RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
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.
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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
alternative term
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.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
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
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Title
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
An alternative label for a given entity such as a commonly used abbreviation or synonym.
has exact 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)
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
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/
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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
has realization
b has realization c =Def c realizes b
As for realizes
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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
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])
(Elucidation) realizes is a relation between a process b and realizable entity c such that c inheres in some d & for all t, if b has participant d then c exists & the type instantiated by b is correlated with the type instantiated by c
A balding process realizes a disposition to go bald; a studying process realizes a student role; a process of pumping blood realizes the pumping function of a heart
participates in
(Elucidation) participates in holds between some b that is either a specifically dependent continuant or generically dependent continuant or independent continuant that is not a spatial region & some process p such that b participates in p some way
Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <https://github.com/BFO-ontology/BFO-2020/tree/master/src/owl/profiles/temporal%20extensions>
has participant
p has participant c =Def c participates in p
preceded by
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
b preceded by c =Def b precedes c
The temporal region occupied by the second half of the match is preceded by the temporal region occupied by the first half of the match
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.
(Elucidation) precedes is a relation between occurrents o, o' such that if t is the temporal extent of o & t' is the temporal extent of o' then either the last instant of o is before the first instant of o' or the last instant of o is the first instant of o' & neither o nor o' are temporal instants
The temporal region occupied by Mary's birth precedes the temporal region occupied by Mary's death.
Each temporal region is its own temporal extent. The temporal extent of a spatiotemporal region is the temporal region it temporally projects onto. The temporal extent of a process or process boundary that occupies temporal region t is t.
Precedes defines a strict partial order on occurrents.
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
b occurs in c =Def b is a process or a process boundary & c is a material entity or site & there exists a spatiotemporal region r & b occupies spatiotemporal region r & for all time 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 occupies spatial region s' at t & s is a continuant part of s' at t
A process of digestion occurs in the interior of an organism; a process of loading artillery rounds into a tank cannon occurs in the interior of the tank
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
environs
b environs c =Def c occurs in b
Mouth environs process of mastication; city environs traffic
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 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 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.
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 relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes
Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.
has measurement unit label
is about
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
The inverse property of is specified input of
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
has specified input
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Alan Ruttenberg
is specified input of
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
The inverse property of is specified output of
The inverse property of is_specified_output_of
has specified output
is_specified_output_of
is specified output of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
A relation between an information content entity and a value specification that specifies its value.
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
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.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
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 relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
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
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
Participates in is a primitive instance-level relation between a continuant and a process in which it participates. For example a scanner participates in a scanning process at some specific time.
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
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)
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the A 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.
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 or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
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.
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes 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
has function
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
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
has role
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
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
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
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
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
innervated_by
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 '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 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 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.
Primitive instance level timing relation between events
before or simultaneous with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
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
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
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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 an anatomical structure 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
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.
Chris Mungall
<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 overlaps B if they share some part in common.
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
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.
David Osumi-Sutherland
<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
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.
life cycle stage of
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.
For use in recording has_part with a cardinality constraint.
placeholder relation to indicate normality/abnormality.
has component
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
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
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
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.
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
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
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
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
capable of
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)".
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.
temporal relation
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
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 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.
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 at the beginning of p.
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
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 anatomical structure 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
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
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
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).
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure 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
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.
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
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.
q inheres in 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
Because part_of is transitive, inheres in is a sub-relation of inheres in 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
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
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
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.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
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
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
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 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
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
Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component
has member is a mereological relation between a collection and an item.
input of
output of
formed as result of
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
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
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
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
This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.
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
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
This relation groups causal relations between material entities and causal relations between processes
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.
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 if and only if p precedes q and p and q are linked in a causal chain
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 both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
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 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
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
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 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 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
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)
'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.
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.
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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
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.
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
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.
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.
molecular interaction relation helper property
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 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
Process(P1) directly regulates process(P2) 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.
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
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 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 organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
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.
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 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
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.
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.
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 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.
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
results in fusion of
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
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'.
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.
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 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.
This property only applies to anatomical entities.
p has anatomical participant c iff p has participant c, and c is an anatomical entity
results in changes to anatomical or cellular structure
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 relation that holds between a polymer and its constituent monomers. P has_constituent_monomer c if and only if P has_component multiple instances of c and each instance of c is covalently attached to another instance of c.
The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows one to indicate the number of instances of c.
See document https://docs.google.com/document/d/15iVMtMyYbQSlvUDgn2XUaDzpwkB0USZI for full definition.
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 is a conduit for y iff y passes through the lumen of x.
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
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
is subject of
A primitive relationship between an instance of an Entity and an instance of an Information Content Entity.
A primitive relationship between an Information Content Entity and some Entity.
designated by
x designated_by y iff y is an instance of Information Content Entity and x is an instance of Entity, such that given some context, y uniquely distinguishes x from other entities.
designates
x designates y iff x is an instance of an Information Content Entity, and y is an instance of an Entity, such that given some context, x uniquely distinguishes y from other entities.
a URL designates the location of a Web Page on the internet
a vehicle identification number designates some vehicle
Given a stronger temporal interpretation, this property may be functional. For more info please refer to https://github.com/BFO-ontology/BFO-2020/tree/master/src/owl/temporal%20extensions.
Number of protons in an atomic nucleus
has atomic number
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
A planned process resulting in a software product involving the creation of source code.
software development
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
entity
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])
(Elucidation) An entity is anything that exists or has existed or will exist
Julius Caesar; the Second World War; your body mass index; Verdi's Requiem
continuant
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]
(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity
A human being; a tennis ball; a cave; a region of space; someone's temperature
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
(Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region
As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant.
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
b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c
An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra
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
(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time
As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region
temporal region
(Elucidation) A temporal region is an occurrent over which processes can unfold
As for zero-dimensional temporal region and one-dimensional temporal region
spatiotemporal region
(Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime
The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite
'Spacetime' here refers to the maximal instance of the universal 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.
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
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]
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
process
event
(Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant
An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer
For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
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 endocitosis and exocitosis
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
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 [89
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]
A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
disposition
internally-grounded realizable entity
(Elucidation) A disposition b is a realizable entity such that if b 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
An atom of element X has the disposition to decay to an atom of element Y; the cell wall is disposed to transport cellular material through endocytosis and exocytosis; certain people have a predisposition to colon cancer; children are innately disposed to categorize objects in certain ways
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 entity
(Elucidation) A realizable entity is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region & which is of a type some instances of which are realized in processes of a correlated type
The role of being a doctor; the role of this boundary to delineate where Utah and Colorado meet; the function of your reproductive organs; the disposition of your blood to coagulate; the disposition of this piece of metal to conduct electricity
quality
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 an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
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]
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
(Elucidation) 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
The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold
specifically dependent continuant
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.
An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white.
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 (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(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]
A continuant [snap: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 specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c
(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates
(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole
For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
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.
A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
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])
b is a role means: b is a realizable entity and 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 and 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]
A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
role
externally-grounded realizable entity
(Elucidation) A role b is a realizable entity such that 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
The priest role; the student role; the role of subject in a clinical trial; the role of a stone in marking a property boundary; the role of a boundary to demarcate two neighbouring administrative territories; the role of a building in serving as a military target
fiat object
fiat object part
(Elucidation) A fiat object part b is a material entity & such that if b exists then it is continuant part of some object c & demarcated from the remainder of c by one or more fiat surfaces
The upper and lower lobes of the left lung; the dorsal and ventral surfaces of the body; the Western hemisphere of the Earth; the FMA:regional parts of an intact human body
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit
The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank
'Exactly' means that there are no parts of the object aggregate other than its member parts.
The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts.
site
(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity
A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist
object
(Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested
An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube
A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide
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
g-dependent continuant
(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share
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; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint
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
(Elucidation) A function is a disposition that exists in virtue of its bearer's physical make-up & 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 artefacts) in order to realize processes of a certain sort
The function of a hammer to drive in nails; the function of a heart pacemaker to regulate the beating of a heart through electricity
process boundary
p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts
The boundary between the 2nd and 3rd year of your life
material entity
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
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
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.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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]
An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part
A human being; the undetached arm of a human being; an aggregate of human beings
continuant fiat boundary
(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity
As for fiat point, fiat line, fiat surface
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
b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part
As for fiat point, fiat line, fiat surface, site
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
(Elucidation) A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by the material part of a material entity
The life of an organism from the beginning to the end of its existence
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.
anatomical entity
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
connected anatomical structure
material anatomical entity
multi-cell-part structure
neuron projection bundle
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
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.
An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included.
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.
The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).
A trace radioisotope of argon with atomic mass of 38.964313 and a half-life of 269 years.
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
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 minor stable isotope of calcium with relative atomic mass 42.95877 and 0.135 atom percent natural abundance.
A stable isotope of molybdenum with relative atomic mass 97.90541, 24.29 atom percent natural abundance and nuclear spin 0.
A major stable isotope of strontium with relative atomic mass 87.90561 and 82.58 atom percent natural abundance.
A stable isotope of rubidium with relative atomic mass 84.91179, 72.17 atom percent natural abundance and nuclear spin 5/2.
A stable isotope of selenium with relative atomic mass 81.91670, 8.82 atom percent natural abundance and nuclear spin 0.
A stable isotope of zinc with relative atomic mass 65.92603, 27.7 atom percent natural abundance and nuclear spin 0.
A stable isotope of nickel with relative atomic mass 59.93079, 26.223 atom percent natural abundance and nuclear spin 0.
A stable isotope of cobalt with relative atomic mass 58.93319, 100 atom percent natural abundance and nuclear spin 7/2.
A stable isotope of manganese with relative atomic mass 54.93804, 100 atom percent natural abundance and nuclear spin 5/2.
A stable isotope of arsenic with relative atomic mass 74.921596, 100 atom percent natural abundance and nuclear spin 3/2.
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.
A carbon group element atom with a symbol Fl and atomic number 114.
A boron group element atom with a symbol Nh and atomic number 113.
A pnictogen atom with a symbol Mc and atomic number 115.
A chalcogen atom with a symbol Lv and atomic number 116.
A halogen atom with a symbol Ts and atomic number 117.
A p-block element atom with a symbol Og and atomic number 118.
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).
Any compound that produces a peak used as reference frequency in the delta chemical shift scale.
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.
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
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.
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 cobalt group element atom that has atomic number 27.
A chromium group element atom that has atomic number 24.
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.
Chemical element (nickel group element atom) with atomic number 28.
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.
The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek pirhoomegatauomicronsigma, first).
The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
The radioactive isotope of hydrogen with relative atomic mass 3.016049 and half-life of 12.33 years (from Greek taurhoiotatauomicronsigma, third).
A divalent inorganic anion resulting from the removal of two protons from ammonia.
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.
The stable isotope of helium with relative atomic mass 3.016029. The least abundant (0.000137 atom percent) isotope of naturally occurring helium.
The stable isotope of helium with relative atomic mass 4.002603. The most abundant (99.99 atom percent) isotope of naturally occurring helium.
Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.
A metallic element first identified and named from the brilliant indigo (Latin indicum) blue line in its flame spectrum.
A metallic element first identified and named from the brilliant green line in its flame spectrum (from Greek thetaalphalambdalambdaomicronsigma, a green shoot).
Alkaline earth metal atom with atomic number 4.
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.
Some people may be uncomfortable calling every proton an atomic nucleus
This is equivalent to CHEBI:33252
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 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.
A radioactive metallic element discovered in 1898 by Marie Sklodowska Curie and named after her home country, Poland (Latin Polonia).
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
A cobalt group element atom of atomic number 45.
Chemical element (nickel group element atom) with atomic number 46.
A copper group element atom with atomic number 111. The the ninth member of the 6d series of transition metals, it is an extremely radioactive, synthetic element. Average mass is around 281.
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 zinc group element atom with a symbol Cn and atomic number 112. All its isotopes are intensely radioactive. Prior to its discovery, it had the placeholder name ununbium (in accordance with IUPAC recommendations). Following its discovery (in Darmstadt, 1996) and subsequent confirmation, the name copernicium was adopted in 2010.
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.
A main group molecular entity containing one or more atoms of any noble gas.
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.
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 amino-acid residue derived from an alpha-amino acid.
The stable isotope of oxygen with relative atomic mass 17.999160 and 0.205 atom percent natural abundance.
The stable isotope of oxygen with relative atomic mass 15.994914. The most abundant (99.76 atom percent) isotope of naturally occurring oxygen.
The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen.
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.
polymer
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 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).
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.
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.
An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Note also that the definition 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 PR:000064867 ("protein-containing molecular entity"). 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 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 hadron with zero or integer spin; a strongly interacting boson. The term is derived from the Greek muepsilonsigmaomicronsigma (medium, middle).
A nucleus or any of its constituents in any of their energy states.
The collective name for zero-spin mesons pi(+), pi(-) and pi(0).
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
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.
The radioactive isotope of oxygen with relative atomic mass 15.003065. The longest-lived oxygen radionuclide with half-life of 122.2 s.
The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen.
The radioactive isotope of nitrogen with relative atomic mass 13.0057386. The longest-lived nitrogen radionuclide with half-life of 9.965 min.
The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen.
The radioactive isotope of fluorine with relative atomic mass 18.000938. The longest-lived fluorine radionuclide with half-life of 109.77 min.
The stable isotope of fluorine with relative atomic mass 18.998403 and nuclear spin (1)/2.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
The radioactive isotope of helium with relative atomic mass 6.01889 and half-life of 806.7 ms.
The radioactive isotope of helium with relative atomic mass 8.03392 and half-life of 119.0 ms.
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'.
The radioactive isotope of polonium with relative atomic mass 209.98286 and half-life of 138.376 days; the only naturally occurring isotope of polonium.
The radioactive isotope of polonium with relative atomic mass 210.986637 and half-life of 0.516 s.
The radioactive isotope of polonium with relative atomic mass 211.988852 and half-life of 0.299 mus.
The radioactive isotope of polonium with relative atomic mass 212.9928425 and half-life of 4.2 mus.
The radioactive isotope of polonium with relative atomic mass 213.995186 and half-life of 164.3 mus.
The radioactive isotope of polonium with relative atomic mass 214.999415 and half-life of 1.781 ms.
The radioactive isotope of polonium with relative atomic mass 216.001905 and half-life of 0.145 s.
The radioactive isotope of polonium with relative atomic mass 217.006253 and half-life of < 10 s.
The radioactive isotope of polonium with relative atomic mass 218.008966 and half-life of 3.10 min.
The radioactive isotope of polonium with relative atomic mass 202.981413 and half-life of 36.7 min.
The radioactive isotope of polonium with relative atomic mass 204.981165 and half-life of 1.66 h.
The radioactive isotope of polonium with relative atomic mass 205.98047 and half-life of 8.8 days.
The radioactive isotope of polonium with relative atomic mass 206.981578 and half-life of 5.80 h.
The radioactive isotope of polonium with relative atomic mass 207.98123 and half-life of 2.898 years.
The radioactive isotope of polonium with relative atomic mass 208.982404 and half-life of 102 years.
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.
The stable isotope of thallium with relative atomic mass 202.9723. The least abundant (29.524 atom percent) isotope of naturally occurring thallium.
The stable isotope of thallium with relative atomic mass 204.9744. The most abundant (70.476 atom percent) isotope of naturally occurring thallium.
The radioactive isotope of thallium with relative atomic mass 200.9708 and half-life of 72.912 hours.
The radioactive isotope of thallium with relative atomic mass 198.9698 and half-life of 7.42 hours.
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.
The stable isotope of aluminium with relative atomic mass 26.98153 and nuclear spin (5)/2.
The radioactive isotope of aluminium with relative atomic mass 25.986892 and half-life of 717,000 years.
The radioactive isotope of aluminium with relative atomic mass 27.981910 and half-life of 2.25 min.
The stable isotope of phosphorus with relative atomic mass 30.973762 and nuclear spin (1)/2.
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
The stable isotope of silicon with relative atomic mass 28.9764947, 4.683 atom percent natural abundancy, and nuclear spin (1)/2.
The stable isotope of silicon with relative atomic mass 27.9769265. The most abundant (92.23 atom percent) isotope of naturally occurring silicon.
The stable isotope of silicon with relative atomic mass 29.9737702. The least abundant (3.09 atom percent) isotope of naturally occurring silicon.
The radioactive isotope of silicon with relative atomic mass 30.975363, half-life of 2.62 hours and nuclear spin (3)/2.
The radioactive isotope of silicon with relative atomic mass 31.974148. The longest-lived silicon radionuclide with half-life of 172 years.
The stable isotope of sulfur with relative atomic mass 31.972071. The most abundant (95.02 atom percent) isotope of naturally occurring sulfur.
The stable isotope of sulfur with relative atomic mass 32.9714585, 0.75 atom percent natural abundance, and nuclear spin (3)/2.
The stable isotope of sulfur with relative atomic mass 33.9678668 and 4.21 atom percent natural abundance.
The stable isotope of sulfur with relative atomic mass 35.9670809. The least abundant (0.02 atom percent) isotope of naturally occurring sulfur.
The radioactive isotope of sulfur with relative atomic mass 34.9690322 and nuclear spin (3)/2. The longest-lived sulfur radionuclide with half-life of 87.5 days.
The radioactive isotope of sulfur with relative atomic mass 36.9711257 and half-life of 5.05 min.
The radioactive isotope of sulfur with relative atomic mass 37.97116 and half-life of 170.3 min.
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 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 steroid substituted by at least one carboxy group.
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 metallic element predicted as eka-aluminium by Mendeleev in 1870 and discovered by Paul-Emile Lecoq de Boisbaudran in 1875. Named in honour of France (Latin Gallia) and perhaps also from the Latin gallus cock, a translation of Lecoq.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
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.
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.
The stable isotope of tin with relative atomic mass 118.903311, 8.59 atom percent natural abundance and nuclear spin (1)/2.
The stable isotope of tin with relative atomic mass 119.902199 and 32.58 atom percent natural abundance.
The stable isotope of tin with relative atomic mass 117.901609 and 24.22 atom percent natural abundance.
The stable isotope of tin with relative atomic mass 115.901747 and 14.54 atom percent natural abundance.
The stable isotope of tin with relative atomic mass 116.902956, 7.68 atom percent natural abundance and nuclear spin (1)/2.
The stable isotope of tin with relative atomic mass 114.903348, 0.34 atom percent natural abundance and nuclear spin (1)/2.
The stable isotope of boron with relative atomic mass 11.009306, 80.1 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of tellurium with relative atomic mass 124.904425, 71.4 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of xenon with relative atomic mass 128.904780, 26.4 atom percent natural abundance and nuclear spin 1/2.
A stable isotope of selenium with relative atomic mass 76.919915, 7.60 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of lithium with relative atomic mass 7.016004, 92.5 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of rubidium with relative atomic mass 86.909184, 27.9 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of niobium with relative atomic mass 92.906378, 100 atom percent natural abundance and nuclear spin 9/2.
The stable isotope of niobium with relative atomic mass 182.950225, 14.3 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of cadmium with relative atomic mass 110.904182, 12.8 atom percent natural abundance and nuclear spin 1/2.
The isotope of cadmium with relative atomic mass 112.904401, 12.2 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of lithium with relative atomic mass 6.015122, 7.5 atom percent natural abundance and nuclear spin 1.
The stable isotope of yttrium with relative atomic mass 88.905848, 100 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of iron with relative atomic mass 56.935399, 2.1 atom percent natural abundance and nuclear spin 1/2.
The stable isotope of antimony with relative atomic mass 120.903818, 57.2 atom percent natural abundance and nuclear spin 5/2.
The stable isotope of antimony with relative atomic mass 122.904216, 42.8 atom percent natural abundance and nuclear spin 7/2.
The stable isotope of lanthanum with relative atomic mass 138.906348, 99.9 atom percent natural abundance and nuclear spin 7/2.
The stable isotope of iodine with relative atomic mass 126.904468, 100 atom percent natural abundance and nuclear spin 5/2.
The stable isotope of potassium with relative atomic mass 38.963707, 93.3 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of molybdenum with relative atomic mass 94.905842, 15.9 atom percent natural abundance and nuclear spin 5/2.
The stable isotope of sodium with relative atomic mass 22.989770, 100 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of scandium with relative atomic mass 44.955910, 100 atom percent natural abundance and nuclear spin 7/2.
The isotope of iodine with relative atomic mass 128.904988, and nuclear spin 7/2.
The stable isotope of europium with relative atomic mass 150.919846, 47.8 atom percent natural abundance and nuclear spin 5/2.
The stable isotope of bromine with relative atomic mass 78.918338, 50.69 atom percent natural abundance and nuclear spin 3/2.
The stable isotope of germanium with relative atomic mass 72.923459, 7.73 atom percent natural abundance and nuclear spin 9/2.
The stable isotope of magnesium with relative atomic mass 24.985837, 10.0 atom percent natural abundance and nuclear spin 5/2.
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.
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.
Any metal that is characterized by its rather high atomic mass and density. Although typically occurring in low concentrations, they can be found all throughout the Earth's crust (Commonly, a density of at least 5 g cm(3) is used to define a heavy metal and to differentiate it from other, ''light'' metals).
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.
An amino-acid residue protonated on nitrogen.
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.
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.
A group that carries an overall positive charge.
A group that carries an overall negative charge.
An amino-acid residue carrying an overall negative charge.
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.
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.
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
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.
A stable isotope of boron with relative atomic mass 10.0129370, 19.9 atom percent natural abundance and nuclear spin 3+.
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.
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.
A zinc atom in which the nucleus contains 35 neutrons. It has a half-life of 244 days, decaying by emission of a positron (beta(+) decay), and is the most abundant and stable of the 25 known radioisotopes of zinc.
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.
Any metal which causes the onset of an allergic reaction.
An information content entity that is output by an assay.
A piece of apparatus that is used to measure a physical quantity.
Measurement of the dose of a substance taken up by an object.
A sensor that is used to measure the dose of a substance taken by up an object.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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.
CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
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).
cell
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
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.
Female germ cell is a germ cell that supports female gamete production.
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.
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 that specializes in secretion of surfactant in the alveoli of the lung.
Epithelial progenitor cell of the lung. Club cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Club cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium.
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.
An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals.
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 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.
Any cell that has characteristic some binucleate.
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.
An epithelial cell found in the trachea.
This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell'
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 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.
A cell that initiates an electrical signal and passes that signal to another cell.
A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
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.
neuron
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 giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
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 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.
A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree.
ciliated columnar cell of tracheobronchial tree
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).
An epithelial cell of the tracheobronchial tree.
epithelial cell of tracheobronchial tree
An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells.
undifferentiated columnar cell of tracheobronchial tree
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.
Connective tissue cells of the endometrium, these cells are fibroblastic in appearance. During decidualization they tranform into decidual (stromal) cells, swellling up and adopt an epithelial cell-like appearance due to the accumulation of glycogen and lipid droplets.
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.
A fat cell 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 hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells.
A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell 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 keratin sulfate.
An endo-epithelial cell of the respiratory tract.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
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
A fat cell 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
A mesenchymal stem cell of the chorionic membrane.
chorionic membrane mesenchymal stem cell
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 glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function.
