.
A vertebral endochondral element in the thoracic region of the vertebral column.
A sphenoid bone or its cartilage or pre-cartilage precursor.
consider merging into myocardial compact layer
perimysial connective tissue of subepicardium
Visceral intrapericardial fat contiguous with the myocardial surface.
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
An eye consisting of multiple light-sensing organs.
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A region of somite adjacent to presomitic mesoderm.
Epithelium located in the intersomitic region.
An anatomical group whose component structures share a common function.
A non-connected functional system that is composed primarily of a gland.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A pancreatic lobule that is in_the_left_side_of a exocrine pancreas.
A pancreatic lobule that is in_the_right_side_of a exocrine pancreas.
A basement membrane of epithelium that is part of a respiratory system.
A zone of skin that is part of a axilla.
The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery.
A hepatic artery that is part of a left lobe of liver.
ramus sinister (arteria hepatica propria)
A hepatic artery that is part of a right lobe of liver.
Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla.
An epithelium that is part of a anal canal.
A smooth muscle tissue that is part of a hypodermis.
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
smooth muscle layer in fatty layer of subcutaneous tissue
An epithelium that is part of a camera-type eye.
An epithelium that is part of a foregut.
A lamina propria that is part of a duodenum.
A hole in the diaphragm through which the esophagus passes.
Is the sensory system for the sense of hearing.
Auditory system is general anatomical term in FMA
Luminal space of the right ventricle of the heart.
An anatomical space that is part of a duodenum.
Luminal space of the left atrium of the heart.
Luminal space of the left ventricle of the heart.
Luminal space of the right atrium of the heart.
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
central nervous system gray matter layer
Mucus produced in the respiratory tract.
Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm).
An roughly circular indentation in a surface.
The dorsal region of the optic cup that gives rise to the dorsal part of the retina.
Primordium that develops into the central nervous system.
Primordium that develops into the nervous system.
Epithelium lining the distalmost portion of the digestive tract.
epithelium of terminal part of digestive tract
Any muscle tissue of the distalmost portion of the digestive tract.
muscle tissue of terminal part of digestive tract
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A muscle layer that is part of the rectum.
Any portion of smooth muscle tissue that is part of the rectum.
Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx).
A zone of skin that is part of a lower lip.
A zone of skin that is part of a upper lip.
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
A muscular coat that is part of a digestive tract.
responsible for gut movement, such as peristalsis
There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]
Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina
The anatomical space within the intestine.
see notes in inclusivity in class 'intestine'
Muscle innervated by the trigeminal nerve (Cranial Nerve V).
muscle innervated by the trigeminal nerve
muscles innervated by the trigeminal nerve
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid.
An exocrine gland that is part of a integumental system.
A portion of organism substance that is secreted by a reproductive gland.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
Serous membrane layer that is adjacent to and lines an organ.
Serous membrane layer that lines to a body cavity.
A specific region of the foregut into the area in which the lung will develop.
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
spinal cord lateral wall ventricular layer
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa.
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
The area of axial mesoderm that develops into the prechordal plate.
Endocardium that is part of the left atrium.
Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts.
Any organ component layer that consists of smooth muscle tissue.
organ region with floating fiat boundary
Any gaseous product of an excretory process.
Any excreted gas that is produced by the digestive tract.
In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum
Any portion of gas located in a part of the respiratory system.
Mesenchyme that is part of a developing jaw [Automatically generated definition].
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
Any of several arteries that arise from the aorta and supply blood to the esophagus.
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
Any chamber of the left side of the heart.
Any chamber of the right side of the heart.
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
The primordial mouth region of the developing head.
A muscle layer that is part of the sigmoid colon.
The sum of epicardial and paracardial fat deposits.
Fat deposits in the mediastinum outside the parietal pericardium .
Any fat deposit surrounding a visceral organ.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity.
A sweet viscid material elaborated out of the nectar of flowers in the honey sac of various bees.
A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract.
respiratory primordium associated mesenchyme
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
An anatomical junction that is between the sigmoid colon and rectum.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
Any gland that is part os the respiratory system.
A notochord that has persisted beyond the embryonic stage.
The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit.
ramus zygomaticotemporalis (Nervus zygomaticus)
ramus zygomaticotemporalis nervus zygomatici
zygomaticotemporal branch of zygomatic nerve
Wall of ventricle which is continuous with the wall of aorta.
Wall of ventricle which is continuous with the wall of pulmonary trunk.
Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle.
myocardium of anterior wall of left ventricle
myocardium of anterior wall of right ventricle
A mucosa that is part of a lip region [Automatically generated definition].
vasculature of central nervous system plus retina
Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees.
An artery that supplies oxygenated blood to the cystic duct.
Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament.
Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament.
A zone of skin that is part of the face.
An anatomical junction between two parts of the digestive tract.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Cartilage which is part of the axial skeleton.
Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse.
the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences
Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA].
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
Dermal, epidermal, glandular and pigment structures of the external head integument.
Dermal, epidermal, glandular and pigment structures of the body integument.
Dermal, epidermal, glandular and pigment structures of the tail integument.
Anatomical projection that is composed of bone or cartilage tissue.
An anatomical surface that is part of a bone.
Any sense organ that is part of some larva.
Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727).
Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730).
Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730).
insect embryonic/larval head sense organ
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles.
Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact.
Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson.
A venule that is located in the anorectum.
An arteriole that is located in the anorectum.
The anatomical junction between the descending colon and the sigmoid colon.
A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery.
A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery.
An anatomical junction between two parts of the intestine.
A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus.
The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum.
A capillary that is part of the anorectum.
A capillary that is part of a small intestine.
blood vessel capillary of small intestine
A submucosal gland found in a respiratory tract.
Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.
Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin).
An anatomical system that eliminates waste products that arise as a result of metabolic activity.
A portion of smooth muscle tissue that is part of the thoracic aorta.
A zone of skin that is above the clavicle zone in the pectoral girdle region.
A zone of skin that is part of the external genitalia.
A muscle tissue that is associated with soft internal organs (viscera).
It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated.
A striated muscle tissue that is associated with soft internal organs (viscera).
A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium.
A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface.
A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung.
A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa.
phenotype
Western Australian Mulga Shrublands Ecoregion
Australasia Ecoregion
Southern central Australia Ecoregion
Simpson Desert Region
Pilbara Shrublands Ecoregion
Carnarvon Xeric Shrublands Ecoregion
Central Ranges Xeric Shrub Ecoregion
Gibson Desert Ecoregion
The Great Sandy-Tanami Desert Ecoregion
Great Victoria Desert Ecoregion
Nullarbor Plains Xeric Shrubland Ecoregion
Afrotropical Ecoregion
Southern Africa: Southern Namibia into South Africa
Succulent Karoo Ecoregion
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
Islands east of the Horn of Africa and south of Yemen Ecoregion
Socotran Archipelago Ecoregion
Red Sea Coastal Desert Ecoregion
Namibian Savanna Woodland Ecoregion
Namib Desert Ecoregion
Nama Karoo Ecoregion
Masai Xeric Grasslands and Shrublands Ecoregion
Madagascar Succulent Woodlands Ecoregion
Madagascar Spiny Thickets Ecoregion
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
Kalahari Xeric Savanna Ecoregion
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
Hobyo Grassland and Shrubland Ecoregion
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
Ethiopian Xeric Grasslands and Shrublands Ecoregion
Eritrean Coastal Desert Ecoregion
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
Aldabra Island Xeric Scrub Ecoregion
Indo-Malay Ecoregion
Southern Asia: Western India into Pakistan
Thar Desert
Southern Asia: Eastern India and western Pakistan
Northwestern Thorn Scrub Forests
A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
Arctic front
A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
Antarctic front
Solar radiation
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)
relation has no temporal argument
researcher, metadata, diseases, University of Maryland
third planet from the Sun in the Solar System
Earth
"Suni, or Jalca, is one of the eight Natural Regions of Peru. It is located in the Andes at an altitude between 3,500 and 4,000 metres above sea level. Suni has a dry and cold weather and there are many glacial valleys. The flora includes gramineous plants and shrubs such as the taya-taya (Caesalpinia spinosa), the quishuar (Buddleja coriacea), and the cantuta (Cantua buxifolia) which was considered sacred by the Incas. Even though it is hard for plants to grow because of the weather, people are able to cultivate such crops as quinoa, qañiwa, broad beans and ulluku (Ullucus tuberosus). The main fauna is the guinea pig and, among numerous other highland birds, the Chiguanco thrush."
Suni
Sol
World Ocean
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
may be present in other parts in other species
conservatively place at deuterostome, excluding acoelomates
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
This can't be added as a property chain because it causes a circularity violation for 'part of'.
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).