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 endometrium.
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 ciliated epithelial cell with many cilium.
MCC
multi-ciliated cell
multiciliated cell
multiciliated epithelial cell
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.
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 epithelial cell that is part of an endometrial gland.
An endothelial cell that is part of a placenta.
A smooth muscle cell that is part of a placenta.
An endothelial cell that is part of a hepatic portal vein.
An endothelial cell that is part of a uterus.
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.
Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
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 nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
Any serous secreting cell that is part of the tracheobronchial epithelium.
tracheobronchial serous cell
Any chondrocyte that is part of the tracheobronchial tree.
tracheobronchial chondrocyte
A smooth muscle cell that is part of any blood vessel.
blood vessel smooth muscle cell
A smooth muscle cell that is part of the tracheobronchial tree.
smooth muscle cell of tracheobronchial tree
tracheobronchial 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 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 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
A fat cell that is part of the epicardial fat.
A fat cell that is part of the epicardial fat of right ventricle.
adipocyte of epicardial fat of right ventricle
A fat cell that is part of the epicardial fat of left ventricle.
adipocyte of epicardial fat of left ventricle
A serous secreting cell that is part of the epithelium of trachea.
A serous secreting cell that is part of the epithelium of bronchus.
A serous secreting cell that is part of the epithelium of terminal bronchiole.
serous cell of epithelium of terminal bronchiole
A serous secreting cell that is part of the epithelium of bronchiole.
serous cell of epithelium of lobular bronchiole
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 oviduct epithelium. Example: peg cells, ciliated cells.
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.
A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua.
Any mesenchymal stem cell that is part of a placenta.
placental amniotic mesenchymal stromal cell
Any capillary endothelial cell that is part of a placenta.
placental villus capillary endothelial cell
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
Any microvascular endothelial cell that is part of a endometrial blood vessel.
endometrial microvascular endothelial cell
Any fibroblast of lung that is part of a bronchus.
A ciliated epithelial cell of the esophagus.
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 material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
This atom is closely related to ChEBI's atom, but not exactly equivalent to.
atom
A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.
This molecular entity is different than ChEBI's 'molecular entity'.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
We would like to have cardinality restrictions on the logic, but there are some technical limitations.
molecule
A part of a multicellular organism that is a collection of cell components that are not all contained in one cell.
gross anatomical part
A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
Includes virus - we will later have a class for cellular organisms.
organism
A material entity processed by human activity with an intent to produce it.
In the COB 2024 workshop there was much disagreement about this label.
processed material entity
completely executed planned process
A complex of two or more molecular entities that are not covalently bound.
A complex of two or more molecules that are not covalently bound.
complex of molecules
A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.
planned process
A planned process that intends to output material entities from input material entities
material processing
A processed material entity which is designed to be capable of a process.
device
A respiratory system disease which involves the lower respiratory tract.
A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle.
Cardiomyopathies
MESH:D009202 added from NeuroDevNet [WAK].
A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney.
An infratentorial cancer that is located_in the lower part of the brain and is a type of primitive neuroectodermal tumor.
CNS PNET
CPNET
brain medulloblastoma
infratentorial primitive neuroectodermal tumor
localized primitive neuroectodermal tumor
A disease of mental health that occur during a child's developmental period between birth and age 18 resulting in retarding of the child's psychological or physical development.
A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs.
lymphoid cancer
A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer.
A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize.
An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction.
A cardiovascular system disease that involves the heart's electrical conduction system.
heart rhythm disease
A prostate cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
cancer of prostate
carcinoma of prostate
A leukemia that has_material_basis_in a B-cell or T-cell lineage involving primarily the bone marrow and the peripheral blood.
lymphoblastic leukaemia
lymphoblastic leukemia
lymphocytic leukaemia
A lymphocytic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood.
B-cell chronic lymphocytic leukaemia
B-cell chronic lymphocytic leukemia
CLL
chronic lymphatic leukaemia
chronic lymphatic leukemia
chronic lymphocytic leukaemia
lymphoplasmacytic leukaemia
lymphoplasmacytic leukemia
B-cell chronic lymphoid leukemia
A gastrointestinal system cancer that is located_in the stomach.
gastric cancer
gastric neoplasm
A tauopathy that is characterized by memory lapses, confusion, emotional instability and progressive loss of mental ability and results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques containing beta-amyloid.
Alzheimer disease
Alzheimers dementia
Xref MGI. OMIM mapping confirmed by DO. [SN].
An urinary system cancer that results_in malignant growth located_in the urinary bladder.
bladder cancer
tumor of the bladder
A cell type cancer that has_material_basis_in abnormally proliferating cells derives from embryonic mesoderm.
connective and soft tissue neoplasm
tumor of soft tissue and skeleton
A cardiovascular system disease that involves the heart.
A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage.
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding.
postpartum coagulation defect
postpartum coagulation defect with delivery
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
disease of subdivision of hemolymphoid system
A cognitive disorder resulting from a loss of brain function affecting memory, thinking, language, judgement and behavior.
A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.
BT - Brain tumour
adult brain tumor
adult malignant brain neoplasm
brain neoplasm
brain neoplasm, adult
malignant brain tumour
malignant primary brain neoplasm
malignant primary brain tumor
malignant tumor of Brain
malignant tumor of adult brain
neoplasm of brain
primary brain neoplasm
primary brain tumor
primary malignant neoplasm of brain
tumor of the Brain
A brain disease that is characterized by loss of structure or function of neurons, including death of neurons and loss of brain tissue.
Brain degeneration
A disease that is characterized by abnormally rapid cell division.
cell process disease
neoplasm
A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture.
A disease of mental health that involve long-term patterns of thoughts and behaviors that cause serious problems with relationships and work.
character disorder
A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism.
disorder of pleura
non-neoplastic pleural disease
A disease of mental health that affects cognitive functions including memory processing, perception and problem solving.
cognitive disease
Organic Mental disorder
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
A thoracic cancer that originates in the mammary gland.
breast tumor
malignant neoplasm of breast
malignant tumor of the breast
mammary cancer
mammary tumor
primary breast cancer
mammary neoplasm
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
malignant neoplasm
malignant tumor
primary cancer
A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart.
vascular tissue disease
A pericardium disease that is characterized by an inflammation of the pericardium and has_symptom chest pain.
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye.
Naevocarcinoma
malignant melanoma
A cognitive disorder that involves an excessive, irrational dread of everyday situations.
anxiety
anxiety state
A female reproductive organ cancer that is located_in the ovary.
malignant Ovarian tumor
malignant tumour of ovary
ovarian neoplasm
ovary neoplasm
primary ovarian cancer
tumor of the Ovary
A cognitive disorder that involves abnormal thinking and perceptions resulting in a disconnection with reality.
mental or behavioural disorder
Basal cell cancer
Basal cell carcinoma of skin
Basal cell neoplasm
Basal cell tumor
Epithelioma basal cell
Rodent ulcer
malignant Basal cell neoplasm
malignant basal cell tumor
An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
Hematologic malignancy
Hematologic neoplasm
Hematological tumors
blood cancer
hematopoietic and lymphoid system tumor
hematopoietic cancer
hematopoietic neoplasm
hematopoietic tumors
malignant hematopoietic neoplasm
A brain disease that is characterized by damage to brain substance located_in cerebellum; has_symptom ataxia, has_symptom dysarthria, and has_symptom cerebellar cognitive affective syndrome.
A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
A nephritis that causes inflammation of the glomeruli located_in kidney.
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from germ cells.
malignant tumor of the germ cell
germ cell neoplasm
germ cell tumour
A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning.
An obstructive lung disease that is characterized by irreversible airflow obstruction due to chronic bronchitis, emphysema, and/or small airways disease.
COLD
COPD
chronic obstructive airway disease
chronic obstructive lung disease
An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles.
CHD
Coronary disease
coronary arteriosclerosis
coronary heart disease
A skin cancer that is located_in tissues of the skin and develops from epithelial cells.
carcinoma of skin
A hepatobiliary system cancer that is located_in the liver.
Ca liver - primary
Resectable malignant neoplasm of Liver
ca liver - primary
hepatic cancer
hepatic neoplasm
malignant hepato-biliary neoplasm
malignant neoplasm of liver
malignant neoplasm of liver, not specified as primary or secondary
malignant neoplasm of liver, primary
malignant tumor of liver
neoplasm of liver
non-resectable primary hepatic malignant neoplasm
primary liver cancer
primary malignant neoplasm of Liver
primary malignant neoplasm of liver
resectable malignant neoplasm of the liver
An integumentary system disease that is located_in skin.
Genodermatosis
skin and subcutaneous tissue disease
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A gastrointestinal system disease that is located_in the mouth.
A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right).
Valvular heart disease
disorder of liver
hepatic disorder
A disease of mental health that involves physical symptoms suggesting a physical illness where the biological or medical cause of the symptoms is indeterminate.
physiological malfunction arising from mental factor
psychophysiologic disorder
psychosomatic disorder
bone marrow disorder
A gastrointestinal system cancer that is located_in the esophagus.
Ca lower third oesophagus
Ca middle third oesophagus
esophagus cancer
malignant neoplasm of distal third of esophagus
malignant neoplasm of lower third of oesophagus
malignant neoplasm of middle third of oesophagus
malignant neoplasm of proximal third of esophagus
malignant neoplasm of upper third esophagus
malignant tumor of Distal Third of esophagus
malignant tumor of Proximal Third of esophagus
malignant tumor of abdominal esophagus
malignant tumor of the middle Third of the esophagus
A disease of mental health that involves disruption of sleep patterns.
Non-organic sleep disorder
A intestinal disease located in the colon.
colon disorder
A urinary system disease that is located_in the kidney.
nephropathy
An eye and adnexa disease that is located_in the eye.
A sarcoma and hematologic cancer that derives_from follicular lymphoma.
histiocytic and dendritic cell
Corneal tumor
malignant Corneal tumor
malignant neoplasm of cornea
malignant tumor of cornea
neoplasm of cornea
A disease that has_material_basis_in genetic variations in the human genome.
A cell type benign neoplasm that is composed_of epithelial tissue in which tumor cells form glands or glandlike structures.
acinar cell adenoma
acinic cell adenoma
adenomas
A disease that manifests in a defined anatomical structure.
An immune system disease that is located_in the lymphatic system.
Adenopathy
Lymphangiopathy
Lymphatic disease
Lymphatic disorder
disease of lympoid system
disorder of lymph node and lymphatics
disorder of lymphatic system
disorder of lymphoid system
lymphatic disorder
lympoid system disease
A lens disease characterized by clouding of the lens inside the eye which leads to a decrease in vision.
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
Updating out dated CUI and removing lung abscess as a synonym.
A myeloid leukemia that is characterized by over production of white blood cells.
CML
CML - chronic Myelogenous Leukemia
Myeloid Leukemia, chronic
chronic granulocytic leukaemia
chronic granulocytic leukemia
chronic myelogenous leukaemia
chronic myelogenous leukemia
chronic myeloid leukaemia
A leukemia that is located_in myeloid tissue.
Non-Lymphocytic Leukemia
leukaemia myelogenous
leukemia myelogenous
myeloid granulocytic leukaemia
myeloid granulocytic leukemia
myeloid leukaemia
A carcinoma that is an early development defined by the absence of invasion of surrounding tissues.
An acute myeloid leukemia that derives from blood-forming tissue in which megakaryocytes proliferate in the bone marrow and circulate in the blood in large numbers.
Megakaryocytic myelosis
Thrombocytic leukaemia
A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells.
AML - acute Myeloid Leukemia
Leukemia, Myelocytic, acute
acute myeloblastic leukaemia
acute myeloblastic leukemia
acute myelogenous leukaemia
acute myelogenous leukemia
acute myeloid leukaemia
A large intestine cancer that is located_in the colon and/or located_in the rectum.
A mouth disease that is characterized by inflammation of the mouth and lips.
A acute leukemia that is characterized by over production of lymphoblasts.
acute lymphoblastic leukaemia
acute lymphocytic leukaemia
precursor lymphoblastic lymphoma/leukemia
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.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A geographical feature associated with water.
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.
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.
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
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.
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
Valleys are typically located between hills our mountains.
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.
Typically found in either Karst (limestone) or chalk terrain.
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.
Subclasses of this class are to be populated by inference. Definition modified from http://en.wikipedia.org/wiki/Ocean_current.
A landform elevated above the surrounding area.
elevation
A part of an astronomical body which is primarily composed of solid material.
Ice mass may need to be resolved from ice field, the former referring simply to an accumulation of ice.
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 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 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 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 biome which is primarily or completely situated on a landmass.
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 facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
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.
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.
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.
A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water.
Sediment which has increased levels of one or more chemical compounds.
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.
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.
Chemically-enriched sediment which has increased levels of organic compounds.
Chemically-enriched sediment which has increased levels of inorganic compounds.
A portion of soil which is found in a forested area.
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.
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/C
A/C unit
air conditioner
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.
A house used for sheltering non-human animals.
While humans are animals, this class does not refer to human houses.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
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.
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 building or collection of co-located buildings constructed for the purpose of undertaking scientific research.
This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed.
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 an agricultural field.
Soil which is part of some elevated land.
This class represents habitations of non-human animals. This distinction may be removed in future releases.
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"
Anthropogenic material in or on which organisms may live.
This term is specific to marine upwellings.
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.
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.
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
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
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
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.
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 savanna biome which is subject to temperate climate patterns.
A subtropical grassland in which dominant ecological communities have reached their climax successional state.
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 tropical 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 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]"
This class' definition is less satisfactory than the other latitudinal conditoins.
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 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.
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
A woodland biome which is subject to temperate climate patterns.
An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration.
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.
Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined.
A coniferous forest biome which includes communities adapted to subpolar conditions.
Note that this class refers to a climatic rather than a positional condition.
A system which has the disposition to environ one or more material entities.
1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. 2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity).
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 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.
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 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.
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.
Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline.
Class should be populated by inference and asserted subclasses redistributed.
A layer that is part of a marine water body.
An endolithic environment is an environment that exists within solid rock.
An environmental system which has its properties and dynamics determined by saline water.
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'.
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 environment whose dynamics are strongly influenced by water.
A rocky slope is a slope which has a surface primarily composed of rock.
An environmental system determined by seawater.
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 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.
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'.
Requested term with preliminary def. See Issue 29 on the envo tracker.
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 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.
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 layer which is determined by a form of vegetation.
A portion of acidic water is a portion of water with a pH less than 7.
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 deciduous broadleaf forest which is subject to temperate climate patterns.
A deciduous needleleaf forest which is subject to temperate climate patterns.
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.
A sclerophyllous forest which is subject to temperate 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.
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
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 whole plant which is relatively young.
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 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.
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?
Missing the class for "aggregate" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid.
"Cement" refers more to a disposition than a specific material.
This is a building part and not the same as a standalone wall, which is a building in its own right.
An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment.
This class is meant to represent roofs which are parts of buildings, rather than a roofs of cave and other natural formations.
Generally used to refer to the masonry unit rather than a material.
A brick exterior wall is an exterior wall that is built from bricks.
A concrete exterior wall is an exterior wall that is composed primarily of concrete.
A sheet-iron building roof is a building roof that is built from sheets of iron.
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 building roof is a building roof that is built using tiles.
"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.
Definition from GEMET - will be refined.
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
motor vehicle
A vehicle is a mobile machine which transports people or cargo.
vehicle
motor
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
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
plant litter
planetary landmass
Adpated from https://en.wikipedia.org/wiki/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 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
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
A role that is realized in some process wherein the bearer is discarded or not utilized further.
waste role
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
Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.
contaminated air
Elastic strain, gravity, chemical reactions, or even the motion of massive bodies can produce earthquakes.
earthquake
tectonic earthquake
A lake which has concentrations of environmental contaminants high enough to harm the ecosystems associated with it.
polluted lake
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
tsunami
geological subsidence
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
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid.
desublimation process
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
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
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
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 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
This class may be split. "urban village" doesn't sit well and prevents relations to village biomes.
village
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
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 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
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
atmospheric wind
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 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
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 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
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
This is the process which typically happens on Earth. Other planets may have different liquids involved in the process.
water-based rainfall
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 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 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 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 located in a region subject to temperate climate patterns.
temperate marine upwelling biome
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 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
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
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
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
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
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
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
A planet that is composed primarily of silicate rocks or metals.
terrestrial planet
animal trap
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
plumbing 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
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 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
A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body.
meteor
A meteor which is primarily composed of water.
hydrometeor
A meteor which is primarily composed of rock.
lithometeor
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
particle 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
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 which has its properties and dynamics determined by soil.
soil 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 an aerosol.
aerosol environment
An environmental system which has its properties and dynamics determined by a saline aerosol.
saline aerosol environment
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 determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
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 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
tectonic movement
tectonic plate
tectonic plate boundary
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
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
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
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
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
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 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 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
ecosystem fragmentation process
active ecosystem management 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
acidic soil
This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO.
algal material
water surface
The surface layer of a mass of sediment.
sediment surface
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
lithification
grassland ecosystem
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 process during which liquid water accumulates in a site, most often in some form of container.
water accumulation process
office building
commercial building
office
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
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
canopy
The correct usage of FLOPO terms in the axiomatisation needs to be confirmed.
forest ecosystem
cropland ecosystem
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
Expand the sites of occurrence listed as axioms as new terms emerge.
agricultural process
A layer which is primarily composed of some liquid material.
liquid layer
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
"Bush" is a rather loosely defined regional term, primarily used in Australia.
bush area
An environmental zone which is part of an atmosphere.
atmospheric zone
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
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 body of water which is primarily composed of saline water.
This class has its subclasses populated by inference.
saline water body
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
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
erosion
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 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 organic environmental material which is primarily composed of gill tissue.
gill tissue material
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
land conversion process
agricultural land conversion process
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
terrestrial mining
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
mining
A mining process which occurs in a marine ecosystem.
marine mining
This may be either terrestrial or marine.
coal mining
usage of an environment for transportation
usage of an environment for infrastructure and utilities
This class does not include environments which are primarily used for commerce or industry.
usage of an environment for residential activity
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
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 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
domestic building
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 vehicle which is able to travel through air in an atmosphere.
aircraft
An elevation which is flattened across its highest surface.
flattened elevation
A pollution process during which artificial light with wavelengths in the visible spectrum is released into the environment.
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
optical radiation from a manufactured product
visible spectrum radiation from a manufactured product
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
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
Soil which is below the freezing point of water.
frozen soil
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
A water surface that is part of a water body.
surface layer of a water body
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
An ecoregion which is located on a landmass.
terrestrial ecoregion
A surface layer which is part of an ocean or sea.
envoPlastics
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
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
cryospheric layer
Permafrost which contains inclusions of water-based ice.
ice-bearing permafrost
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 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
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
An aerosol that is suspended in an atmosphere.
atmospheric aerosol
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
A surface layer which is composed primarily of some liquid or gas.
fluid surface layer
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
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 weather front which separates air masses of tropical and polar origin.
envoAtmo
envoPolar
polar front
tropical environment
subtropical environment
polar environment
subpolar environment
temperate environment
An advective transport process during which a fluid moves.
mass fluid flow
straight-line wind
This is a very general concept, and should likely be elevated to OBO Core rather than held in ENVO.
structural collapse process
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
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 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
aquatic ecosystem
marine ecosystem
An ecosystem which primarily occurs on land.
terrestrial ecosystem
A broadleaf forest which is subject to tropical climate conditions.
tropical 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 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
A grassland which is subject to subtropical climatic conditions.
subtropical grassland
temperate 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
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 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 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 arid environmental conditions.
arid biome
A process during which one entity loses energy to another entity.
energy transfer process
A material accumulation process during which the volume of liquid entity increases.
liquid accumulation process
wind gust
The concentration of carbon dioxide when measured in air that is part of an atmosphere.
concentration of carbon dioxide in an atmosphere
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 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 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
convective transport process
convective
advective
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
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 primarily of some metallic material.
Dust which is derived from clay material.
nuclear reactor
nuclear power reactor
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
fluid environmental material
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
desertification
flooding
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
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.
Prior to afforestation, the land cover of a region must not include forests.
To be populated through inference. Do not use for annotation.
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 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.
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 water.
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 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
The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486
geographic basin
soot
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
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
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 desublimation process during which water vapour is frozen into water ice.
desublimation of water vapour into ice
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
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
acidic water-based rain
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
health facility
medical facility
healthcare facility
radioactive material
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]
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
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
not placing under 'pond' class becasue contents may not be primarily be composed of water. consider revising 'pond' semantics
tailings pond
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 seawater.
concentration of carbon dioxide in seawater
soil organic matter
A surface layer which is composed primarily of soil.
soil surface layer
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 layer that is composed primarily of soil.
soil layer
Texture which inheres in soil.
soil texture
Water-holding capacity which inheres in some soil.
soil water-holding capacity
water-holding capacity of soil
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 liquid water when measured in soil.
soil moisture content
soil water content
The concentration of a salt when measured in soil.
The concentration of a soil organic matter when measured in soil.
concentration of soil organic matter in soil
The temperature of some environmental material.
The quality of a environmental system process.
soil pH
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 that binds nucleons to form the atomic nucleus (and nuclear reactions).
Potential energy which is stored in the fields of propagated by electromagnetic radiation.
Kinetic energy which is realised through the microscopic motion of particles.
A form of disordered mechanical energy.
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.
An environment which is determined by an anatomical entity.
The concentration of dioxygen when measured in liquid water.
concentration of dioxygen in liquid water
The concentration of dioxygen when measured in sea water.
The concentration of oxygen when measured 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 sodium molecular entity when measured in soil.
soil sodium molecular entity concentration
concentration of sodium molecular entity in soil
The concentration of organic molecular entity when measured in soil.
soil organic molecular entity concentration
concentration of organic molecular entity in soil
A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).
useful organizational term to collect entities that have genomes/genotypes.
organismal entity
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.
Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid.
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.
The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative 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.
cell morphogenesis involved in 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 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 set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
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.
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 process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
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.
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
Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
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 directed movement of sodium ions (Na+) by the renal system.
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.
The progression of the conus arteriosus over time, from its formation to the mature structure. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.
The process in which the conus arteriosus is generated and organized. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.
The developmental process pertaining to the initial formation of the conus arteriosus from unspecified parts. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.
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 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 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.
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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
This is the same as GO molecular function
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.
gene product or complex activity
Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
nuclear membrane vesicle binding to chromatin
Binding to an RNA molecule or a portion thereof.
Exportin-5 recognizes 3' overhang of pre-miRNA
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 reaction: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1); RNA-template-directed extension of the 3'-end of a DNA strand by one deoxynucleotide at a time.
Binds to and stops, prevents or reduces the activity of an enzyme.
This term should only be used in cases when the regulator directly interacts with the enzyme.
Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
hematopoietin/interferon-class (D200-domain) cytokine receptor binding
hematopoietin/interferon-class (D200-domain) cytokine receptor ligand
Binding to a vascular endothelial growth factor receptor.
vascular endothelial growth factor receptor ligand
vascular endothelial growth factor receptor binding
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 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
malate [mitochondrial matrix] + orthophosphate [cytosol] <=> malate [cytosol] + orthophosphate [mitochondrial matrix]
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 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
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
Binding to collagen, 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%).
Binding to D- or L-enantiomers of glucose.
Binding to a glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues.
Binding to hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine.
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
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).
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
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.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that 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 ND, no data, is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use 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 homotrimer of alpha1(II) chains; type II collagen triple helices associate to form 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.
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 double lipid bilayer that encloses the nucleus, separating its contents from the cytoplasm. It consists of an inner and outer nuclear membrane, with an intermembrane space (20-40 nm wide, also called the perinuclear space) between them. The envelope is supported by the nuclear lamina and contains nuclear pore complexes, which regulate molecular transport.
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 glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
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 process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Any process that modulates the frequency, rate or extent of DNA repair.
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 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 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.
The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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 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 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.
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 indicating damage to its DNA from environmental insults or errors during metabolism.
cellular response to DNA damage stimulus
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 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 set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
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 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.
Binding to a microtubule, a filament composed of tubulin monomers.
Viral UL47:UL48 Proteins Bind HCMV Tegumented Virion to Host Microtuble and Dynein complexs
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
Binds to and increases the activity of an enzyme.
The directed movement of organelles or molecules along microtubules in neuron projections.
Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
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.
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
A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.
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. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the 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'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
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
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 mitochndrial intermebrane 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
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
A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
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.
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 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.
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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
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 a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
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 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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
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.
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, 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 modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
regulation of cellular carbohydrate metabolic process
Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
positive regulation of cellular carbohydrate metabolic process
Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
negative regulation of cellular carbohydrate metabolic process
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 modulates 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.
regulation of cell morphogenesis involved in differentiation
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 involved in differentiation
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 involved in differentiation
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 modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
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
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
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
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
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 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)
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.
Binding to monomeric or multimeric forms of tubulin, including microtubules.
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 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
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.
membrane
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. Cell migration is a central process in the development and maintenance of multicellular organisms.
Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum.
Binding to an amino acid, organic acids containing one or more amino substituents.
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
Binding to a peptide with hormonal activity in animals.
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
Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Binds to and stops, prevents or reduces the activity of a kinase.
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.
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
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-).
Glyoxylate metabolism and glycine degradation
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 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.
A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
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 process in which relatively unspecialized cells, e.g. embryonic or regenerative 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. 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.
Binds to and modulates the activity of an enzyme.
Formation of myofibrils, the repeating units of striated muscle.
Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides 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. Cyclitols are generally not regarded as carbohydrates.
Binding to a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
polysaccharide assembly with MHC class II protein complex
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.
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
Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
A vesicle found in the cytoplasm of a cell.
Binding to an alkali metal ion; alkali metals are those elements in group Ia of the periodic table, with the exception of hydrogen.
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
Binding to a bile acid, a steroid carboxylic acids occurring in bile.
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 stops, prevents, or reduces the frequency, rate or extent of protein binding.
Any process that activates or increases the frequency, rate or extent of protein binding.
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
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 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-RNA complex into its constituent components.
The process in which cellular structures, including whole cells or cell parts, are generated and organized.
The process in which the anatomical structures of a cell part are generated and organized.
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.
This is not covalently bonded, which conflicts with changes to the parent definition.
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.
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
Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
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.
Binding to a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-).
Any process that modulates the frequency, rate or extent of collagen binding.
Any process that stops, prevents, or reduces the frequency, rate or extent of collagen binding.
Any process that activates or increases the frequency, rate or extent of collagen binding.
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 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 indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
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.
The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell.
cellular polysaccharide biosynthetic process
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 an ion is transported across a membrane.
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 resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells.
cellular carbohydrate biosynthetic process
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 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, carried out by individual cells.
cellular biopolymer biosynthetic process
cellular macromolecule biosynthetic 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 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
signal transduction via intracellular signaling cascade
Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
negative regulation of chromatin binding
Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
positive regulation of chromatin binding
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 progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct.
The progression of an epithelium of the uterus over time from its initial formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
The process in which anatomical structures of the oviduct are generated and organized. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.
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 a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.
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.
Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
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 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.
Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
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.
Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor.
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.
The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
The regrowth of the endometrium and blood vessels in the uterus following menstruation, resulting from a rise in progesterone levels.
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.
cell projection
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.
neuron projection
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.
Binding to a complex of RNA and protein.
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
Any process involved in the maintenance of a steady-state level of a surface-active agent that maintains the surface tension of a liquid.
regulation of surface tension of a liquid
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
Binding to an ion, a charged atoms or groups of atoms.
Binding to an anion, a charged atom or group of atoms with a net negative charge.
Binding to a cation, a charged atom or group of atoms with a net positive charge.
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.
Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group.
Binding to an organic acid, any acidic compound containing carbon in covalent linkage.
Binding to a vascular endothelial growth factor receptor 2.
vascular endothelial growth factor receptor 2 binding
Binding to sulfate, SO4(2-), a negatively charged small molecule.
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-bounded organelle
intracellular non-membrane-enclosed 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 modulates the frequency, rate or extent of protein binding.
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
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates, carried out by individual cells.
regulation of cellular 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.
Binding to insulin, 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 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 polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, as carried out by individual cells.
cellular polysaccharide catabolic process
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 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, as carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
main pathways of carbohydrate metabolic process
main pathways of carbohydrate metabolism
The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells.
cellular polysaccharide metabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells.
cellular macromolecule catabolic process
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 resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
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
Any constituent part of a virion, a complete fully infectious extracellular virus particle.
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 biological process that directly contributes to the process of producing new individuals, involving another organism.
A multicellular organism process which involves another multicellular organism of the same or different species.
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
A protein complex that plays a role in the process of DNA packaging.
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 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.
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
Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
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.
synapse
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
Binding to cadherin, a type I membrane protein involved in cell adhesion.
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
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair.
Any process that activates or increases the frequency, rate or extent of DNA repair.
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.
Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
The directed movement of substances within a cell.
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.
Binding to a monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
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 process whose specific outcome is 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.
A developmental process, independent of morphogenetic (shape) change, that is required for a 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
Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
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.
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
adhesive extracellular matrix constituent
Binding to a component of the extracellular matrix.
extracellular matrix constituent binding
A organ system process carried out by any of the organs or tissues of neurological system.
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 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 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.
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
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
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
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 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 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
Binding to serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
Binding to norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), 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 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 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
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
Phosphate bond hydrolysis by NUDT proteins
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 reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure.
The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.
A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother.
embryonic process involved in female pregnancy
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.
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 biological process whose specific outcome is the progression of a bronchus from an initial condition to its mature state. This process begins with the formation of the bronchus and ends with the mature structure. The bronchus is the portion of the airway that connects to the lungs.
The process in which the bronchus is generated and organized. The bronchus is the portion of the airway that connects to the lungs.
The biological process whose specific outcome is the progression of a bronchiole from an initial condition to its mature state. This process begins with the formation of the bronchiole and ends with the mature structure. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi.
The process in which a bronchiole is generated and organized. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi.
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 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 a club cell. A club cell is an unciliated epithelial cell found in the respiratory and terminal bronchioles.
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 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 whose specific outcome is the progression of lung 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.
The process in which the bronchus cartilage is generated and organized. The bronchus cartilage is the connective tissue of the portion of the airway that connects to the lungs.
The process whose specific outcome is the progression of the tracheal 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.
The process in which the anatomical structures of cartilage in the trachea are generated and organized.
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.
Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
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
The process in which the embryonic placenta is generated and organized.
The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer.
branching involved in labyrinthine layer morphogenesis
The process in which a trophoblast cell acquires specialized features of an epithelial cell of the placental labyrinthine layer.
epithelial cell differentiation involved in embryonic placenta development
Any process that mediates the transfer of information from one cell to another.
cell-cell signalling involved in placenta development
cell-cell signaling involved in placenta development
The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure.
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 process in which a relatively unspecialized cell acquires specialized features of the embryonic placenta.
cell differentiation involved in embryonic placenta development
The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.
The process in which the labyrinthine layer of the placenta is generated and organized.
The developmental process pertaining to the initial formation of the labyrinthine layer of the placenta.
The process whose specific outcome is the progression of a blood vessel of the labyrinthine layer of the placenta over time, from its formation to the mature structure. The embryonic vessels grow through the layer to come in close contact with the maternal blood supply.
labyrinthine layer blood vessel development
The biological process whose specific outcome is the progression of a chorion from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The chorion is an extraembryonic membrane.
The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
chorionic trophoblast cell differentiation
The process whose specific outcome is the progression of the chorionic trophoblast 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.
The multiplication or reproduction of cells, resulting in the expansion of the population in the embryonic placenta.
cell proliferation involved in embryonic placenta development
Any process that modulates the rate, frequency, or extent of cell proliferation involved in embryonic placenta development.
regulation of cell proliferation involved in embryonic placenta development
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
Any process that modulates the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state.
regulation of cell differentiation involved in embryonic placenta development
Any process that decreases the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state.
negative regulation of cell differentiation involved in embryonic placenta development
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 anatomical structures of the uterus are generated and organized.
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
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 progression of the trachea submucosa over time from its formation to the mature structure. The trachea submucosa is made up of the glands and elastic tissue that lie under the mucosa in the trachea.
The progression of a trachea gland over time, from its formation to the mature structure. Trachea glands are found under the mucus of the trachea and secrete mucus, and agents that help protect the lung from injury and infection.
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 paramesonephric duct over time, from its formation to the mature structure. Mullerian ducts (or paramesonephric ducts) are paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, cervix, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin.
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 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 remodelling.
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
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.
Binding to fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade.
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 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.
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide or use of neuron-specific markers) show that neuron death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the neuron 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'), and the cell type captured as an annotation extension; or the term GO:0051402 'neuron apoptotic process' may be considered, if appropriate.
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
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 an abiotic (non-living) stimulus.
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.
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 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.
cellular response to electromagnetic radiation stimulus
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 ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
cellular response to ionizing radiation stimulus
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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
cellular response to X-ray radiation stimulus
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 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 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.
The part of a cell encompassing the cell cortex, 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 frequency, rate or extent of a cellular response to stress. Cellular response to stress is 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 indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
regulation of cellular response to stress
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
A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
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.
A region of a chromosome at which DNA damage has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.
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.
Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
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.
The multiplication or reproduction of chorionic trophoblast cells, resulting in the expansion of their population.
chorionic trophoblast cell proliferation
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
Small finger-like extension of a Schwann cell that contacts the nodal membrane.
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 cation is transported across a membrane.
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.
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
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.
Any vesicle-mediated transport that occurs in a synapse.
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.
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 an environmental stimulus.
cellular response to environmental stimulus
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
The process in which the anatomical structures of the pharynx are generated and organized.
Any process that modulates the frequency, rate or extent of pharynx morphogenesis, the process in which the anatomical structure of the pharynx is generated and organized.
Any process that stops, prevents, or reduces the frequency, rate or extent of pharynx morphogenesis.
negative regulation of pharynx morphogenesis
Any process that activates or increases the frequency, rate or extent of pharynx morphogenesis.
positive regulation of pharynx morphogenesis
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 modulates the frequency, rate or extent of placenta blood vessel development.
regulation of placenta blood vessel development
Any process that activates or increases the frequency, rate or extent of placenta blood vessel development.
positive regulation of placenta blood vessel development
Any process that stops, prevents or reduces the frequency, rate or extent of placenta blood vessel development.
negative regulation of placenta blood vessel development
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 consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.
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.
Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes.
Overlaps with some cellular components from GO
Binding to somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin.
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 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
A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
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.
The biosynthetic process resulting in the formation of a nucleic acid.
A protein complex capable of activating an enzyme. Activating subunits may dissociate from the catalytic unit before the enzyme is active.
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 signalling 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 signalling 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.
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 a protein or other molecule binding to a receptor.
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
down regulation of receptor-associated protein activity
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
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 lipid binding.
Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding.
Any process that activates or increases the frequency, rate or extent of lipid binding.
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 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 neuron death.
Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
negative regulation of neuron cell death
negative regulation of neuronal cell death
Any process that activates or increases the frequency, rate or extent of neuron death.
positive regulation of neuron cell death
positive regulation of neuronal cell death
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
Any process that modulates the frequency, rate or extent of chorionic trophoblast cell proliferation.
regulation of chorionic trophoblast cell proliferation
Any process that stops, prevents or reduces the frequency, rate or extent of chorionic trophoblast cell proliferation.
down regulation of chorionic trophoblast cell proliferation
down-regulation of chorionic trophoblast cell proliferation
downregulation of chorionic trophoblast cell proliferation
inhibition of chorionic trophoblast cell proliferation
negative regulation of chorionic trophoblast cell proliferation
Any process that activates or increases the frequency, rate or extent of chorionic trophoblast cell proliferation.
up regulation of chorionic trophoblast cell proliferation
up-regulation of chorionic trophoblast cell proliferation
upregulation of chorionic trophoblast cell proliferation
activation of chorionic trophoblast cell proliferation
positive regulation of chorionic trophoblast cell proliferation
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 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 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
The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell.
multi-ciliated epithelial 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 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 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
The process whose specific outcome is the progression of an uterine gland over time, from its formation to the mature structure.
glandular part of endometrium development
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 modulates the frequency, rate or extent of microtubule binding.
regulation of microtubule severing activity
regulation of microtubule/chromatin interaction
Any process that stops, prevents or reduces the frequency, rate or extent of microtubule binding.
down regulation of microtubule severing activity
down regulation of microtubule/chromatin interaction
down-regulation of microtubule severing activity
down-regulation of microtubule/chromatin interaction
downregulation of microtubule severing activity
downregulation of microtubule/chromatin interaction
inhibition of microtubule severing activity
inhibition of microtubule/chromatin interaction
negative regulation of microtubule severing activity
negative regulation of microtubule/chromatin interaction
negative regulation of microtubule binding
Any process that activates or increases the frequency, rate or extent of microtubule binding.
activation of microtubule severing activity
activation of microtubule/chromatin interaction
positive regulation of microtubule severing activity
positive regulation of microtubule/chromatin interaction
up regulation of microtubule severing activity
up regulation of microtubule/chromatin interaction
up-regulation of microtubule severing activity
up-regulation of microtubule/chromatin interaction
upregulation of microtubule severing activity
upregulation of microtubule/chromatin interaction
positive regulation of microtubule binding
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
The process whose specific outcome is the progression of an allantois over time, from its formation to the mature structure.
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 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
Any process that modulates the frequency, rate or extent of RNA binding.
Any process that stops, prevents or reduces the frequency, rate or extent of RNA binding.
Any process that activates or increases the frequency, rate or extent of RNA binding.
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 intracellular signal transduction that is involved in positive regulation of cell growth.
intracellular signal transduction involved in up regulation of cell growth
intracellular signal transduction involved in up-regulation of cell growth
intracellular signal transduction involved in upregulation of cell growth
intracellular signaling chain involved in positive regulation of cell growth
intracellular signaling chain involved in up regulation of cell growth
intracellular signaling chain involved in up-regulation of cell growth
intracellular signaling chain involved in upregulation of cell growth
intracellular protein kinase cascade involved in activation of cell growth
intracellular protein kinase cascade involved in positive regulation of cell growth
intracellular protein kinase cascade involved in stimulation of cell growth
intracellular protein kinase cascade involved in up regulation of cell growth
intracellular protein kinase cascade involved in up-regulation of cell growth
intracellular protein kinase cascade involved in upregulation of cell growth
intracellular signal transduction involved in activation of cell growth
intracellular signal transduction involved in stimulation of cell growth
intracellular signal transduction pathway involved in activation of cell growth
intracellular signal transduction pathway involved in positive regulation of cell growth
intracellular signal transduction pathway involved in stimulation of cell growth
intracellular signal transduction pathway involved in up regulation of cell growth
intracellular signal transduction pathway involved in up-regulation of cell growth
intracellular signal transduction pathway involved in upregulation of cell growth
intracellular signaling chain involved in activation of cell growth
intracellular signaling chain involved in stimulation of cell growth
protein kinase cascade involved in activation of cell growth
protein kinase cascade involved in positive regulation of cell growth
protein kinase cascade involved in stimulation of cell growth
protein kinase cascade involved in up regulation of cell growth
protein kinase cascade involved in up-regulation of cell growth
protein kinase cascade involved in upregulation of cell growth
signal transmission via intracellular cascade involved in activation of cell growth
signal transmission via intracellular cascade involved in positive regulation of cell growth
signal transmission via intracellular cascade involved in stimulation of cell growth
signal transmission via intracellular cascade involved in up regulation of cell growth
signal transmission via intracellular cascade involved in up-regulation of cell growth
signal transmission via intracellular cascade involved in upregulation of cell growth
intracellular signaling cascade involved in activation of cell growth
intracellular signaling cascade involved in positive regulation of cell growth
intracellular signaling cascade involved in stimulation of cell growth
intracellular signaling cascade involved in up regulation of cell growth
intracellular signaling cascade involved in up-regulation of cell growth
intracellular signaling cascade involved in upregulation of cell growth
intracellular signaling pathway involved in activation of cell growth
intracellular signaling pathway involved in positive regulation of cell growth
intracellular signaling pathway involved in stimulation of cell growth
intracellular signaling pathway involved in up regulation of cell growth
intracellular signaling pathway involved in up-regulation of cell growth
intracellular signaling pathway involved in upregulation of cell growth
signal transduction via intracellular signaling cascade involved in activation of cell growth
signal transduction via intracellular signaling cascade involved in positive regulation of cell growth
signal transduction via intracellular signaling cascade involved in stimulation of cell growth
signal transduction via intracellular signaling cascade involved in up regulation of cell growth
signal transduction via intracellular signaling cascade involved in up-regulation of cell growth
signal transduction via intracellular signaling cascade involved in upregulation of cell growth
intracellular signal transduction involved in positive regulation of cell growth
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 cellular response to gamma radiation.
regulation of cellular response to gamma ray
regulation of cellular response to gamma-ray photon
regulation of cellular response to gamma radiation
Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to gamma radiation.
down regulation of cellular response to gamma radiation
down-regulation of cellular response to gamma radiation
downregulation of cellular response to gamma radiation
inhibition of cellular response to gamma radiation
down regulation of cellular response to gamma ray
down regulation of cellular response to gamma-ray photon
down-regulation of cellular response to gamma ray
down-regulation of cellular response to gamma-ray photon
downregulation of cellular response to gamma ray
downregulation of cellular response to gamma-ray photon
inhibition of cellular response to gamma ray
inhibition of cellular response to gamma-ray photon
negative regulation of cellular response to gamma ray
negative regulation of cellular response to gamma-ray photon
negative regulation of cellular response to gamma radiation
Any process that activates or increases the frequency, rate or extent of cellular response to gamma radiation.
up regulation of cellular response to gamma radiation
up-regulation of cellular response to gamma radiation
upregulation of cellular response to gamma radiation
activation of cellular response to gamma radiation
activation of cellular response to gamma ray
activation of cellular response to gamma-ray photon
positive regulation of cellular response to gamma ray
positive regulation of cellular response to gamma-ray photon
up regulation of cellular response to gamma ray
up regulation of cellular response to gamma-ray photon
up-regulation of cellular response to gamma ray
up-regulation of cellular response to gamma-ray photon
upregulation of cellular response to gamma ray
upregulation of cellular response to gamma-ray photon
positive regulation of cellular response to gamma radiation
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
The developmental process by which a pharyngeal gland is generated and organized.
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).
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 cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
regulation of cellular macromolecule biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
negative regulation of cellular biopolymer biosynthetic process
negative regulation of cellular macromolecule anabolism
negative regulation of cellular macromolecule biosynthesis
negative regulation of cellular macromolecule formation
negative regulation of cellular macromolecule synthesis
negative regulation of cellular macromolecule biosynthetic 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 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 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 cellular response to X-ray.
regulation of cellular response to X-ray radiation stimulus
regulation of cellular response to X-ray
Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to X-ray.
negative regulation of cellular response to X-ray radiation stimulus
negative regulation of cellular response to X-ray
Any process that activates or increases the frequency, rate or extent of cellular response to X-ray.
positive regulation of cellular response to X-ray radiation stimulus
positive regulation of cellular response to X-ray
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 cellular senescence.
Any process that stops, prevents or reduces the frequency, rate or extent of cellular senescence.
negative regulation of cellular senescence
Any process that activates or increases the frequency, rate or extent of cellular senescence.
positive regulation of cellular senescence
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 response to gamma radiation.
regulation of response to gamma-ray photon
regulation of response to gamma radiation
Any process that stops, prevents or reduces the frequency, rate or extent of response to gamma radiation.
negative regulation of response to gamma ray
negative regulation of response to gamma-ray photon
negative regulation of response to gamma radiation
Any process that activates or increases the frequency, rate or extent of response to gamma radiation.
positive regulation of response to gamma ray
positive regulation of response to gamma-ray photon
positive regulation of response to gamma radiation
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
General characterisation of the ancestry of a population or individual
ancestry status
Ancestry that is the result of cultural or geographic isolation. Generally characterised by increased genetic homogeneity and reduced genetic variation
genetically isolated ancestry
Ancestry which is an admixture of more than one defined ancestral population. The degree and type of admixture may vary within a population and the accuracy of classification requires well-defined reference samples
admixed ancestry
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
a data item is 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.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
Pier: 'data, information or knowledge'. OR 'representation'
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
scalar measurement datum
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
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)
PERSON:Bill Bug
source code module
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
OBI branch derived
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
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.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
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.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
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.
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
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.
Barry Smith, Werner Ceusters
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
Mus (commonly mice) is a small mammal belonging to the order of rodents.
Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.
Saccharomyces cerevisiae 'var. diastaticus'
Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, 1883
A quantitative confidence value that refers to an interval give values within which there is a high probability (95 percent by convention) that the true population value can be found. The calculation of a confidence interval considers the standard deviation of the data and the number of observations. Thus, a confidence interval narrows as the number of observations increases, or its variance (dispersion) decreases.
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns.
set of data sets
WEB: https://en.wikipedia.org/wiki/Matrix_(mathematics)
A data item that consists of two or more data sets that are produced as the output of a data transformation.
set of transformed data sets
A data set that is produced as the output of a data transformation.
transformed data set
A data item that is produced as the output of a data transformation.
transformed data item
A categorical value specification that is used to record the destruction of an organism cells or tissues by the organisms' own enzymes or processes with nominal categories ranging from none to severe.
Add instances 0-non, 1-slight, 2-moderate, 3-severe
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A data item that contains the outcome of a survey.
Alice Nzinga
survey data
A plan specification that is realized by process of gathering information (e.g. by asking questions).
survey plan specification
A planned process that realizes the concretization of a survey to generate an output(survey data.)
survey execution
A specimen that is normal.
normal specimen
A Homo sapiens who contributes specimen.
sample donor
specimen donor
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO.
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
obsolete planned process
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
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.
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
measuring
scientific observation
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
A protocol is an information entity which is a set of instructions that describe an how an experiment is done.
a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
A planned process with the objective to produce a processed material which will have a function for future use.
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
A clustered data set is the output of a K means clustering data transformation
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site
A planned process with the objective of collecting a specimen.
A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
Definition updated following discussion on 2024-10-07 OBI dev call.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
A objective specification to obtain a material entity for potential use as an input during an investigation.
OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
James Malone
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
A person or organization that has a manufacturer role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
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.
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
A device which has a function to emit light.
A device that is used to generate X-rays.
A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828
PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A specimen composed of an individual organism to be studied in an investigation.
A length measurement datum between a point at sea or ground level and some point above it.
Adapted from https://www.merriam-webster.com/dictionary/altitude
A person or organization that provides material supplies to other people or organizations.
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.
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. E.g Drosophila melanogaster
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.
Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.
WEB: http://en.wikipedia.org/wiki/Organism
obsolete organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
A material entity that has the specimen role.
A material entity that is collected for potential use as an input upon which measurements or observations are performed.
GROUP: OBI Biomaterial Branch
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
leave one out cross validation method
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
PERSON: Elisabetta Manduchi
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
Generation of a heatmap from a microarray dataset
A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations.
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves)
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
planned irradiation
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
material entity role
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
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 resistance to pressure, being broken, or pierced
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 quality of an entity that is descriptive or observational, typically not represented numerically.
TODO: define this or obsolete it and move children somewhere else.
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 morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
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 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 hardness quality of being rigid and resistant to pressure.
A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
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 inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
A quality inhering in a bearer by virtue of the bearer's existence.
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 quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
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.
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 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 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 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 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.
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.
A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis.
A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed.
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
See comments of relational quality of a physical 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.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
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 morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
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 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 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.
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 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 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 mass which is higher than normal or average.
A physical quality that is the ability to contract or shrink.
A contractility which is relatively high.
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
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.
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 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 retain foliage.
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 of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited.
Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose, but this is an over simplification.
A quality of a substance inhering in a bearer by virtue of it being currently or previously exposed to electromagnetic radiation,
This may refer to incident external irradiation or internal radiation from an ingested or otherwise internal source.
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 composition quality inhering in a bearer by virtue of the bearer's containing granules.
A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome.
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 concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions).
A shape quality in a bearer by virtue of the bearer's curving inward.
A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
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 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 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 quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A quality inhering in a bearer by virtue of its constitution.
A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
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 shape that inheres in a 3 dimensional entity.
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 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).
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 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.
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.
A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen.
A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching.
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.
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
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 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
A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.
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.
A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.
pair of interacting organisms
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
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 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.
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)
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.
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).
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 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.
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).
'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'.
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.
Generally the below ground portion of a vascular plant.
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
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.
portion of phyllome primordium tissue (exact)
The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.
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'.
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.
The phyllome anlagen is only detectable by gene expression, not morphology.
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).
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.
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 native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
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.
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).
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 with 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
A molecule 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.
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 molecular 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:000050565).
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)
Ionizing radiation classified by the material entity which generates or emits it.
ionizing radiation categorized by source
Radiation originating outside the Earth's atmosphere.
One of the principal sources of ground radiation is radon gas.
Radiation produced on Earth or on another planetary body by natural or artificial means.
Material presenting, when irradiated, interaction properties similar to those of soft tissue.
ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material)
Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons.
Ionization chambers and silicon solid state detectors can be used as active dosimeters.
A radiation measuring device which records dose at the time of detection, with data available in real time
Thermoluminescent dosimeters and plastic nuclear track detectors are passive detectors.
A radiation measuring device which integrates the amount of radiation to which it is exposed. Passive detectors are interrogated at a later time to determine the dose.
The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra
The effective dose was calculated to be 300 mSv.
The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv).
The samples were exposed to a mixed radiation field consisting of several ions at different energies.
The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously.
An environment the occupation of which results in exposure to radiation.
That part of the Earth exposed to the Earth atmosphere.
The region between the Earth's surface and an altitude of approximately 100 km
The region of outer space between the Earth's atmosphere and the innermost Earth radiation belt
That part of outer space beyond the Earth's radiation belts.
A radiation dose administered in two or more exposures at specified time intervals
A unit of absorbed dose equal to 1/1000 of a rad
The equivalent dose was calculated to be 300 mSv.
The product of the mean absorbed dose in an organ or tissue and the radiation weighting factor (w_R )of the radiation type of interest
The total dose was administered in five dose fractions.
The absorbed radiation dose administered in a single one of a series comprising a fractionated radiation exposure
Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space
Galactic cosmic radiation is one of the principal sources of radiation dose outside low-earth orbit
Galactic cosmic radiation consists of high-energy charged particles originating from outside the solar system
Solar cosmic radiation contributes to the radiation dose to humans in space.
Solar cosmic radiation is high-energy charged particles that originate from the sun.
The measurement datum representing a dose to an organism or object per unit time.
The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972.
Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space.
The experiment was conducted in the International Space Station module Columbus
The experiment was conducted on the Russian module of the ISS.
A self-contained unit of the International Space Station.
Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia.
A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies.
The HIMAC accelerator has a beamline dedicated for radiation biology experiments.
The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes.
Radiation produced by a particle accelerator.
Radiation produced by a nuclear reactor.
High energy photons emitted during nuclear decay of the Cesium-137 isotope.
High energy photons emitted during nuclear decay of the Cobalt-60 isotope.
High energy photons emitted during nuclear decay of the Cobalt-57 isotope.
Isotopes that exhibit radioactivity and undergo radioactive decay. (From Grant & Hackh's Chemical Dictionary, 5th ed & McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A series of radioactive elements from ACTINIUM, atomic number 89, to and including LAWRENCIUM, atomic number 103
A trivalent radioactive element and the prototypical member of the actinide family. It has the atomic symbol Ac, and atomic number 89. Its principal isotope is 227 and it decays primarily by beta-emission.
A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy
A man-made radioactive actinide with atomic symbol Cf, atomic number 98, and atomic weight 251. Its valence can be +2 or +3. Californium has medical use as a radiation source for radiotherapy
A radioactive element of the actinide metals family. It has the atomic symbol Np, and atomic number 93.
A naturally radioactive element of the actinide metals series. It has the atomic symbol Pu, and atomic number 94. Plutonium is used as a nuclear fuel, to produce radioisotopes for research, in radionuclide batteries for pacemakers, and as the agent of fission in nuclear weapons.
A radioactive element of the actinide series of metals. It has an atomic symbol Th, atomic number 90, and atomic weight 232.04. It is used as fuel in nuclear reactors to produce fissionable uranium isotopes. Because of its radioopacity, various thorium compounds are used to facilitate visualization in roentgenography.
A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors.
Electromagnetic radiation with photon energies approximately 3-120 eV. High energy UV radiation can be ioinizing.
A substance present at the time of irradiation that mitigates or prevents the biological effects of irradiation.
Richard T. Hoppe, Theodore Locke Phillips, Mack Roach, Leibel and Phillips Textbook of Radiation Oncology (Third Edition), W.B. Saunders, (2010), ISBN 9781416058977, https://doi.org/10.1016/B978-1-4160-5897-7.00093-7.
Radionuclide chelators are small organic molecules or in some cases larger peptides that chemically sequester the radionuclide ion by forming a complex that determines the thermodynamic stability and kinetic inertness of the radionuclide.
A co-carcinogen is generally a chemical that promotes the effects of a carcinogen in the production of cancer. In some circumstances exposure to radiation or physical trauma is considered to be co-carcinogenic.
Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors.
Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009.
Radiation response modifiers that are peptides.
Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.â€ Future oncology (2021): doi/10.2217/fon-2020-0577
Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577
Radiation response modifiers that are small molecules.
small molecule radiation response modifier
A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers.
Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1
Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1
The theme or modality of an experimental, theoretical, critical or summative study involving radiation, radioactive materials including their impacts on orgnisms and society.
An epidemiological study is the study (scientific, systematic, and data-driven) of the distribution (frequency, pattern) and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations (neighborhood, school, city, state, country, global)
A study of the impact of radiation on the composition of or processes within the natural or anthropogenic environment.
A study who endpoint is the lifespan of the organism under investifgation.
A study of the effect of agents including radiation, seperately or together, on the incidence or type of neoplasia or pre-neoplasia.
A study in which the structural or processual damage to normal tissue caused by radiation is assessed. Often by histopathology or molecular profiling.
A study of the mechanism or effects of radiation on dna damage and its repair.
A study of the effects of internal or external radiation on cellular or organismal physiology.
A study of the effects of radiation on the integrity, composition and quality of adult, fetal or embryonic anatomical structures.
A study of the effects of external irradiation on an organism.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application.
A study of the effects of external irradiation on an organism where the most of the dose is given in a single or small number of fractions closely in time.
A study of the effects of external irradiation on an organism where the dose is given over a protracted time period either continuously or in many fractions. Often these are lose dose studies.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. The dose is delivered over a long period of time, often continuously and generlly at low dose. For example long term Radon exposure by inhalation.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. Most of the dose is given over a short period of time and is generally unfractionated, such as in brachytherapy.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Acute exposure involves usually a single exposure over a short period of time with no fractionation.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Chronic exposure involves usually a continuous or highly fractionated exposure over a long period of time.
A study of the effects of radiation on gene expression.
A study of the effects of radiation on the proteome or individual proteins.
A study that aims at the discovery of protein, RNA or other molecular entities or modifcations that can act as reliable surrogates for the prediction or measurement of the effects of radiation or the response of the organism to radiation.
A study that aims at the discovery, development or assessment of efficacy of therapeutic agents or processes designed to mitigate or cure the effects of radiation exposure.
A study that uses survival as an endpoint. Generally applicable to animal studies rather than human studies which would use the "lifespan" measure (RBO:00000085)
A study of the effects of radiation on the metabolome or individual metabolites.
A study of the contributing factors consequences and prevention of nuclear accidents
A study of the toxicity of chemical or biological agents on cells or whole organisms.
A study of the effects of radiation on the endocrine system or of endocrine hormones on the effects of radiation.
A study of the effects of radiation on the offspring of an irradiated animal or plant.
A study of the distribution and metabolism orf drugs or biologicals used for therapeutic purposes.
A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Professionâ€ can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society.
A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society.
Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1].
NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf
X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale.
Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom
A device that is used to measure the amount of ionizing radiation exposure or absorption.
Particle or electromagnetic radiation with sufficient energy to liberate one or more electrons from an atom.
Charged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)
electromagnetic radiation with photon energies greater than approximately 100 keV
A device used to impart kinetic energy to subatomic particles by means of electric and magnetic fields
A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation.
Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
The process by which an entity is exposed to electromagnetic or acoustic radiation radiation energy internally or externally.
Unplanned exposure to radiation of any type in any environment or otherwise planned process.
Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally or externally.
Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a diagnosis of disease.
Exposure to naturally occurring radiation (NORM) of any type in any environment .
exposure to naturally ocurring radioactive material
Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a cure or mitigation of disease.
Unplanned exposure to anthropogenic radiation of any type in any environment ; for example radiation from nuclear waste, nuclear industry discharge or weapons.
accidental non-medical anthropogenic radiation exposure
Exposure to ionising radiation created by a man-made machine or exposure to a fixed source. For example a cobalt source, an X ray machine, an acceleratororf a nucler weapon.
Planned exposure to radiation generated through a device or exposure to a source emitting ionising radiation
planned anthropogenic radiation exposure
Accidental or incidental exposure to radiation from a man made process or machine. Covers both radiation accidents and routine occupational exposure.
accidental anthropogenic radiation exposure
Accidental exposure occurring during medical therapy or diagnostics, for example medical radiation accidents or overdoses.
accidental medical anthropogenic radiation exposure
Incidental exposure to naturally occurring radiation in a natural or anthropogenic environment, such as geographical areas with high background levels of radiation or specific locations such as Uranium mines.
unplanned naturally occurring radiation exposure
Deliberate or knowing exposure to naturally occurring radiation in a natural or anthropogenic environment, such as a radon spa.
planned naturally occurring radiation exposure
Studies relating to human society and the interrelation of social and educational factors with individual thought and behaviour including mental illness.
Studies on the distribution of information or opinion by technological means of communication that reach large numbers of people.
Studies on the civil, legal, and political preparedness for accidental or deliberate release of radioactive materials or radiation into the environment.
Studies in which research is conducted with human subjects or on material of human origin in which the investigator directly interacts with human subjects, including the dveelopment of new technologies, understanding of the mechanisms of disease, therapy, clinical trials, epidemiology behaviousrand health services research.
Study of the laws, statutes, ordinances, government or international treaty regulations or authoritative guidelines, as well as for legal controversy and court decisions, relating to the regulation of radiation safety, movement and containment of radioactive materials and the consequences for human health or the natural environment of radioactive contamination.
Studies relating to organisations and processes concerned with freedom from or resilience towards potential harm caused by hostile intent or circumstances (for example terrorism and illegal release of radioactive substances or radiation) towards the natural environment or human population, and the enforcement of relevant laws and international treaties.
A study whose intention is to discover knowledge concerning the origins, nature diagnosis or therapy for neoplastic disease and cancer. This includes studies in humans, model organisms, the laboratory and in silico. This class includes experimental and epidemiological studies specifically aimed at cancer.
The specific manner, characteristic, pattern of application, or the employment of any technology, approach or formal procedure to implement the study plan to generate a study type.
Studies of the presence of radiation of any type in the natural or anthropogenic environment and its impact on animals, plants, and microorganisms. This includes studies measuring nuclide transfer in the environment, and interaction with meteorological phenomena. This excludes occupational exposure and the human working environment.
Studies concerned with the regulation, monitoring and operation of the nuclear industry. For example nuclear power station and reprocessing plants, isotope purification and manufactore, weapons manufacture and testing. This includes occupation health studies, impact of accidental or deliberate release on the natural or man made environment and impact on organisms specifically affected directly or indirectly by contamination.
Research done in a laboratory. A laboratory study may use special equipment and cells or animals to investigate the effects of an experimental perturbation, discover fundamental molecular mechanisms, assay biological substances, or find out if a drug, procedure, or treatment is likely to be useful in humans. A laboratory investigation is often characterised by a hypothesis and is carried out with controls.
Study of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ethicolegal constructs surrounding radiation and radiation safety and regulation.
Study concerning exchange or transmission of thoughts, messages, or information between people or between authorities and the general public (for example educational information, risk communication, safety communication) concerning exposure to and use of radiation.
A study focussed on a set of people with some shared characteristic. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. For example communities collectively exposed to radioactive environmental contamination.
The study of political involvement in radiation and nuclear regulation, military use, and safety as shown by inclusion in political manifestos and messaging by established or informal groups and its impact on voting patterns and democracy.
A study measuring "psychological" aspects of a person such as knowledge, skills, abilities, attitudes, or personality using defined scales.
A study of human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology.
A study dealing with group relationships, patterns of collective behavior, and social organization.
Studies involving fields of inquiry into human constructs and concerns as opposed to natural processes . These are traditionally the study of literature, philosophy, and religion. Included in this definition are sociological studies, especially those concerned with the social impact of the humanities.
Specifically an attitudinal study looking at how perception, for example of risk, and expectations affect behaviour.
perceptions, expectations and behaviours study
Sociological, attitudinal, ethocolegal and regulatory approaches to governance of radiation and radioactive substance use.
Studies on policy concerning socially and ethically responsible research and innovation
responsible research and innovation study
Studies of the engagement between an organisational entity and those groups or individuals potentially or actually impacted by the actions of that entity over a range of activities and approaches.
Study concerning the modes, efficacy and response to communication of risk and health impacts of radiation in all aspects.
Studies concenring the attitudes to and practices of radiological protection in defined groups of people. For example the nuclear industry of a country or within a specific laboratory.
Genetic study done at the population level or among population groups, generally to find the cause, incidence or spread of a disease or to see the response to a treatment, nutrition or environment.
A type of study in which participants are enrolled into the study before they develop the disease or outcome in question.
Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) An observational study that is also considered to be a Patient Registry.
A study looking backwards in time using observations collected predominantly prior to subject selection and enrolment
A study of the number of new cases of a given disease during a given period in a specified population. It also is used for the rate at which new events occur in a defined population. this class also includes PREVALENCE, which refers to all cases in the population at a given time.
Studies concerning the optimisation of situation awareness through gathering and analysing information, and methodologies for making decisions on that awareness, such as estimating the path of a radioactive fallout with respect to weather and population density and making a decision to evacuate a population.
situation awareness and decision support study
A study concerning the protection of the population from unexpected radioactive discharge or contamination, such as a dirty bomb, and civil safetyy coningency plans, such as deployment of emergency services and evacuation.
Studies on planning for unexpected natural or man-made radiological catastrophe of substantial extent causing significant property damage or destruction, loss of life or sometimes permanent changes to the natural environment. Broader scope than civil protection as may relate to livestock, food and water shortage, disease outbreak and extensive traumas caused by precipitating or consequential damage.
Studies on plannig for or analysing a nuclear accident with release of airborn or waterborn contamination into the environment. Narrower than Disaster planning study but may be used to qualify an annotation to Disaster planning study if the source of contamination is a nuclear accident. A nuclear accident is not necessarily a disaster.
A controlled study designed to assess the safety and efficacy of new drugs, devices, treatments, or preventive measures in humans by comparing two or more interventions or regimens
Study of the effects of radiation used in a medical therapeutic or diagnostic context. Inlcudes radiation accidents in this context, excludes occupational exposure for health professionals.
A study concerned with health and safety policy development, implementation and practice in the workplace including investigating accidents at work, and chronic occupational exposure. Includes monitoring compliance with health and safety legislation and study of the promotion and maintenance of physical and mental health in the work environment.
Study on the efficacy, outcomes and adverse consequences of exposure to medical diagnostic procedures using internal or external irradiation.
Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment.
A study involvingdevelopment of agents or procedures intended to produce an effect that is intended to mitigate or stop a pathologic process.
A study of the macroscopic and microscopic anatomical changes in diseased tissue.
Study of legal and statutory instruments and legislation designed to regulate the safety, use and transport of radioactive materials, release of such materials into the environment, or external radiation.
Study of the policy approaches and their implementation concerned with harmonising regulatory guidelines and legislation dealing with radiation and radioactive substances between legislatures, generally internationally.
Study of the development, implementation and monitoring of nuclear non proliferation treaties between states.
Studies concerning intentional release of organisms (germs), toxic chemicals, or radioactive substances with intent to harm or kill people or the environment, or to inflict panic within a population.
Study of strategies and their implementation towards defence against radiation used as a weapon conducted by military powers and institutions. May also include civil defence where the military has a significant operational role, but not disaster preparedness.
Study of biological processes that involve adding/removing chemical moieties to/from DNA, including methylation, phosphorylation, dephosphorylation, etc. Includes interventional DNA modification.
Study of biological processes that involve adding/removing chemical moieties to/from histones, including methylation, acetylation,phosphorylation, dephosphorylation, etc.
Study conducted by means of structured or unstructured interviews of persons of interest.
A study of genetic variation and the inheritance of a trait or traits within a population or an individual including examination of genetic material for the presence or absence of cytogenetic or molecular genetic abnormalities.
A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques.
Study concerned with the construction, analysis, evaluation, refinement etc. of mathematical or statistical models of the properties or behaviour of a set of entities, such as molecules, physiological processes, environmental processes such as nuclide transfer, such that functions are developed to reliably predict the behaviour of those entities.
A study usually conducted in a laboratory where non human animals are used to model aspects of a disease process or its therapy to provide insights into human biology or pathobiology.
Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides.
monitoring technologies and metrology study
Study of the chemistry of radioactive materials including radioactive tracer studies of metabolic processes
Study of the development and implementation of public policy towards issues involving radiation
Study of the effects of acoustic radiation on cellular and organismal physiology and the effects of acoustic radiation emitted in response to exposure to ionising radiation.
Study of radiation levels and effects in the human built environment.
environmental study_ abiotic_anthropogenic
Study of radiation levels and effects in the natural environment.
The development and use of mathematical models and systems analysis for the description of naturally occurring non-human populations, and applications to measuring the effects of radiological contamination.
The study of environmental contamination with radiation and radioactive substances and the toxic effects on the ecosystem either through chemical toxicity or radiation exposure.
The study of environmental contamination with radon and the toxic effects on biota including humans. Both natural and anthropogenic environments. Includes radiometrics, safety policies and mitigation technologies.
Mathematical modelling of radionuclide transfer and dispersal processes in water, earth or air, either directly or through the mediation of biota.
Study of the ocurrence, levels and effects of naturally occurring radioactive materials such as Radon.
naturally occurring radioactive materials study
Study involving the measurement of radiation levels, or concentration of radionuclides, in the natural or man made environment. Usually in a time series.
environmental radiation monitoring study
Study concerned with the measurement of transfer of radionuclides to biota from the environment.
environmental radionuclide transfer study
Any study concenrd with the prevalence or effects on non-ionising radiations such as UV, acoustic, or RF.
non ionising electromagnetic radiation study
Study concerning the safety, regulation, activities and engineering of nuclear installations including power stations, waste processing plant, radionuclide generation and purification plant, and military nuclear establishments. May include occupational health studies if broader than just occupationaal health in scope.
Study of the process of generation of nuclear waste, its monitoring, regulation, disposal and inadvertent discharge.
Study of the engineering of nuclear installations such as power plants.
Study of the process, regulation and monitoring of mines where exposure to naturally occurring radiation presents an occupational hazard for workers or the process itself, for example run off water or spoil, constitutes an environmental hazard.
A study using cells derived from an organism grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent.
A study using an organ, part of an organ or an organoid culture, derived from an organism and grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. The system differs from cell culture in the generation or maintenance of multiple cell types with the spatial and functional relationship between them derived from or reflecting the normal organisation in vivo.
Any study involving the manipulation, measurement, or characterisation of DNA or RNA in a cell or organism.
Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations.
A study using an intact organism, plant, animal, or microorganism
Study of the cellular phenomenon which radiation energy is not been directly deposited in cells by transfer of medium, proximity/justaposition, or other means, but results in their behaving as if they had been irradiated.
A study of heritable phenotype changes that do not involve alterations in the DNA sequence. This may be in intact organisms or in cells and includes population analysis of epigenetic phenomena and molecular analysis of gene expression and epigenetic modifications of chromatin such as DNA methylation and histone acetylation.
Study of the frequency of induction , nature and consequences of the production of genetic or epigenetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods.
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or regulation of the nuclear industries.
attitudinal study of nuclear industry risk perception
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic ionising radiation in the environment.
attitudinal study towards ionising radiation in the environment
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic non-ionising radiation in the natural environment.
attitudinal study towards non-ionising radiation in the environment
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety and efficacy in a clinical context where radiation is used for diagnostic or therapeutic procedures..
attitudinal study towards medical radiation procedures
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety towards natural or anthropogenic non-ionising radiation in the occupational environment.
attitudinal study towards radiation in the occupational environment
Study of social and individual trust in the position and activities of legal or other competent advisory or regulatory authorities.
Study on the modality, efficacy and responses to communcation of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context.
Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context.
Study on the modality, efficacy and responses to communication of information or advice to populations on any aspect of radiation, conceived of as an educational programme, and including a wider scope than just safety and risk. For example basic nuclear physics, emergency action advice.
Study involving attitudes, health status, social organisation of defined communities identified by common characteristics such as occupation type, geography, gender identity, with respect to radiation.
social affairs and community health study
Studies involving creation and assessment of plans for the future physical arrangement, well being, efficiency and condition of a community. It may have the goals of improving health, promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. In the context of radiation this may be concerned with community planning for dealing with mitigation measures for local NORM, or organised community-wide continegency measures for nuclear accident or recovery from such.
Study concerned with eliciting information in a structured way concerning issues of interest from members of a community defined by common characteristics, for example occupation, geographical location, personal history or gender.
A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology at the level of slected individuals. May be carried out by observation or as individual responses to a questioannaire or interview in the case of humans where the person records their own assessment of their behaviour.
A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology within substantial populations of individuals. Likely to be carried out by mass observation or indirect inference.
Mathematical modelling for theraputic regime optimisation and for optimal tumor response, for example modelling spatiotemporal dynamics of tumor and blood volume fraction, and predicting response to radiation therapy. Also studies for beam modelling and multiimaging techniques.
Study of the radiolonuclide components and emissions from building materials
building materials radiological safety study
Studies on radiological safety within buildings. Primary purpose os for buildings not specifially designed to hold radioactive materials but anaylyis and mitigation of risks from radioactive exposure from the local environment or materials.
Study of the weather and atmospheric dynamics mainly with respect to dissemination of radionuclides.
Study of non-living objects in the environment, such as soils or rocks.
Study of non-human biota in the natural environment.
Study which may include human and non-human biota in the environment.
Study of the measurement, effects and regulation of wireless communication signals, for example mobile phone radiation and microwave communication.
The sample was irradiated with Cs-137 gamma ray photons.
Photons having energies that are greater than tens of thousands of electron volts (eV).
The sample was irradiated with x-ray photons.
A photon with energies from about 100 eV (electron volts) to 1 MeV (million electron volts).
Irradiation of the sample was with x-ray photons.
An energy transfer process in which energy in the form of particles or waves is transferred from one entity to another
A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus
Irradiation that is not the result of a planned process
Unplanned irradiation that is of anthropogenic origin
Unplanned irradiation that is non-anthropogenic in origin
Environmental monitoring that includes continual assay for radiation dose or quality.
Monitoring within an environment which was not man-made.
Monitoring within a man-made or constructed environment
Monitoring for radiation dose or quality within a man-made or constructed environment such as a building or a vehicle.
anthropogenic environment radiation monitoring
Monitoring for radiation dose or quality within a natural environment.
natural environment radiation monitoring
A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles.
Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10.
Heavy ion radiation has several notable characteristics and contexts: High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation.Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10.
Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means
A particle with a positive or negative electric charge
An atomic nucleus with 26 protons and 30 neutrons
An atomic nucleus with 14 protons and 14 neutrons
An atomic nucleus with 6 protons and 6 neutrons
An atomic nucleus with 2 protons and 2 neutrons
An atomic nucleus with 10 protons and 10 neutrons
Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere.
The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium.
The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium per unit time.
The kinetic energy carried by a particle or photon of ionizing radiation.
Electromagnetic radiation with photon energies approximately between 0.1 and 120 keV. The upper end of the x-ray spectrum overlaps with the lower end of the gamma ray spectrum.
Sham irradiation refers to a procedure in which participants or subjects in an experiment are exposed to simulated radiation, mimicking precisely the conditions of actual irradiation. The purpose of using sham irradiation is to create a control group that experiences the non-specific effects of the experimental setup, while excluding the specific effects associated with radiation exposure.
A protocol for administering a total radiation dose in two or more increments separated by a specified time interval
The region of space between the Earth and the Moon
A region of space defined by a regular, repeating path of a specified object about Earth's moon
The area of the lunar landmass exposed to space
The region of space between the Earth and Mars
A region of space defined by a regular, repeating path of a specified object about Mars
The area of the Mars landmass exposed to the Martian atmosphere
The region of space in the Solar System between planets
The outermost solid or liquid area of a planet
An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation
A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation)
An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument
A protocol for administering radiation to a sample
One of the series of individual doses administered to a sample in a fractionated irradiation.
Time between fractions in a fractionated irradiation.
The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude.
The class should be used in cases where it is clear that the control sample was treated in precisely the same way as the experimental samples or sham irradiation is specified. It is therefore a more restricted quality definition than "non-irradiated". It is likely to be used more often with external radiation exposure or exposure to a beam, and with a biological rather than abiotic sample.
A quality of a biotic or abiotic sample or individual which is part of an experiment that tests the effects of radiation on organisms or materials by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. In sham irradiation the precise treatment of the sample must be identical to that of the experimental samples and should be made explicit in the description of the method.
An aircraft which flies a series of parabolic arcs to simulate micrgravity.
An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes.
An research aircraft designed to operate without crew members, either autonomously or under control from a ground station
Fully ionized atomic nucleus with 2 or more protons and energies in excess of tens of MeV per nucleon
A study of a response to radiation conditioned by prior administration of radiation of a different type and/or at a different dose or dose rate
The total dose administered in a series of radiation fractions divided by the elapsed time between the beginning of the first exposure fraction and the end of the last exposure fraction
A device which exposes samples to gamma radiation.
The electric charge of a particle used in an irradiation
The measurement of the amount of radiation taken up by a sample.
A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations.
An atomic nucleus with 41 protons and 52 neutrons
An atomic nucleus with 47 protons and 60 neutrons
An atomic nucleus with 54 protons and 75 neutrons
An atomic nucleus with 73 protons and 108 neutrons
An atomic nucleus with 79 protons and 118 neutrons
An atomic nucleus with 7 protons and 7 neutrons
An atomic nucleus with 8 protons and 8 neutrons
An atomic nucleus with 18 protons and 22 neutrons
An atomic nucleus with 22 protons and 26 neutrons
An atomic nucleus with 36 protons and 48 neutrons
A derived absorbed dose unit which is equal to one milligray absorbed per second
This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen.
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 which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell
The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671
The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. Löffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671
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 radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells.
Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component.
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 exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells.
indirect cellular response to ionising radiation
A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes.
High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level.
non-targeted effects of ionising radiation
Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001)
One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials.
A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen
NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)
Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints.
The reduction of radiation intensity upon passage of radiation through matter
Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident.
Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that
The bystander effect can be studied by identifying cells that were traversed by a charged particle.
The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one.
Delta ray energies increase with the velocity of the incident particle.
Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a
The average annual dose equivalent for crew members on the ISS is approximately 300 mSv.
The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv)
The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included
The sample was irradiated with fast neutrons.
Neutrons of energies above a few hundred kiloelectron volts (keV)
The value of the fluence was approximately 1 particle per cm2.
The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2]).
The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0.
The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].)
An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions.
In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)
Biological effects are a function of LET.
The energy deposited by an ionizing charged particle or photon in any medium per unit path length.
Radiation protection standards take into account organ dose as well as whole body dose.
The mean absorbed radiation dose in a specified tissue or organ of the human body.
Neutrons have a high quality factor compared to photons.
Dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed
The samples received a dose of 1 Gy. (The use of the gray unit implies that "dose" refers to a measured quantity, typically absorbed dose or organ dose.)
The samples received a dose of 1 Sv. (The use of the sievert unit implies that "dose" refers to a der
A measurement datum of the quantity of radiation absorbed by a substance or organism. The term "radiation dose" may for example refer to absorbed dose, organ dose, dose equivalent or equivalent dose, depending upon context and weighting factor(s).
Radiation weighting factors may change as more data on biological effects are obtained.
A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated.
Neutrons have been found to have a higher RBE than electrons.
Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r
Tissue equivalent materials can be used to study radiation effects at depth in the human body.
Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue.
An active radon dosimeter that uses a phosphor-coated zinc sulfide screen or a liquid scintillator that emits light when hit by alpha particles from radon decay. The emitted light is measured with a photomultiplier tube. They have high sensitivity, fast response time.
An active radon dosimeter that measure the concentration of radon decay products (polonium-218, lead-214, and bismuth-214) using alpha spectroscopy or particle collection on a filter. They provide working level (WL) values, which indicate the potential radiation dose from radon decay products.
Provides direct measurement of biologically relevant radiation exposure. Expensive, mainly used in occupational settings.
continuous working level radon dosimeter
An active radon dosimeter that uses various sensors (e.g., scintillation detectors, ion chambers, or solid-state silicon detectors) to measure radon decay in real-time. They typically record radon levels at hourly intervals.
Provides near real-time results, detects fluctuations over time, useful for home inspections.
A passive radon dosimeter that contain an electret (a charged Teflon disc) inside an ionization chamber. Radon decay ionizes the air, causing a measurable voltage drop in the electret, which correlates with radon concentration.
Can be read without a lab, provides both short- and long-term measurements.
A passive radon dosimeter in which a container filled with activated charcoal absorbs radon from the air. After exposure (typically 2–7 days), the canister is sealed and sent to a lab for gamma spectroscopy, which measures radon decay products.
A passive radon dosimeter in which a small plastic film or polycarbonate chip is exposed to radon gas. When radon decays, it emits alpha particles that leave microscopic tracks on the film. After exposure, the film is chemically etched to reveal the tracks, which are counted under a microscope to determine radon levels.
Alpha track radon dosimeters are used domestically for radon monitoring over long periods of time.
Nuclear reactors primarily used to produce neutrons for the study of materials at the atomic level, the biological effects of radiation, the production of radioisotopes for medicine, industry and research, and the imaging of objects’ internal structure.
Definition adapted from: https://www.iaea.org/bulletin/what-are-research-reactors-how-do-they-contribute-to-sustainable-development
A nuclear reactor primarily used to generate and supply power.
This conceptualization of nuclear power reactor emphasizes its role as a radiation source. For use to emphasize its roles in energy production, recommend use of identically named concept ENVO:02000137
A nuclear reactor used for military purposes such as plutonium production.
A nuclear reactor used for more than one purpose.
An x-ray source operating at a voltage of 160 kV.
An x-ray source operating at a voltage of 320 kV.
A facility designed and constructed so as to minimize exposure to natural background radiation.
A facility located below the earth's surface in order to minimize natural background radiation
underground low background radiation laboratory
An energy transfer process in which radiation intensity is reduced by modifying the composition, and/or energy of incident radiation.
Radiation shielding that require using an external power or energy source, such as an electrostatic or electromagnetic field.
The role of materials used in radiation shielding such as concrete, lead, or polyethylene, with no requirement for external power or operator intervention
The power per unit solid angle delivered by radiation incident on a given location.
The role of a material in reducing radiation intensity by modifying the composition, and/or energy of incident radiation.
Radiation shielding using materials such as concrete, lead, or polyethylene, with no requirement for external power or operator intervention
A serious human disease that occurs when the entire body (or a large portion of it) is exposed to a high dose of penetrating radiation—typically more than 1 Gray (Gy)—over a short period (minutes to hours).Key features: Prodromal Phase (hours to days): Nausea, vomiting, diarrhoea, fatigue. Latent Phase (hours to weeks): Apparent improvement or absence of symptoms. Manifest Illness Phase: Depending on dose, damage to rapidly dividing cells leads to one or more syndromes: Hematopoietic syndrome (1–10 Gy): Bone marrow failure, infection, bleeding. Gastrointestinal syndrome (5–20 Gy): Severe GI tract damage, fluid loss, sepsis. Neurovascular syndrome (≥20 Gy): Neurological impairment, confusion, convulsions; usually fatal within days. Recovery or Death: If dose is survivable and supportive care is provided, recovery can occur over weeks to months; higher doses carry a poor prognosis.
Dainiak, N., & Albanese, J. (2022). Medical management of acute radiation syndrome. Journal of radiological protection : official journal of the Society for Radiological Protection, 42(3), 10.1088/1361-6498/ac7d18. https://doi.org/10.1088/1361-6498/ac7d18. https://www.icrpaedia.org/Acute_radiation_syndrome
An environment in which there is human-created radiation.
Includes terrestrial and non-terrestrial environments. Includes environments created for investigations, and those used for other purposes including those created by humans for habitation, manufacture, storage, clinical practice and transport. Will include mines and other environments actively created by humans by the manipulation of natural materials
A radiation environment resulting from natural processes.
The radiation environment below the surface of the Earth, consisting of radiation from naturally occurring radioactive elements; particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field, atmosphere and materials in the Earth's crust to enable them to penetrate below the Earth's surface; particles produced by interactions of primary radiation with the Earth's crust; and anthropogenic sources of radiation such as buried nuclear waste. The composition and strength of the radiation at a given point under the Earth's surface depends strongly on depth below the surface and composition of the surrounding crustal material.
terrestrial subsurface radiation environment
The radiation environment at the surface of the Earth, consisting of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements on the surface; and anthropogenic radiation. The composition and strength of the radiation at a given point on the Earth's surface depends on factors including altitude, the composition of the surface material, and the temporal variation in incident space radiation, e.g. with solar cycle.
terrestrial surface radiation environment
The radiation environment in the Earth's atmosphere , consisting of particles originating in space which are sufficiently energetic and/or weakly interacting to penetrate the Earth's magnetic field; particles produced by interactions of space radiation with the Earth's atmosphere and albedo radiation from interactions of incident radiation with the Earth's crust; and anthropogenic radiation. The composition and strength of the radiation at a given point in the Earth's atmosphere depends on factors including altitude and the temporal variation in incident space radiation, e.g. with solar cycle.
terrestrial atmosphere radiation environment
The quality of neutrons or charged particles, such as protons or alpha particles, such that they can produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1].
The quality of X and gamma rays or light charged particles such as electrons such that they can only produce sparse ionizing events far apart on a molecular scale.
Microdosimetry is a radiobiology study type that deals with the study of the distribution of energy deposition on a micrometer scale in biological systems exposed to ionizing radiation. It focuses on understanding how radiation interacts with cellular and sub-cellular structures and the resulting effects on biological systems.
A study of the biological effects of low acute or protracted doses of ionising radiation defined as being below 500 mSv, less than 100mGy, or at dose rates less than 5mGy per hour. ( https://www.nationalacademies.org/our-work/developing-a-long-term-strategy-for-low-dose-radiation-research-in-the-united-states)
The radiation environment consisting of the water at the surface of the Earth, including all of Earth’s water: oceans and seas, lakes and rivers (freshwater), groundwater, and atmospheric water. Some frameworks treat the cryosphere (ice, snow, glaciers) as a sub-part of the hydrosphere. Radiation in water consists of particles originating in space which are sufficiently energetic and/or weakly interacting with the Earth's magnetic field and atmosphere to reach the surface; particles produced by interactions of space radiation with the Earth's atmosphere; decays of naturally occurring radioactive elements dissolved or suspended in water, those on the substrate where there is body of water and from the subsurface. This includes anthropogenic radiation carried in water by means of direct discharges, precipitation and other transfer routes. The composition and strength of the radiation in water at a given point on the Earth's surface depends on factors including underlying geology, water chemistry and elemental composition, and the temporal variation in incident space radiation, e.g. with solar cycle.
A measurement of the amount of energy deposited by ionizing radiation per unit length of a medium. . It represents the average energy transferred to the material per unit length along the path of the particle in a specified micrometric ( or smaller) site divided by the mean chord length of the site volume. Lineal energy is typically expressed in units of keV/?m (kilo-electron volts per micrometer) or MeV/cm (mega-electron volts per centimeter)
The ionization cluster size is a measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle.
In the case of ionization cluster size per unit length, the common unit is "ion pairs per micrometer" (ion pairs/µm) or "ion pairs per millimeter" (ion pairs/mm). This unit represents the average number of ion pairs produced within a length of one micrometer or one millimeter along the path of the ionizing particle. For ionization cluster size per unit volume, the unit may be "ion pairs per cubic micrometer" (ion pairs/µm³) or "ion pairs per cubic millimeter" (ion pairs/mm³). This unit represents the average number of ion pairs produced within a volume of one cubic micrometer or one cubic millimeter."
A measure of the spatial extent or size of the ionized region created by the passage of radiation through a medium. It measures the number of ion pairs that are produced within a localized volume or track of the radiation particle.
ionisation cluster size measurement datum
ionization cluster size measurement datum
The particle track penumbra is the region where secondary electrons released by the primary particle, transitioning a medium, are the exclusive agents of energy deposition due to multiple scattering and energy loss of the charged particles as they interact with the atoms and molecules of the medium." Makes sense to define this a s a spatial region ( BFO:000006) as it has extent that can be measured but is a concept rather than a material entity.
Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed. See Chatterjee, A., Schaefer, H.J. ( 1976) Rad Env Biophys 13, 215-227 https://ntrs.nasa.gov/api/citations/19750020623/downloads/19750020623.pdf
In the theory of particle track structure, the narrow central zone with a radius in matter far below 1 micron where energy deposition occurs mainly in processes of ionisation, excitation and collective oscillation of the atoms of the medium related to the passage of the primary particle.
That energy which is transferred in space and time as part of the process of radiation (ENVO:01001023).
Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)
An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers
See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259ï¿½265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006.
See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006.
Usually a track structure assay at nm scale
An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers
Usually a track structure assay at micrometre scale
Nuclear decay in which an alpha particle is emitted.
Radioactive decay in which a beta particle is emitted or in which orbital electron capture occurs.
Processes in which electrons or components of the atomic nucleus are participants.
Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers
In microdosimetry the specific energy, z, is the energy deposited by radiation ( in one or more deposition events) in a specified micrometric (or smaller) site divided my the mass of the site. Measured in Gy.
The path of a particle in matter, delineated by sites where the particle deposits energy.
A pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers.
The complete set of spatial coordinates of energy deposition events along a particle track in matter
A group of ionization events closely related in time and space, occurring in a specified target volume and originating from a single primary ionizing particle.
Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers.
A volume of matter characterised by linear dimensions of the order of 0.5- 10's of microns, referred to as the "site" in microdosimetry.
A control specimen role of a biotic or abiotic sample or individual describes a specimen by its purpose, and therefore treatment, within a planned experimental process that tests hypotheses by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. The quality of control inhering in the sample role exists as a result of the historical treatment of the sample. In a controlled experiment, two or more virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena. A control may have been subject to treatments during the experiment that might alter its state or behaviour and is therefore distinguishable from the sample as initial input into the experiment. However such treatments should in all cases but that of the variable under scrutiny, be the same as the experimental sample.
Sham irradiation in which an identical irradiation protocol (with the exception of the administration of the radiation exposure) is not followed in every respect.
Use approximate sham irradiation when at least one aspect of the irradiation (with the exception of the administration of the radiation exposure) is not followed precisely. For example, Not placing an organism or sample in a beam line for the same length of time as the irradiated organism(s) or sample(s) were left in the beam.
Experimental internal radiation exposure of rodents to radon gas through inhalation.
Exposure to an inhaled, ingested, injected or implanted source of radiation of any origin as part of a planned or accidental process.
Mice exposed to external radiation from a Sr source.
Exposure to an external source of radiation of any origin or type.
Sham irradiation in which an identical irradiation protocol is followed in every respect, with the exception of the administration of the radiation exposure.
Use complete sham irradiation when all steps of an irradiation protocol are followed for sham control group (with the exception of administration of the radiation exposure).
Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally by the ingestion, inhalation or implantation of a source of radiation.
Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure
internal experimental radiation exposure
The direct or indirect transfer of energy from radiation to a medium through ionisation or excitation of the atoms of the medium.
A mixed irradiation study typically involves exposing a sample or system to a combination of different types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A mixed ion and photon irradiation study typically involves exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A mixed ion and photon simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
mixed ion and photon simultaneous irradiation study
A mixed ion and photon sequential irradiation study typically involves sequentially exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
mixed ion and photon sequential irradiation study
A multiple ion irradiation study typically involves exposing a sample or system to a combination of different types of charged particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A multiple ion simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of ions. This could include exposure to various forms of particle radiation, for example ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
multiple ion simultaneous irradiation study
A multiple ion sequential irradiation study involves exposing a sample or system to a combination of different ions. This could include exposure to various forms of particle radiation such as ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
multiple ion sequential irradiation study
Radiation present in an experimental or therapeutic process, other than that produced as part of that planned process.
anthropogenic ionizing background radiation
Radiation originating in the terrestrial or extra-terrestrial environment.
The types and characteristics of particles or waves that make up the radiation produced or emitted by a radiation source for use in a particular exposure context or protocol. The source may be artificial as in a particle accelerator or natural, in a controlled environment, such as a collimated beam from a radioactive isotope.
The space radiation field in the solar system consists of particle and electromagnetic radiation from the sun, electromagnetic radiation originating from extra-solar sources, and galactic cosmic radiation.
The mix of charged and neutral atomic and subatomic particles and electromagnetic radiation suffusing a defined volume in an extraterrestrial environment at a given time.
The process by which an entity is exposed to two or more species of accelerated ions sequentially or simultaneously.
The term is often used as jargon, in which cases it is taken to imply sequential exposure to multiple ion types, and not parallel exposures. (perhaps include reference to NSRL)
Radiation field composition refers to the spectrum of types and characteristics of radiation present in a specific area or region where radiation is being used, emitted, absorbed, or measured. It describes the combination of different types of particles or waves that make up the radiation in a given field.
A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV.
a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV.
The ambient radiation in a defined environment emanating from natural or anthropogenic sources.
For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought.
Background radiation that does not result in ionization of target material
anthropogenic non-ionizing background radiation
Non-ionizing background radiation that is the result of a human planned process.
natural non-ionizing background radiation
Non-ionizing background radiation that is not the result of a human planned process.
The toroidal zones surrounding the Earth, comprised of charged particles trapped by the Earth's magnetic field. There are two permanent belts, an inner and an outer belt. A transient third belt may form during periods of high solar activity.
The emission and acceleration of large numbers of energetic charged particles, mainly protons, from the Sun. Sources include solar flares and coronal mass ejections (CME).
The geomagnetosphere is the region of space surrounding Earth where the dominant magnetic field is the magnetic field of Earth, rather than the magnetic field of interplanetary space. The geomagnetosphere is formed by the interaction of the solar wind with Earth’s magnetic field.
A radiation exposure in which the delivery of energy to the target is considered to be "high dose rate" in a given context.
The context here is determined by the type of radiation and application of the exposure.
A radiation environment outside a commonly defined boundary marking the beginning of space (frequently the Karman line).
Senescence caused by radiation and associated with the dismantling of a cell as a response to oxidative stress, e.g. high levels of reactive oxygen species, such as superoxide anions, hydrogen peroxide, and hydroxyl radicals.
A radiation detector which, when exposed to ionizing radiation, stores energy and when stimulated with light, releases the stored energy as luminescence, the intensity of which depends on the amount of radiation absorbed.
optically stimulated luminescence dosimeter
A device which measures ionizing radiation dose by storing and then releasing the energy produced by the radiation. Energy is stored in the form of excited electrons. When the dosimeter is heated the electrons return to the ground state, resulting in the emission of light. The intensity of the emitted light directly corresponds to the radiation dose received, allowing for quantifiable measurements.
An active dosimeter in which ionizing radiation creates electron-hole pairs in a semiconductor which are collected by electrodes across which a voltage is applied. The resulting current is proportional to the energy deposited in the semiconductor by the incident radiation.
An active dosimeter which estimates the amount of incident ionizing radiation by measuring the number of electrons liberated from the gas molecules by the radiation in a suitable housing.
A senolytic is a type of drug or compound that selectively induces the death, removal or both of senescent cells—cells that have stopped dividing but often remain metabolically active, often secreting inflammatory and harmful molecules. These cells accumulate with age and contribute to aging-related diseases, chronic inflammation, and tissue dysfunction.
Senolytics work by targeting specific survival pathways that senescent cells rely on, such as the BCL-2 family proteins, PI3K/AKT pathway, or p53-related mechanisms. By eliminating these cells, senolytics have shown potential in improving tissue function, delaying age-related diseases, and enhancing healthspan in preclinical studies.
See: Lelarge, V., Capelle, R., Oger, F. et al. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment. npj Aging 10, 12 (2024). https://doi.org/10.1038/s41514-024-00138-4
In radiation science, a dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed
Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose. Rossi, Harald H. Specification of Radiation Quality. Radiation Research, vol. 10, no. 5, Radiation Research Society, 1959, pp. 522 31, https://doi.org/10.2307/3570787. But this is an over simplification.
Is a quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited.
NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) and see https://melodi-online.eu/wp-content/uploads/2021/04/02-What-is-radiation-quality-Goodhead.pdf
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
Devices, manned and unmanned, which are designed to be placed into an orbit about the Earth or into a trajectory to another celestial body.
A vehicle operating or capable of operating in an extraterrestrial environment between the Earth's atmosphere and the innermost Earth radiation belt
There is no universally accepted definition of where space begins. Some definitions use the K�rm�n line, a somewhat arbitrary boundary approximately 62 miles (100 kilometers) above sea level. The US FAA (https://www.faa.gov/space/human_spaceflight) does not define where space begins, but recognizes "any flight crew or space flight participant who is on an FAA-licensed launch or reentry vehicle and reaches 50 statute miles above the surface of the Earth" by listing their name on the FAA Commercial Human Space Flight Recognition web page (https://www.faa.gov/space/human_spaceflight/recognition/).
Activity carried out by crewed or robotic vehicles outside the Earth's atmosphere but inside the Earth's inner radiation belt.
The natural radiation environment of a region of a cis-lunar space environment
The natural radiation environment of a region of a cis-mars space environment
The natural radiation environment of a region of interplanetary space
interplanetary space radiation environment
The natural radiation environment in lunar orbit. Contributions to the lunar orbit radiation environment include: free space radiation, partially shielded by the body of the Moon; albedo radiation produced by interactions of free space radiation with the lunar crust; and, particles produced by decays of radioactive elements in the lunar crust.
The natural radiation environment on or adjacent to the surface of the moon. Contributions to the lunar surface radiation environment include: free space radiation, partially shielded by the body of the Moon; albedo radiation produced by interactions of free space radiation with the lunar crust; and, particles produced by decays of radioactive elements in the lunar crust.
The natural radiation environment in Mars orbit. Contributions to the Mars orbit radiation environment include: free space radiation, partially shielded by the planetary body; albedo radiation produced by interactions of free space radiation with the Mars crust and modulated by interactions with the Martian atmosphere; and, particles produced by decays of radioactive elements in the Martian crust modulated by interactions with the Martian atmosphere.
The natural radiation environment on or adjacent to the surface of Mars. Contributions to the lunar surface radiation environment include: free space radiation partially shielded by the planetary body and modulated by interactions with the Martian atmosphere; albedo radiation produced by interactions of free space radiation with the Martian crust; and, particles produced by decays of radioactive elements in the Martian crust.
The natural radiation environment of a region of a planetary surface
The natural radiation environment on or adjacent to the surface of a planet or moon, comprising: the free space radiation environment partially shielded by the planet or moon and modulated by interactions with the planet's or moon's crust, and atmosphere and magnetic field, if any, and radiation produced by naturally occurring radioactive elements in the planet's or moon's crust. A surface radiation environment can include both ionizing radiation and non-ionizing radiation such as UVA, UVB and visible light, but often is used to refer to biologically damaging ionizing radiation such as galactic cosmic radiation and solar particles.
The natural radiation environment in the vicinity of Mars comprising: the free space radiation environment, radiation produced by interactions of the free space radiation environment with the Martian atmosphere and crust, and radiation produced by naturally occurring radioactive elements in the Martian crust. The Martian radiation environment varies with location and time--for example with proximity to the Martian surface, shielding by the planetary body, and with the solar cycle and periodic solar particle events. It can include both ionizing radiation and non-ionizing radiation such as UVA, UVB and visible light, but often is used to refer to biologically damaging ionizing radiation such as galactic cosmic radiation and solar particles.
The natural radiation environment on or in the vicinity of the Earth's moon, comprising: the free space radiation environment, radiation produced by interactions of the free space radiation environment with the lunar surface, and radiation produced by naturally occurring radioactive elements in the lunar crust. The lunar radiation environment varies with location and time--for example with proximity to the lunar surface, shielding by the Moon itself, and with the solar cycle and periodic solar particle events. It can include both ionizing radiation and non-ionizing radiation such as UVA, UVB and visible light, but often is used to refer to biologically damaging ionizing radiation such as galactic cosmic radiation and solar particles.
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
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.
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.
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].
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.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
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 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 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.
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).
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.
Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].
Portion of connective tissue that connects bone or cartilage.[TAO]
Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]
this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament
PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)
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
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].
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
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.
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 mucosa that is part of a bronchus [Automatically generated definition].
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
An anatomical wall that is part of a uterus [Automatically generated definition].
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.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
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]
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.
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
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
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 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)
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]
in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
tubular parts of female reproductive system
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688
The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
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.
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
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
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
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.
in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
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.
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].
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.
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 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
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]
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].
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.
The organism subdivision that includes the pelvic 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 pelvic girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
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 glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy.
The mucous membrane lining the uterus. [TFD][VHOG]
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead
in FMA this is subdivided into basal and outer
TODO - check for parallel structure with peritoneum
A fallopian tube that is part of a right side of organism [Automatically generated definition].
non-functional in monotremes[ISBN:978-0226870137]
A fallopian tube that is part of a left side of organism [Automatically generated definition].
Muscle (organ) which is a part of the pelvis. Examples: levator ani,.
The anus and surrounding regions. Encompasses both internal and external regions, where present.
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 a pelvis [Automatically generated definition].
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]
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].
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].
Any muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
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 bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted].
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
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 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]
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)
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)
The epithelial lining of the trachea which contains numerous ciliated cells.
An epithelium that is part of a small intestine [Automatically generated definition].
Intestinal epithelium which lines the lumen of the mid intestine.[TAO]
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 hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP].
A submucosa that is part of a bronchus [Automatically generated definition].
An epithelium that lines a terminal bronchiole.
bronchiolus terminalis epithelial tissue
epithelial tissue of bronchiolus terminalis
epithelial tissue of terminal bronchiole
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)
Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011
Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.
DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Excretion in semisolid state processed by the intestine.[FMA]
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783].
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]
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.
An epithelium that is part of a bronchus [Automatically generated definition].
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]
An epithelium that is part of a bronchiole [Automatically generated definition].
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].
The upper conducting airways of the lung; these airways arise from the terminus of the trachea.
Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching.
lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer
In FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however, there are two distinct terms for the corresponding epithelium.
In some texts/references/ontologies, bronchiole has been used as an exact synonym of 'lobular bronchiole'. However, a 'lobular bronchiole' is a segment of a bronchiole.
The last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls.
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
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
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]
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.
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.
check the FMA placement here; ncit placement of body cavity here probably not correct
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
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.
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]
The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle.
A lamina propria that is part of a bronchus [Automatically generated definition].
lamina propria mucosa of bronchial trunk
lamina propria mucosae of bronchial trunk
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].
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.
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 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]
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
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
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]
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.
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
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)
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 mucous secreting gland associated with the mucuous membrane lining the uterus.
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
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
The outermost extraembryonic membrane of amniotes.
The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]
The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252].
The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584]
This term refers to the amniote structure. It is distinct from the concept of chorion in insects
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
An elongated tube which carries air to and from the lungs.[AAO]
The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]
In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409
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].
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
An endothelium that is part of a trachea.
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 pelvic appendage bud.
An unilaminar epithelium that surrounds a pectoral appendage bud.
An extraembryonic structure that develops_from a ectoderm and is part of a chorion.
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 portion of smooth muscle tissue that is part of a trachea [Automatically generated definition].
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 pelvic appendage bud.
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 nerve that is part of a pelvis [Automatically generated definition].
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 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 a trachea.
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 pelvis [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 bronchiole that is part of a right lung [Automatically generated definition].
A bronchiole that is part of a left lung [Automatically generated definition].
A terminal bronchiole that is part of a right lung [Automatically generated definition].
A terminal bronchiole that is part of a left lung [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 trachea.
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 bronchus [Automatically generated definition].
bronchial trunk portion of connective tissue
portion of connective tissue of bronchial trunk
portion of connective tissue of bronchus
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 pelvis [Automatically generated definition].
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].
The ring-shaped cartilaginous structures that support the trachea.
check whether to classify as part of splanchoncranium
in mammals the rings are incomplete, in avians the rings are complete.
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].
An elastic tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk elastic connective tissue
bronchial trunk textus connectivus elasticus
elastic connective tissue of bronchial trunk
textus connectivus elasticus of bronchial trunk
textus connectivus elasticus of bronchus
An elastic tissue that is part of a trachea [Automatically generated definition].
cartilaginous trachea elastic connective tissue
cartilaginous trachea textus connectivus elasticus
elastic connective tissue of cartilaginous trachea
elastic connective tissue of vertebrate trachea
textus connectivus elasticus of cartilaginous trachea
textus connectivus elasticus of vertebrate trachea
textus connectivus elasticus of windpipe
vertebrate trachea elastic connective tissue
vertebrate trachea textus connectivus elasticus
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.
A mesentery that is part of a uterus [Automatically generated definition].
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
Initial section of the oviduct through which the ova pass from the ovary to the uterus.
Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]
Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559
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
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 placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood.
Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ]
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.
Blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate.
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
A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP].
Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]
Kardong says absent in adult tetrapods, check AAO
we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally
The funnel-like expansion of the abdominal extremity of the uterine tube[MP].
The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube].
In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct.
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]
That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate.
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.
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]
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.
The embryonic vessels grow through the layer to come in close contact with the maternal blood supply.
blood vessel of labyrinthine layer of placenta
labyrinthine layer of placenta blood vessel
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 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 bronchus [Automatically generated definition].
A portion of smooth muscle tissue that is part of a fallopian tube [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 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 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
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]
a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]
part_of embryo in EHDAA2 - note differences in humans
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
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].
Any collection of muscles that is part of a pelvic girdle [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 portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition].
A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition].
smooth muscle tissue of terminal bronchiole
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
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 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 posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
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 oviduct [Automatically generated definition].
in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label
columnar epithelium of the fallopian tube
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 an endometrium [Automatically generated definition].
In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)
epithelium of tunica mucosa of endometrium
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 future body wall - underlies the ectoderm[WP].
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.
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.
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 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 submucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a cystic duct [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 right uterine tube [Automatically generated definition].
A mucosa that is part of a left uterine tube [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].
A mucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a terminal bronchiole [Automatically generated definition].
mucosa of organ of bronchiolus terminalis
mucous membrane of bronchiolus terminalis
A mucosa that is part of a fallopian tube [Automatically generated definition].
A mucosa that is part of a uterine tube infundibulum [Automatically generated definition].
mucosa of infundibulum of fallopian tube
mucosa of organ of uterine tube infundibulum
mucous membrane of uterine tube infundibulum
organ mucosa of uterine tube infundibulum
uterine tube infundibulum mucosa of organ
uterine tube infundibulum mucous membrane
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].
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 or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
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 tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen.
These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents.
An external ectoderm that is part of a optic eminence [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.
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.
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
A limb bud that develops into a hindlimb or pelvic fin.
Fin bud that develops into the pelvic fin.[TAO]
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
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
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
pelvic 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
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.
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 limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
pelvic 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.
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
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.
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 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]
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 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 tube that is part of a excretory 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 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 muscle layer that is part of a fallopian tube.
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'
An anatomical space that surrounded_by a trachea.
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
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
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
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively
The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
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 serous membrane that is part of a uterine tube infundibulum.
serosa of infundibulum of fallopian tube
A muscle layer that is part of a uterine tube infundibulum.
muscle layer of infundibulum of fallopian tube
muscularis of infundibulum of uterine tube
muscle layer of infundibulum of uterine tube
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 structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
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.
A pre-cartilage condensation that is part of a trachea.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of a pelvic appendage.
Musculature that is part of the pelvic fin.[TAO]
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The collection of all skeletal elements in a pelvic appendage region.
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 cartilage tissue that is part of a pelvic appendage.
Cartilage which is part of the pelvic 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
A ciliated columnar epithelium that is part of a oviduct.
A cuboidal epithelium that is part of a oviduct.
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 bone element or fused bone that is part of pelvic girdle.
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
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
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333
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
The part of the ventral body cavity that is within the pelvis.
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.
Epithelium pertaining to the trachea and bronchi.
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.
Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified].
logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]
Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624].
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]
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].
An organism containing a developing embryo, fetus, or unborn offspring within the body.
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
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.
Mesenchyme that is part of a developing trachea.
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 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 basement membrane that is part of a bronchus.
MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108
A basement membrane that is part of a trachea.
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.
The vascularized and branched structures arising from the rodent trophoblast-derived epithelium that allow an increase its surface area for the efficient exchange of nutrients and wastes between the maternal and fetal circulation.
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 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.
Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli.
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.
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
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic 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). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior 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 bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
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].
A skeleton of pelvic girdle that is part of a right pelvic girdle region.
A skeleton of pelvic girdle that is part of a left pelvic girdle region.
A pelvic girdle region that is in the right side of a multicellular organism.
A pelvic girdle region that is in the left side of a multicellular organism.
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 pelvic girdle region.
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'
The submucous layer of the wall of the uterine tube.
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
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.
An anatomical cavity that is part of a bronchus.
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
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 broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis.
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 collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior 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.
A serous membrane that is part of a fallopian tube.
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
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.
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
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
FMA class may only represent the uterine portion
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].
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
An organ cavity that is part of a uterus.
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.
The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta.
Classification notes: May be considered an external sphincter[PMID:8224664]
A crus of diaphragm that is in_the_right_side_of a diaphragm.
A crus of diaphragm that is in_the_left_side_of a diaphragm.
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 pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin.
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).
Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic 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 blood vessel that is part of a endometrium.
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.
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.
The layer of endometrial epithelium adjacent to the uterine 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.
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].
A post-anal tail that attaches outside the tail.
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.
The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon.
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.
An anatomical surface that is part of a bone.
One of the main divisions of the whole organism of arthropods formed from groups of segments.
Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods.
Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052).
Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727).
Any sense organ that is part of some larva.
Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004).
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.
An anatomical junction between two parts of the intestine.
A submucosal gland located in a bronchus.
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.
An endothelium that is part of the placental artery.
A zone of skin that is above the clavicle zone in the pectoral girdle region.
A zone of skin that is above the iliac crest in the pelvic girdle bone/zone.
A zone of skin that is part of the external genitalia.
Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue.
A unit of measurement is a standardized quantity of a physical quality.
"A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia]
A unit which is a standard measure of the distance between two points.
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
A unit which is a standard measure of the amount of matter/energy of a physical object.
"A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]
A unit which is a standard measure of the dimension in which events occur in sequence.
"A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia]
"A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction." [Wikipedia:Wikipedia]
"A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST]
A derived unit is a unit which is derived from base units.
A unit which is derived from base units.
"A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG]
"A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of angular movement about an axis; the angle rotated in a given time." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]
"A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG]
"A unit which is a standard measure of the luminous intensity impinging on a given area." [Wikipedia:Wikipedia]
"A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the quantity of motion measured by the product of mass and velocity." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the number of rotations in a given time." [NIST:NIST]
"A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG]
"A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG]
"A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
"A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST]
"A unit which is a standard measure of the force is applied when a mass is accelerated." [NIST:NIST]
"A unit which is a standard measure of the force applied to a given area." [NIST:NIST]
"A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST]
"A unit which is a standard measure power or the rate of doing work." [NIST:NIST]
"A unit which is a standard measure of the luminous flux incident on a unit area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the flow of radiant energy." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of the action of a catalyst." [NIST:NIST]
"A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the angle formed by three or more planes intersecting at a common point." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source." [OCRBS:OCRBS]
"A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance." [DEFRA:DEFRA]
A derived unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue.
"A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue." [DEFRA:DEFRA]
"A unit which is a standard measure of the expression of dose in terms of its biological effect." [ORCBS:ORCBS]
"A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured." [ORCBS:ORCBS]
"A unit which is a standard measure of the power of electromagnetic radiation at a surface, per unit area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the intensity of light." [NIST:NIST]
"A unit which is a standard measure of the intensity of electromagnetic radiation." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves." [Wikipedia:Wikipedia]
"A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd]
"A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia]
"A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object." [Wikipedia:Wikipedia]
"A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia]
"A dimensionless unit which denotes a simple count of things." [MGED:MGED]
"A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia]
"A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]
"A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
"A concentration unit which a measure of plaque forming units in a given volume." [UOC:GVG]
"A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet]
"A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet]
"A unit which is a standard measure of the amount of information." [Wikipedia:Wikipedia]
"An information unit which is a standard measure of the detail an image holds." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces." [NIST:NIST]
"A unit which is a standard measure of the internal resistance of fluids to flow." [UOC:GVG]
"A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG]
"A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG]
"A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature." [Wikipedia:Wikipedia]
"The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
"A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG]
"A prefix in the metric system denoting a factor of ten to the power of 9." [UO:GVG]
"A prefix in the metric system denoting a factor of million." [UO:GVG]
"A prefix in the metric system denoting a factor of one thousand." [UO:GVG]
"A prefix in the metric system denoting a factor of one tenth." [UO:GVG]
"A prefix in the metric system denoting a factor of one hundred." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -6." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -9." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -12." [GVG:UO]
"A prefix in the metric system denoting a factor of 10 to the power of -15." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -18." [UO:GVG]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
einstein per square meter per second based unit
watt per steradian per square meter based unit
colony forming unit per milliliter based unit
plaque forming unit per milliliter based unit
The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource.
A list of types used to categorize the nature or genre of the content of the resource.
DCMI Type Vocabulary
A set of date encoding schemes and/or formats
Date Encoding Schemes
A set of format encoding schemes.
Format Encoding Schemes
A set of resource identifier encoding schemes and/or formats
Resource Identifier Encoding Schemes
A set of language encoding schemes and/or formats.
Language Encoding Schemes
A set of resource relation encoding schemes and/or formats
Resource Relation Encoding Schemes
A set of source encoding schemes and/or formats
Source Encoding Schemes
A set of geographic place encoding schemes and/or formats
Place Encoding Schemes
A set of subject encoding schemes and/or formats
Subject Encoding Schemes
A set of encoding schemes for the coverage qualifier "temporal"
Encoding Schemes for temporal characteristics
A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage
This branch will be replaced by, and if necessary merged with an Uberon import in future.
129 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
Simpson E. M., Linder C. C., Sargent E. E., Davisson M. T., Mobraaten L. E., and Sharp J. J. (1997) Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice. Nature Genet. 16, 19-27.
BALB/c is a mouse strain of albion mice.
Description from https://www.jax.org/strain/000651: BALB/c mice are particularly well known for the production of plasmacytomas following injection with mineral oil forming the basis for the production of monoclonal antibodies. Although not all BALB/c substrains have been examined for plasmacytoma induction, substrains derived from the Andervont (An) lineage (which includes BALB/cByJ) typically are susceptible, while those descended from BALB/cJ are resistant (see: Potter M, 1985). Mammary tumor incidence is normally low but infection with mammary tumor virus by fostering to MMTV+ C3H mice dramatically increases tumor number and age of onset. BALB/c mice develop other cancers later in life including reticular neoplasms, primary lung tumors, and renal tumors. Rare spontaneous myoepitheliomas arising from myoepithelial cells of various exocrine glands have been observed in both BALB/cJ and BALB/cByJ substrains. White et al. reported a variation in thioglycolate medium-induced peritoneal leukocyte recruitment in 4 analyzed strains. The response of total leukocyte recruitment, from greatest to least, was C57BL/6J>BALB/c>CD1>129X1/SvJ. Variations were also found in the timeline of response and cell types most impacted. BALB/c mice immunized with PLP180-199 develop an atypical form of experimental autoimmune encephalomyelitis (EAE) in which susceptibility is determined by location. In the spinal cord 60-70% mice develop pathological lesions and in the brain and cerebellum 100% of mice develop sever lesions. Dorso-ventral vaginal septa is observed in some BALB/cJ females, and may contribute to non-productive females in this strain. (Cunliffe-Beamer T, Lab Anim Sci, 1976)
BALB is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/001026.html
A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000646.html
C3H/HeJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000659.html
CB6F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100007.html
B6C3F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100010.html
A designator of mouse strain information indicating the genetic homo or heterogenetity e.g. inbred strain
An inbred strain carrying one or more phenotypic mutations. For example, the mutant strain C3H/H3eSn-bc3J/J carries the bouncy 3 Jackson phenotypic mutation.
Property of an organism which indicates that the organism's parents were genetically related (potentially for several generations). Inbreeding results in closer homozygosity.
Anatomical structure which has as its parts one or more ordered aggregates of nucleotide, amino acid fatty acid or sugar molecules bonded to one another.
The original group of Swiss mice that served as progenitors of this stock consisted of two male and seven female albino mice derived from a non-inbred stock in the laboratory of Dr. de Coulon, Centre Anticancereux Romand, Lausanne, Switzerland.
Inbred Strain TJL Mating System: Sibling x Sibling (Female x Male) Species: laboratory mouse H2 Haplotype: d Generation: F219p (14-DEC-06) Appearance: dilute brown Related Genotype: a/a Tyrp1b/Tyrp1b Myo5ad/Myo5ad Important Note This strain is homozygous for Cdh23ahl, the age related hearing loss 1 mutation, which on this background results in progressive hearing loss that is already severe by 3 months of age. Strain Description DBA/2J is a widely used inbred strain that is valuable in a wide number of research areas including cardiovascular biology, neurobiology, and sensorineural research.
Beck, J.A., et al., Genealogies of mouse inbred strains (2000), Nature, Jan2000, v24, p23
Originally inbred at the Rockefeller Institute, AKR mice are widely used in cancer research for their high leukemia incidence (60-90%) and in immunology as a source of the Thy1.1 (theta AKR) antigen. AKR/J mice are viremic from birth, and express the ecotropic retrovirus AKV in all tissues. The hair interior defect (hid) mutation, a strain characteristic of AKR mice, causes alterations in hair development that is only evident microscopically. Adrenocortical lipid depletion (ald) in AKR mice is caused by a mutation in sterol O-acyltransferase 1 (Soat1), and leads to a truncated SOAT1 protein. AKR/J mice are relatively resistant to aortic lesion formation on a semi-synthetic high fat diet and are hyporesponsive to diets containing high levels of fat and cholesterol.
Both CAST/EiJ and CASA/RkJ (Stock No. 000735) were derived from wild mice trapped in Thailand. CAST is often combined with the common laboratory strains to generate F1 hybrids with high levels of heterozygosity for use in genetic mapping. Unlike the wild-derived strain SPRET, male F1 mice from a CAST cross are fertile. Like CASA, CAST is resistant to flavivirus infection. The flavivirus family includes pathogens responsible for dengue, yellow fever and several forms of encephalitis. Most common laboratory mice are sensitive to flavivirus infection. Resistance/sensitivity is conferred through the oligoA synthase Oas1b locus. In a comparison of multiple strains, CASA and CAST exhibit reduced numbers of retinal ganglion cells as compared to common laboratory strains and other wild-derived strains. In a 2015 study comparing CAST/Ei and the other Collaborative Cross inbred strains (A/J, C3H/HeJ, C57BL/6J, DBA/2J, 129S1/SvImJ, NOD/LtJ, NZO/HlLtJ, and WSB/EiJ), dorsal root ganglion neurons from CAST/Ei mice demonstrate a significantly improved ability to regenerate axons in an inhibitory environment as determined by an increase in number of neurons with neurites and longer axonal process per neuron under both naive and pre-injured conditions. In addition, as compared to neurons from C57BL/6 mice, CAST/Ei neurons exhibit more extensive axonal regeneration in the spinal cord and optic nerve following injury and show greater sprouting following ischemic stroke. Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research.
FVB/NJ was inbred for the Fv1b allele which confers sensitivity to the Friend leukemia virus B strain. Due to the prominent pronuclei in their fertilized eggs and the large litter size, FVB/NJ mice are commonly used for transgenic injection. Compared to many other inbred strains, FVB/NJ is highly susceptible to asthma-like airway responsiveness with significant generation of antigen-specific IgE. Despite having the H2q MHC haplotype, FVB/NJ are resistant to collagen-induced arthritis. This resistance stems from coding polymorphisms in Tcra-V11.1 and a genomic deletion of some Tcrb-V genes that includes Tcrb-V8.2. FVB/NJ have higher than average activity, anxiety, and basal body temperature, low stress-induced hyperthermia, and are homozygous for the Pde6brd1 allele, which results in early onset retinal degeneration. Although FVB/N typically do not develop spontaneous tumors, they are highly susceptible to chemically induced squamous cell carcinomas with a high rate of malignant conversion from papilloma to carcinoma.
NZO mice of both sexes exhibit high birth weights and are significantly heavier at weaning age. Severe obesity (including both visceral and subcuatneous fat depots) develops even when mice are maintained on a standard diet containing 4.5% fat. Both males and females of the NZO/Hl substrain exhibit impaired glucose tolerance (IGT), but subsequent type 2 maturity onset (NIDDM) diabetes development is limited to males, with a phenotype penetrance of 50% or less. NZO/Hl mice also show anti-insulin receptor antibodies, a defect in leptin transport, and hypertension. The genetic lesion appears to be within the islets of Langerhans as transfer of pancreatic islets from normal mice returns body weights and blood glucose levels to within normal range. Ovarian granulosa cell tumors, lymphomas, duodenal, and lung tumors have also been noted to occur in NZO mice at an elevated frequency. F1 hybrids of NON/ShiLt and NZO/Hl provide a new model of obesity-induced diabetes. Male (NON/ShiLt x NZO/Hl)F1 hybrids are obese (BW = 53.5 g by 16 weeks) and almost all develop maturity onset NIDDM. F1 males on a 4% diet will develop hyperglycemia around 20 to 24 weeks of age; increasing the fat content of the diet accelerates diabetes onset to 16 to 20 weeks of age. (NZO/Hl x NON/ShiLt)F1 hybrids will develop diabetes slightly faster than their reciprocal cross due to the NZO maternal environment; however this cross is difficult to produce due to the inherently poor breeding performance of NZO/HlJ female mice. F1 females exhibit a weight gain similar to the NZO parent, and have impaired glucose tolerance but are resistant to diabetes development. Diabetes development can be accelerated to eight to 12 weeks by fostering onto an F1 dam. Reciprocal backcrosses to the parental strains and analysis of (NON/ShiLt x NZO/Hl)F2 mice has led to the identification of a number of complex diabetes-predisposing ("diabesity") QTLs. Dr. Leiter's research group at The Jackson Laboratory is currently developing a series of nine recombinant congenic strains (RCS) made by backcrossing the (NZO/Hl x NON/ShiLt)F1 for two generations onto the NON/ShiLt background before inbreeding (~12% NZO/Hl, 88% NON/ShiLt genomes). Preliminary analysis indicates that body weight gains of all RCS are higher than NON/ShiLt, but none are as obese as NZO/Hl; some of these RCS develop NIDDM while others are resistant. These new strains will be useful to further analyze diabesity QTLs and as new models for type 2 (NIDDM) diabetes. An additional benefit of the RCS is better breeding performance than NZO/Hl.
PWK was derived from wild mice trapped near Prague, Czech Republic. PWK has a biochemical profile that is similar to the inbred strain PWD (also originating from the Czech Republic - Stock No. 004660) with the exception of the isoenzyme variant esterase 13 (Es13b). Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research.
Watkins Star Line B (WSB) was derived from wild mice trapped in Eastern Shore, Maryland. WSB is characterized by a distinct and consistent white head blaze, variable ventral spotting and a slight coat dilution on the agouti background. The variation in pigment is the result of the spontaneous mutation blaze (Kitlblz).Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research.
LP/J mice display a high susceptibility to audiogenic seizures. This strain is also reported to have a fairly high incidence of tumors that develop later in life, including mammary tumors, lymphoma, lung and soft-tissue sarcomas. LP/J mice are also homozygous for the spontaneous mutation piebald in the endothelin receptor type B gene (Ednrbs). The piebald spontaneous mutation is the result of a mutation in the endothelin receptor type B gene, Ednrb. Mice show irregular white spotting, the amount of which is greatly influenced by minor modifying genes. They also have dark eyes. The white areas of the coat are completely lacking in neural crest-derived melanocytes, and there is a reduction in the number of melanocytes in the choroid layer of the eye.
The wild-derived inbred strain SPRET/Ei is often used in crosses with common inbred strains to create highly polymorphic panels for genetic mapping. SPRET/Ei mice are resistant to high doses of tumor necrosis factor alpha (TNFa) (Staelens et al 2002). Mice from a C57BL/6 x SPRET/Ei F1 cross were protected from TNFa-induced arthritis and partially protected against induced allergic asthma (Staelens et al 2004). SPRET/Ei may be useful in understanding certain inflammatory diseases.
CBA/J inbred mice are widely used as a general purpose strain. CBA/J strain is the only CBA substrain that carries the Pde6brd1 mutation, which causes blindness by wean age. CBA/J mice are not histocompatible with the CBA/CaJ (Stock No. 000654) substrain (Green and Kaufer, 1965). The CBA/J inbred mouse strain is used to study granulomatous experimental autoimmune thyroiditis (G-EAT), are relatively resistant to diet-induced atherosclerosis (Paigen et al. 1990), and develop a mild hearing loss late in life, with most of the hearing loss occurring in the higher frequencies (Sweet et al. 1988). Renal tubulointerstitial lesions have been observed in this strain at a high frequency (Rudofsky 1978). Some CBA/J mice spontaneously develop exocrine pancreatic insufficiency syndrome (Eppig and Leiter 1977, Leiter et al. 1977).
CAROLI was derived from wild mice trapped in Thailand and is from the species Mus caroli, which is distantly related to laboratory mice and does not breed with laboratory mice. These mice are characterized by black feet. This wild derived mouse strain is genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and is a valuable tool for sequence comparison, evolution and systematics research.
ICR/HaJ is a mouse strain as described in Jackson Laboratory strain index. This inbred strain is derived from the outbred strain ICR. It may be useful in therapeutic drug testing and genetic analysis of carcinogen-induced colon cancer.
A Mus musculus individual that is a substrain of C57BL/6J (mother) and CAST/EiJ (father).
DBA
CBA
Measurement Unit of Flow
A Measurement Unit that is used as a standard for measurement of the rate at which portions of a substance pass per unit of time.
In traditional astronomical usage, civil time is mean solar time as calculated from midnight as the beginning of the Civil Day.
Note that Civil Time Reference System is more accurately represented as a Temporal Reference System that participates in an act of usage that is sanctioned by an appropriate civil authority. As such, it should be represented as a defined class.
Civil Time Reference System
A Temporal Reference System that is a statutory time scale as designated by civilian authorities to determine local time(s).
Measurement Unit of Acceleration
A Measurement Unit that is used as a standard for measurement of the rate at which objects change their velocities per unit of time.
feet per second per second, kilometers per second per second
Measurement Unit
A Descriptive Information Content Entity that describes a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.
Solar Time Reference System
A Temporal Reference System that is based on the position of the Sun in the sky.
The type of particle quantified is typically either atoms or molecules, but may also be protons, neutrons, electrons, quarks, or other particles. The type of particle being measured should always be specified along with the measurement and its unit.
Measurement Unit of Amount of Substance
Measurement Unit of Chemical Amount
Measurement Unit of Enplethy
A Measurement Unit that is used as a standard for measurement of the number of a specified type of particle in a portion of matter.
Measurement Unit of Sound Level
A Measurement Unit that is used as a standard for measurement of the level (the loudness) of sounds.
Measurement Unit of Area
A Measurement Unit that is used as a standard for measurement of two-dimensional regions or Geospatial Regions.
square feet, square meters, acre, hectare
Measurement Unit of Power
A Measurement Unit that is used as a standard for measurement of rates of work.
Measurement Unit of Mass
A Measurement Unit that is used as a standard for measurement of an object's resistance to Acceleration when a Force is applied to the object.
A single Clock Time System does not provide a complete means for identifying or measuring times. Depending on the particular Clock Time System, it may be compatible for use with one or more other Temporal Reference Systems.
Clock Time System
A Temporal Reference System that is a convention for keeping and displaying the Time of Day.
Note that, while reference systems and reference frames are treated as synonyms here, some people treat them as related but separate entities. See: http://www.ggos-portal.org/lang_en/GGOS-Portal/EN/Topics/GeodeticApplications/GeodeticReferenceSystemsAndFrames/GeodeticReferenceSystemsAndFrames.html
Spatial Reference System
Coordinate System
Spatial Coordinate System
Spatial Reference Frame
A Reference System that describes a set of standards for uniquely identifying the position of an entity or the direction of a vector within a defined spatial region by means of measurements along one or more Coordinate System Axes.
Solar Calendar System
A Calendar System that is designed to organize and identify dates based on the cycles of an Astronomical Body's Orbit around the Sun.
Unless otherwise specified, a Solar Calendar System is assumed to be relative to the Orbit of the Earth around the Sun.
Measurement Unit of Volumetric Flow Rate
A Measurement Unit of Flow that is used as a standard for measurement of the rate at which volumes of fluid pass per unit time.
cubic metres per second, standard cubic centimeters per minute, cubic feet per second, gallons per minute
Spatial Region Identifier
A Designative Information Content Entity that designates some Spatial Region.
Reference System
A Descriptive Information Content Entity that describes a set of standards for organizing and understanding data of the specified type or domain.
Temporal Region Identifier
A Designative Information Content Entity that designates some Temporal Region.
Measurement Unit of Energy
A Measurement Unit that is used as a standard for measurement of the Amount of work that is available in an object.
Geospatial Coordinate Reference System
Geographic Coordinate System
A Spatial Reference System that is used to determine and identify the location of a point or object at or near the surface of the Earth.
Measurement Unit of Force
A Measurement Unit that is used as a standard for measurement of interactions in which the Motion or Velocity of an object is changed, unless the interaction is opposed.
Measurement Unit of Area Moment of Inertia
Measurement Unit of Second Area Moment
A Measurement Unit that is used as a standard for measurement of the distribution of Mass of an object with respect to an axis.
A measure of an object’s resistance to bending or deflection.
Measurement Unit of Currency
A Measurement Unit used in measurements of financial values.
U.S. Dollar, Euro, Yuan, South African Rand
Measurement Unit of Rotational Inertia
Measurement Unit of Moment of Inertia
Measurement Unit of Rotational Mass
A Measurement Unit that is used as a standard for measurement of the distribution of Mass of an object with respect to its axis of rotation.
A measure of an object’s resistance to change in its state of rotation.
Universal Time Reference System
A Solar Time Reference System that is based on the average speed of the Earth's rotation and which uses the prime meridian at 0° longitude as a reference point.
Measurement Unit of Torque
Measurement Unit of Moment of Force
Measurement Unit of Rotational Force
A Measurement Unit that is used as a standard for measurement of the rate of change of angular momentum of an object.
Designative Information Content Entity
Designative ICE
An Information Content Entity that consists of a set of symbols that denote some Entity.
Measurement Unit of Angle
A Measurement Unit that is used as a standard for measurement of the angle between two lines or planes in relation to a vertex.
Measurement Unit of Density
A Measurement Unit that is used as a standard for measurement of the mass of an object per unit of its total volume.
Standards of date, time, and time zone data formats: ISO/WD 8601-2 (http://www.loc.gov/standards/datetime/iso-tc154-wg5_n0039_iso_wd_8601-2_2016-02-16.pdf) W3C (https://www.w3.org/TR/NOTE-datetime)
There is no class 'Time Zone' (the region), only 'Time Zone Identifier' (the designator for some region). Instances of 'Time Zone Identifier' should be related to instances of 'Information Bearing Entity' by means of the object properites 'uses time zone identifier' and 'time zone identifier used by' as appropriate. This is supposed to be analogous to the way we represent the relationship between measurement values and measurement units, where the relevant instance of Information Bearing Entity 'uses measurement unit' some instance of Measurement Unit (i.e., an instance of Information Content Entity).
Time Zone Identifier
A Spatial Region Identifier that designates the region associated with some uniform standard time for legal, commercial, or social purposes.
Measurement Unit of Temperature
A Measurement Unit that is used as a standard for measurement of the thermal energy in an object.
Measurement Unit of Work
A Measurement Unit that is used as a standard for measurement of displacements of points to which Forces have been applied.
Descriptive Information Content Entity
Descriptive ICE
An Information Content Entity that consists of a set of propositions that describe some Entity.
Calendar System
A Temporal Reference System that is designed to organize and identify dates.
Calendars typically organize dates through the use of naming and temporal conventions based on Days, Weeks, Months, and Years.
Measurement Unit of Momentum
A Measurement Unit that is used as a standard for measurement of the Momentum of a portion of matter that is in Motion.
Information Content Entity
ICE
A Generically Dependent Continuant that generically depends on some Information Bearing Entity and stands in relation of aboutness to some Entity.
Information Content Entity is here intended to be a class of Entities whose instances are the informational content of Information Bearing Entities. For example, three instances of information bearers -- such as a bar chart, color-coded map, and a written report -- each of which lists the GDP of Countries for the year 2010 are each different carriers of the same information content. It is this content that is generically dependent upon its carrier. This treatment of Informational Content Entity (cf. the Information Artifact Ontology) leads to a principle of subtyping based upon the relationship that ICE's have with the Entity they are about rather than characteristics such as format, language, measurement scale, or media. The latter are treated here as being Qualities of bearers.
Measurement Unit of Frequency
A Measurement Unit that is used as a standard for measurement of the number of times an event repeats per unit of time.
Measurement Unit of Speed
A Measurement Unit that is used as a standard for measurement of the rates at which objects traverse distance.
miles per hour, kilometers per hour, knot, mach
Measurement Unit of Electromagnetic Force
A Measurement Unit that is used as a standard for measurement of the electromagnetic force between electrically charged entities.
Measurement Unit of Pressure
A Measurement Unit that is used as a standard for measurement of Force applied perpendicular to a surface per unit area.
pascal, atmosphere, pound-force per square inch
Military Time Zone Identifier
A Time Zone Identifier that designates a spatial region where the local time is calculated according to the specified offset from Zulu time, which has no offset from Coordinated Universal Time.
Measurement Unit of Length
A Measurement Unit that is used as a standard for measurement of one-dimensional regions or Geospatial Regions.
Measurement Unit of Mass Flow Rate
A Measurement Unit of Flow that is used as a standard for measurement of the rate at which the Mass of a substance passes per unit time.
kilogram per second, slug per second, pound per second
Measurement Unit of Volume
A Measurement Unit that is used as a standard for measurement of sites or three-dimensional regions or Geospatial Regions.
Temporal Reference System
Temporal Reference Frame
Time Scale
A Reference System that describes a set of standards for measuring time as well as understanding the context of and organizing temporal data.
Measurement Unit of Impulse
A Measurement Unit that is used as a standard for measurement of the integral of a Force applied to a portion of matter over a temporal interval.
Cartesian Coordinate System
Rectangular Coordinate System
A Spatial Reference System that identifies each point in a spatial region of n-dimensions using an ordered n-tuple of numerical coordinates that are the signed (i.e. positive or negative) distances measured in the same unit of length from the zero point where the fixed perpendicular Coordinate System Axes meet.
Greenwich Mean Time (GMT) is the mean solar time at the Royal Observatory in Greenwich, London and has been superseded by Coordinated Universal Time (UTC).
Greenwich Mean Time Zone Identifier
A Time Zone Identifier that designates a spatial region where the local time is calculated according to the specified offset from Greenwich Mean Time.
Measurement Unit of Time
A Measurement Unit that is used as a standard for measurement of temporal regions.
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
exploratory term
exemplar term
example to be eventually removed
failed exploratory term
The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
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
The term was created to ease viewing/sorting terms for development purposes, but 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
The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
terms merged
The term has been combined with one or more other terms to create a more encompassing (merged) term.
An editor note should explain what were the merged terms and the reason for the merge.
The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
term imported
The term has been replaced by a term imported from another ontology.
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.
This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
term split
The term has been split into two or more new terms.
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.
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. The deprecated term should reference the replacement terms with obo:IAO_0100001.
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.
requires discussion
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.
An confidence interval with 95 percent probability that the true population value can be found.
95% confidence interval
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
person:Jennifer Fostel
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
An organization which supplies technology, tools and protocols for use in high throughput applications
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
0-non autolyis
An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
1-slight autolysis
An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
2-moderate autolysis
An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
3-severe autolysis
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
An organization that is developing and selling nanopore sequencing products and is based in the UK.
An organization that manufactures mosquito traps and other mosquito control products.
A manufacturer of rapid point-of-care assay devices.
A manufacturer of in vitro diagnostic assay kits in India.
A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases.
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.
This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
The samples were irradiated using the NSRL Galactic Cosmic Ray Simulation.
The NSRL Galactic Cosmic Ray Simulation is comprised of seven different species of ion, and fourteen different energies of H and He for 33 separate beams in a single GCRSim exposure. (https://www.bnl.gov/nsrl/userguide/GCRSim.php)
The experiment was conducted at the NSRL
A particle accelerator beamline located at Brookhaven National Laboratory
A particle accelerator at the National Institute of Radiological Sciences in Chiba, Japan
The experiment was conducted aboard the International Space Station
An instance of an Earth-orbiting space station that went operational in the year 2000.
The experiment was conducted on the Mir space station
An instance of an Earth-orbiting space station, operational from1986 to 2001, operated by the Soviet Union and later by Russia.
The biological payload was carried into orbit by the Space Shuttle
An instance of a reusable spacecraft designed to carry passengers and equipment into low Earth orbit and return to Earth. Operated by the United States and operational from 1981 to 2011.
The experiment was conducted aboard the Bion-MI satellite.
An instance of a Russian-operated Earth satellite carrying biological samples. Launched April 19, 2013 and returned to Earth May 19, 2013
The samples were flown on the Foton-M4 satellite
An instance of a Russian-operated Earth satellite carrying biological samples. Launched July 19, 2014 and returned to Earth September 1, 2014
The experiment was conducted on the Shenzhou-8 space station
An instance of a Chinese-operated Earth satellite carrying biological samples. Launched October 31, 2011 and returned to Earth November 17, 2011.
The experiment was conducted in the US Laboratory on the ISS
An instance of a module on the International Space Station, operated by the United States
The experiment was conducted on the Japanese Experiment Module
A Japanese science module for the International Space Station developed by JAXA. It is the largest single ISS module, and is attached to the Harmony module. The first two pieces of the module were launched on Space Shuttle missions STS-123 and STS-124.
The experiment was conducted on the Columbus module on the ISS
An instance of a module on the International Space Station, operated by the European Space Agency.
The experiment was conducted in the Zvezda module of the ISS.
An instance of a module on the International Space Station, operated by the Russian Space Agency.
The experiment was carried out at the SIS-18 accelerator.
An particle accelerator located at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germay.
The samples were irradiated using the NSRL Solar Particle Event Simulation.
The NSRL SPE simulatoris based on the fluence of the August 1972 event, with an energy spectrum similar to the March 1989 event. The majority of the protons are at very low energies, below 1 MeV, and pose little to no risk to astronauts in a space craft or space suit. The SPESim begins with 50 MeV protons, which amounts to 91.66% of the total dose. Then the beam energy increments in steps of 10 MeV up to 150 MeV where 0.14% of the total dose is delivered.
The samples were irradiated using the NSRL Simplified Galactic Cosmic Ray Simulation.
The NSRL Simplified Galactic Cosmic Ray Simulation uses 6 beams and 5 different ions including protons at two different energies. https://www.bnl.gov/nsrl/userguide/SimGCRSim.php
NSRL Simplified Galactic Cosmic Ray Simulation
The samples were irradiated with thermal neutrons at the KUR-HWNIF
A heavy water tank of approximately 2 m3 adjacent to the core of the Kyoto University Research Reactor (KUR), a light-water moderated tank-type reactor.
Kyoto University Research Reactor-Heavy Water Neutron Irradiation Facility
The samples were irradiated with fast neutrons at the HIRRAC.
A neutron generator at the Research Institute for Radiation Biology and Medicine, Hiroshima University (RIRBM). Monoenergetic neutrons of which energy is less than 1.3 MeV are generated by the 7Li(p,n)7 Be reaction at proton energies up to 3 MeV.
Hiroshima University Radiobiological Research Accelerator
The Gamma Radiation Facility known as GRSF houses a cesium-137 gamma ray source which can provide gamma rays at a variety of dose rates. The gamma source is an industry standar dJ.L. Shepherd Mark I Model 68A 137Cs ? Irradiator. The photon energy from the source is 662 keV, with a Lineal Energy Transfer (LET) in water of approximately 0.8 keV/um. (https://www.bnl.gov/nsrl/grsf/)
Brookhaven National Laboratory Gamma Radiation Source Facility
A specific instance of Faxitron CP160 x-ray source.
A specific instance of an X-Rad320 x-ray source.
A particle accelerator located at Brookhaven National Laboratory, Upton, NY, capable of delivering protons and heavier ions at energies between several hundred MeV/nucleon and several GeV/nucleon.
Brookhaven National Laboratory Alternating Gradient Synchrotron
An instance of an underground low background radiation laboratory located near the Baksan Neutrino Laboratory
Deep Underground Low Radiation Background Laboratory
An instance of an underground low background radiation laboratory
Mark 1 model 68A gamma irradiator at ARC
An underwater habitat and research laboratory deployed on the ocean floor at a depth of 62 feet/19 meters and located 3.5 miles/6.5 km from Key Largo, FL. The installation consists of a surface-level life support buoy, the 45ft/14m x 9.8ft/3m habitat with living quarters, life-support systems, and laboratory space, and two underwater waystations supplying air for aquanauts on extended dives outside the habitat. The habitat includes a wet entry porch, a pressurizable main cabin, and a sealable entry lock connecting the two pressure zones. Saturation diving allows crews of up to six people to conduct extended missions while living in the habitat. Aquarius enables spaceflight analog studies approximating extreme space environments, extravehicular activity, and isolation and confinement of crew.
References: Sandra H�uplik-Meusburger and Sheryl Bishop, Space Habitats and Habitability: Designing for Isolated and Confined Environments on Earth and in Space (Cham, Switzerland: Springer Nature Switzerland, 2021). NASA NEEMO page: [https://www.nasa.gov/mission/neemo/]
The NEK facility is located at the Institute of Biomedical Problems (IBMP) at the Russian Academy of Sciences in Moscow, Russia. It is a multi-compartment, pressurized facility that is used to capture subjects' emotional and mental state in long-duration isolated and confined environment to advance understanding of behavioral risks associated with this type of spaceflight analog. Subjects are physically isolated and have limited communication to the outside world. This enables subjects to feel as if they are in an actual spaceflight environment. The two areas of study are behavioral health and biochemistry, which will monitor subjects� psychological health and cortisol levels, respectively.
:envihab is a state-of-the-art research facility located in Cologne, Germany.
The HERA facility is located at the Johnson Space Center in Houston, Texas and consists of a unique three-story closed habitat that is designed to serve as an analog for isolation, confinement, and remote conditions in exploration scenarios. Subjects� emotional and mental states in a short-duration, isolated, and confined environment are captured to advance understanding of behavioral risks associated with this type of spaceflight analog. The two areas of study are behavioral health and biochemistry, which monitor subjects� psychological health and cortisol levels, respectively.
A collection is an aggregation of items. The term collection means that the resource is described as a group; its parts may be separately described and navigated.
Collection
A dataset is information encoded in a defined structure (for example, lists, tables, and databases), intended to be useful for direct machine processing.
Dataset
An event is a non-persistent, time-based occurrence. Metadata for an event provides descriptive information that is the basis for discovery of the purpose, location, duration, responsible agents, and links to related events and resources. The resource of type event may not be retrievable if the described instantiation has expired or is yet to occur. Examples - exhibition, web-cast, conference, workshop, open-day, performance, battle, trial, wedding, tea-party, conflagration.
Event
An image is a primarily symbolic visual representation other than text. For example - images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that image may include both electronic and physical representations.
Image
An interactive resource is a resource which requires interaction from the user to be understood, executed, or experienced. For example - forms on web pages, applets, multimedia learning objects, chat services, virtual reality.
Interactive Resource
An inanimate, three-dimensional object or substance. For example -- a computer, the great pyramid, a sculpture. Note that digital representations of, or surrogates for, these things should use Image, Text or one of the other types.
Physical Object
A service is a system that provides one or more functions of value to the end-user. Examples include: a photocopying service, a banking service, an authentication service, interlibrary loans, a Z39.50 or Web server.
Service
Software is a computer program in source or compiled form which may be available for installation non-transiently on another machine. For software which exists only to create an interactive environment, use interactive instead.
Software
A sound is a resource whose content is primarily intended to be rendered as audio. For example - a music playback file format, an audio compact disc, and recorded speech or sounds.
Sound
A text is a resource whose content is primarily words for reading. For example - books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre text.
Text
The DCMI Box identifies a region of space using its geographic limits.
DCMI Box
Dewey Decimal Classification
DDC
The Internet media type of the resource.
IMT
ISO 3166 Codes for the representation of names of countries
ISO 3166
ISO 639-2: Codes for the representation of names of languages.
ISO 639-2
Library of Congress Classification
LCC
Library of Congress Subject Headings
LCSH
Medical Subject Headings
MeSH
A specification of the limits of a time interval.
DCMI Period
The DCMI Point identifies a point in space using its geographic coordinates.
DCMI Point
Internet RFC 1766 'Tags for the identification of Language' specifies a two letter code taken from ISO 639, followed optionally by a two letter country code taken from ISO 3166.
RFC 1766
Internet RFC 3066 'Tags for the Identification of Languages' specifies a primary subtag which is a two-letter code taken from ISO 639 part 1 or a three-letter code taken from ISO 639 part 2, followed optionally by a two-letter country code taken from ISO 3166. When a language in ISO 639 has both a two-letter and three-letter code, use the two-letter code; when it has only a three-letter code, use the three-letter code. This RFC replaces RFC 1766.
RFC 3066
The Getty Thesaurus of Geographic Names
TGN
Universal Decimal Classification
UDC
A URI Uniform Resource Identifier
URI
W3C Encoding rules for dates and times - a profile based on ISO 8601
W3C-DTF
Haiti Gourde
Yemeni Rial
Mauritania Ouguiya
Minute of Arc Measurement Unit
Arcminute
MOA
amin
arcmin
Kenyan Shilling
Slug Measurement Unit
slug
Erg Measurement Unit
erg
GMT-8
PST
Pacific Standard Time
Tablespoon Measurement Unit
Papua New Guinea Kina
Newfoundland Standard Time
Viet Nam Dong
Centimeter Measurement Unit
Global Area Reference System
Ghana Cedi
Sri Lanka Rupee
South Africa Rand
Kilogram Per Liter Measurement Unit
Offset from Universal Coordinated Time = UTC+2
Bravo Time Zone
Afghanistan Afghani
GMT-2
BET
Brazil Eastern Time
Australian Central Standard Time
Shaft Horsepower Measurement Unit
shp
Offset from Universal Coordinated Time = UTC-11
X-ray Time Zone
Singapore Dollar
Guyana Dollar
Pound Force Measurement Unit
lbf
Offset from Universal Coordinated Time = UTC+0
GMT
Greenwich Mean Time
Milligram Measurement Unit
TT is an astronomical time standard that is a theoretical ideal designed to be free of the irregularities in Earth's rotation and is primarily used for time measurements of astronomical observations made from the surface of Earth. It was formerly called Terrestrial Dynamical Time (TDT), which was formulated to replace Ephemeris Time (ET).
Terrestrial Time
Swiss Franc
Cubic Centimeter Measurement Unit
cm^3
ET is an astronomical time scale that was adopted as a standard in 1952 by the IAU but has since been superseded and is no longer actively used. ET is based on the ephemeris second, which was defined as a fraction of the tropical year for 1900 January 01 as calculated using Newcomb's 1895 tables of the Sun. ET was designed to avoid problems caused by variations in Earth's rotational period and was used for Solar System ephemeris calculations until being replaced by Terrestrial Dynamical Time (TDT) in 1979.
Ephemeris Time
Kilogram-Mole Measurement Unit
kg-mol
kilogram-mole
GMT+5
PLT
Pakistan Lahore Time
Dominican Peso
Offset from Universal Coordinated Time = UTC-6
Sierra Time Zone
Quart Measurement Unit
Deciliter Measurement Unit
Offset from Universal Coordinated Time = UTC+1
Alpha Time Zone
Miles Per Second Measurement Unit
mi/s
Chinese Renminbi
Canadian Dollar
Kilometers Per Hour Measurement Unit
km/h
Gram-Mole Measurement Unit
g-mol
gram-mole
Offset from Universal Coordinated Time = UTC+6
Foxtrot Time Zone
Offset from Universal Coordinated Time = UTC-10
Whiskey Time Zone
Kilogram Force Per Centimeter Square Measurement Unit
Kilogram Per Square Centimeter Measurement Unit
Kilopond Per Centimeter Square Measurement Unit
Mile Measurement Unit
GMT+1
ECT
European Central Time
Colombian Peso
Universal Time 1 D
Liter Measurement Unit
Litre
Square Yard Measurement Unit
yd^2
Twenty-Four-Hour Clock Time System
24-Hour Clock
24-Hour Clock Time System
Military Time
Military Time System
Twenty-Four Hour Clock Time System
Twenty-Four-Hour Clock
A Clock Time System for time keeping in which the Day runs from midnight to midnight and is divided into 24 Hours, indicated by the Hours passed since midnight, from 0 to 23.
GMT-9
AST
Alaska Standard Time
Rwanda Franc
Week Measurement Unit
Albania Lek
Year Measurement Unit
Centiliter Measurement Unit
Mike Time Zone is the same local time as Yankee Time Zone, but is 1 Day (i.e. 24 Hours) ahead of Yankee Time Zone as they are on opposite sides of the International Date Line.
Offset from Universal Coordinated Time = UTC+12
Mike Time Zone
CFP Franc
Malawi Kwacha
Czech Koruna
Volt Measurement Unit
Milliampere Measurement Unit
Indian Rupee
Binary Degree Measurement Unit
Binary Radian
Brad
Offset from Universal Coordinated Time = UTC+11
Lima Time Zone
Bolivia Boliviano
Square Mile Measurement Unit
mi^2
Offset from Universal Coordinated Time = UTC-4
Quebec Time Zone
Costa Rica Colon
Pound Per Second Measurement Unit
lb/s
Mauritius Rupee
TDB is a linear scaling of Barycentric Coordinate Time (TCB) and is a relativistic coordinate time scale used in astronomy as a time standard that accounts for time dilation when calculating Orbits and Ephemerides of Astronomical Bodies and interplanetary Spacecraft in the Solar System. TDB is a successor of Ephemeris Time (ET) and is nearly equivalent to the time scale Teph used for DE405 planetary and lunar ephemerides generated by the Jet Propulsion Laboratory.
Barycentric Dynamical Time
Twenty Foot Equivalent Unit
Kilomole Measurement Unit
kilomole
kmol
Uzbekistan Sum
Namibia Dollar
Revolutions Per Day Measurement Unit
r/day
GMT-4
PRT
Puerto Rico and US Virgin Islands Time
GMT+10
AET
Australia Eastern Time
Kilometers Per Second Measurement Unit
km/s
Megahertz Measurement Unit
MHz
Square Centimeter Measurement Unit
cm^2
Cubic Millimeter Measurement Unit
mm^3
Euro
Atmosphere Measurement Unit
atm
Kilohertz Measurement Unit
kHz
GMT+4
NET
Near East Time
Kilogram Measurement Unit
Angstrom Measurement Unit
Angstrom
Ångström
Angolan Kwanza
Offset from Universal Coordinated Time = UTC+9
India Time Zone
Macao Pataca
Algerian Dinar
One mole contains exactly 6.02214076×10^23 elementary entities.
Mole Measurement Unit
Bangladesh Taka
Surinamese Dollar
Square Kilometer Measurement Unit
km^2
Peru Nuevo Sol
Offset from Universal Coordinated Time = UTC-7
Tango Time Zone
Radian Measurement Unit
Bulgarian Lev
Universal Time 1 A
Lebanese Pound
Kilonewton Measurement Unit
Yard Measurement Unit
yrd
Sone Measurement Unit
sone
Square Meter Measurement Unit
m^2
Kuwaiti Dinar
Fiji Dollar
Kiloliter Measurement Unit
Offset from Universal Coordinated Time = UTC+5
Echo Time Zone
Tanzania Shilling
Decibel Isotropic Measurement Unit
Decibels Relative to an Isotropic Reference Antenna
Hungary Forint
Newton Meter Measurement Unit
Uruguay Peso
Universal Time 1 F
Lesotho Loti
Brunei Dollar
Belarussian Ruble
Tonga Pa anga
Meters Per Second Measurement Unit
m/s
South Sudanese Pound
Mexican Peso
Laos Kip
Liberian Dollar
Offset from Universal Coordinated Time = UTC-2
Oscar Time Zone
Nicaragua Cordoba Oro
Madagascar Malagasy Ariary
Turkish Lira
Zambia Kwacha
Philippine Peso
Square Foot Measurement Unit
ft^2
Pint Measurement Unit
GMT-11
MIT
Midway Islands Time
Newton Measurement Unit
Mach Measurement Unit
Offset from Universal Coordinated Time = UTC+8
Hotel Time Zone
Kilogram Meter Per Second Measurement Unit
kg m/s
"TCG is a coordinate time standard intended to be used as the independent variable of time for all calculations pertaining to precession, nutation, the Moon, and artificial satellites of the Earth. It is equivalent to the proper time experienced by a clock at rest in a coordinate frame co-moving with the center of the Earth: that is, a clock that performs exactly the same movements as the Earth but is outside the Earth's gravity well. It is therefore not influenced by the gravitational time dilation caused by the Earth." From: (https://en.wikipedia.org/wiki/Geocentric_Coordinate_Time)
Geocentric Coordinate Time
Cubic Meter Per Second Measurement Unit
Botswana Pula
Egyptian Pound
Hour Measurement Unit
GMT+7
VST
Vietnam Standard Time
Sudanese Pound
Second Measurement Unit
UTC is a variant of Universal Time that is calculated by combining Universal Time 1 with International Atomic Time by occasionally adding leap seconds to TAI in order to maintain UTC within 0.9 seconds of UT1. The difference between UTC and UT1 is called DUT1 and always has a value between -0.9 seconds and +0.9 seconds. Coordinated Universal Time is the current basis for civil time and is the reference time for time zones, whose local times are defined based on an offset from UTC.
Coordinated Universal Time
Meters Per Second Per Second Measurement Unit
m/s/s
m/s^2
Tajikistan Somoni
Israel Shekel
GMT+12
NST
New Zealand Standard Time
Paraguay Guarani
Decimeter Measurement Unit
Short Ton Measurement Unit
Net Ton
ton (US)
Swaziland Lilangeni
Democratic Republic Of Congo Franc
Syrian Pound
UT1R is a variant of Universal Time that is a smoothed version of UT1 by filtering out periodic variations due to tidal waves.
Universal Time 1 R
Dyne Measurement Unit
dyn
The Julian Calendar was proposed by Julius Caesar as a reform of the Roman Calendar, took effect on 1 January 46 BC, and was the predominant Calendar System in Europe until being largely replaced by the Gregorian Calendar.
Julian Calendar
A Solar Calendar System that has a regular Year of 365 24-Hour Days divided into 12 Months with a leap day added at the end of February every 4 Years such that the average length of a Julian Year is 365.25 Days.
Cubic Foot Measurement Unit
ft^3
Gram Measurement Unit
GMT+6
BST
Bangladesh Standard Time
GMT-10
HST
Hawaii Standard Time
Pound Foot Measurement Unit
Samoa Tala
Pound Foot Second Square Measurement Unit
New Zealand Dollar
Pascal Measurement Unit
Calorie Measurement Unit
cal
Uganda Shilling
Cambodian Riel
Horsepower Measurement Unit
Decigram Measurement Unit
GMT-5
EST
Eastern Standard Time
IET
Indiana Eastern Standard Time
Watt Measurement Unit
Ounce Measurement Unit
Gram Per Cubic Centimeter Measurement Unit
Kilogram Per Cubic Meter Measurement Unit
GMT+2
EET
Eastern European Time
Day Measurement Unit
Kelvin Measurement Unit
Teaspoon Measurement Unit
Revolutions Per Minute Measurement Unit
r/min
rpm
CFA Franc
Milliliter Measurement Unit
Ukraine Hryvnia
Nepalese Rupee
Liter Per Second Measurement Unit
l/s
Offset from Universal Coordinated Time = UTC-3
Papa Time Zone
The ITRS definition fulfills the following conditions: 1. It is geocentric, the center of mass being defined for the whole earth, including oceans and atmosphere. 2. The unit of length is the metre (SI). This scale is consistent with the TCG time coordinate for a geocentric local frame, in agreement with IAU and IUGG (1991) resolutions. This is obtained by appropriate relativistic modelling. 3. Its orientation was initially given by the BIH orientation at 1984.0. 4. The time evolution of the orientation is ensured by using a no-net-rotation condition with regards to horizontal tectonic motions over the whole earth. From: (https://www.iers.org/IERS/EN/Science/ITRS/ITRS.html)
International Terrestrial Reference System
Universal Transverse Mercator Reference System
Feet Per Second Measurement Unit
ft/s
World Geographic Reference System
Newton Second Per Kilogram Measurement Unit
Ns/kg
Poland Zloty
Bayre Measurement Unit
GMT+9
JST
Japan Standard Time
Cubic Inch Measurement Unit
in^3
TAI is a time standard the values of which are generated by calculating the weighted average of the measurements of more than 400 atomic clocks and is based on the International System of Units (SI) definition of one second equals the time it takes a Cesium-133 atom at the ground state to oscillate exactly 9,192,631,770 times. TAI is extremely precise, but does not perfectly synchronize with Earth times, which is why TAI and UT1 are both used to determine UTC. TAI serves as the main realization of TT.
International Atomic Time
Offset from Universal Coordinated Time = UTC-8
Uniform Time Zone
Kazakhstan Tenge
Ethiopian Birr
North Korean Won
Swedish Krona
Kilogram Per Second Measurement Unit
GMT+11
SST
Solomon Standard Time
Kilometer Measurement Unit
Iran Standard Time
Iran Time
Guinean Franc
United Kingdom Pound
Miles Per Hour Measurement Unit
mi/h
mph
Offset from Universal Coordinated Time = UTC-1
November Time Zone
Degree Measurement Unit
Argentine Peso
Degree Celsius Measurement Unit
Offset from Universal Coordinated Time = UTC-9
Victor Time Zone
Pound-Mole Measurement Unit
lb-mol
lbmol
pound-mole
Gradian Measurement Unit
Gon
Grad
Grade
Thai Baht
Gallon Measurement Unit
gal
Bar Measurement Unit
bar
Kilovolt Ampere Measurement Unit
kVA
Moldovan Leu
GMT-7
MST
Mountain Standard Time
PNT
Phoenix Standard Time
Gambian Dalasi
Nigeria Naira
United States Dollar
Solomon Island Dollar
Macedonian Denar
Pakistani Rupee
Armenian Dram
Romanian Leu
Offset from Universal Coordinated Time = UTC+7
Golf Time Zone
UT0 is a variant of Universal Time that is measured by observing the diurnal motion of stars or extragalactic radio sources at a specific location on Earth. It does not take into consideration distorting factors, in particular polar motion, such that its value will differ based on the location it is measured at.
Universal Time 0
Twelve-Hour Clock Time System
12-Hour Clock
12-Hour Clock Time System
Twelve Hour Clock
Twelve Hour Clock Time System
Twelve-Hour Clock
A Clock Time System for keeping the Time of Day in which the Day runs from midnight to midnight and is divided into two intervals of 12 Hours each, where: the first interval begins at midnight, ends at noon, and is indicated by the suffix 'a.m.'; the second interval begins at noon, ends at midnight, and is indicated by the suffix 'p.m.'; and the midnight and noon Hours are numbered 12 with subsequent Hours numbered 1-11.
HongKong Dollar
Offset from Universal Coordinated Time = UTC-12
Yankee Time Zone is the same local time as Mike Time Zone, but is 1 Day (i.e. 24 Hours) behind Mike Time Zone as they are on opposite sides of the International Date Line.
Yankee Time Zone
Nautical Mile Measurement Unit
nmi
"WGS 84 is an Earth-centered, Earth-fixed terrestrial reference system and geodetic datum. WGS 84 is based on a consistent set of constants and model parameters that describe the Earth's size, shape, and gravity and geomagnetic fields. WGS 84 is the standard U.S. Department of Defense definition of a global reference system for geospatial information and is the reference system for the Global Positioning System (GPS). It is compatible with the International Terrestrial Reference System (ITRS)." From: (http://www.unoosa.org/pdf/icg/2012/template/WGS_84.pdf)
World Geodetic System 1984
Seychelles Rupee
South Korean Won
Vanuatu Vatu
GMT-1
CAT
Central African Time
Bosnia And Herzegovina Convertible Mark
Phon Measurement Unit
phon
Nanometer Measurement Unit
Nanometre
Comoros Franc
Indonesia Rupiah
Myanmar Kyat
Kilogram Meter Square Measurement Unit
Millimeter Measurement Unit
Millibar Measurement Unit
mbar
Cubic Feet Per Second Measurement Unit
ft^3/s
Square Inch Measurement Unit
in^2
Knot Measurement Unit
Feet Per Second Per Second Measurement Unit
ft/s/s
ft/s^2
Earth-Centered Earth-Fixed Coordinate System
Conventional Terrestrial Coordinate System
ECEF
ECR
Earth Centered Earth Fixed
Earth Centered Rotational Coordinate System
Earth-Centered Earth-Fixed
Earth-Centered, Earth-Fixed
A Geospatial and Cartesian Coordinate System that identifies positions using an x-axis, y-axis, and z-axis coordinate where the zero point is the center of the Earth, the z-Axis extends toward the North Pole but does not always coincide exactly with the Earth's Axis of Rotation, the x-Axis extends through the intersection of the Prime Meridian and the Equator, the y-Axis completes the right-handed system, and all three axes are fixed to the Earth such that they rotate along with the Earth.
Mongolia Tugrik
Tunisian Dinar
Gram Per Second Measurement Unit
g/s
Russian Rouble
Joule Measurement Unit
Iranian Rial
Cape Verde Escudo
Newton Second Measurement Unit
N s
Newton second
Trinidad and Tobago Dollar
Teph (the 'eph' is written as subscript) is an ephemeris time argument developed and calculated at the Jet Propulsion Laboratory (JPL) and implemented in a series of numerically integrated Development Ephemerides (DE), including the currently used DE405. Teph is characterized as a relativistic coordinate time that is nearly equivalent to the IAU's definition of TCB, though Teph is not currently an IAU time standard. Teph is used by the JPL to generate the ephemerides it publishes to support spacecraft navigation and astronomy.
Jet Propulsion Laboratory Ephemeris Time Argument
JPL Ephemeris Time
Turn Measurement Unit
Cycle
Full Circle
Revolution
Rotation
This global main field model provides magnetic field values for any location on Earth, e.g. for navigational purposes (declination) or as a standard for core field subtraction for aeromagnetic surveys. An updated version is adopted by International Association of Geomagnetism and Aeronomy (IAGA) every 5 years).
International Geomagnetic Reference Field
Alken, P., Thébault, E., Beggan, C.D. et al. International Geomagnetic Reference Field: the thirteenth generation. Earth Planets Space 73, 49 (2021). https://doi.org/10.1186/s40623-020-01288-x , https://www.iaga-aiga.org/
GMT+8
CTT
China Taiwan Time
Mozambique Metical
Cubic Meter Measurement Unit
m^3
Decibel Measurement Unit
Georgian Lari
"Barycentric Coordinate Time (TCB, from the French Temps-coordonnée barycentrique) is a coordinate time standard intended to be used as the independent variable of time for all calculations pertaining to orbits of planets, asteroids, comets, and interplanetary spacecraft in the Solar system. It is equivalent to the proper time experienced by a clock at rest in a coordinate frame co-moving with the barycenter of the Solar system: that is, a clock that performs exactly the same movements as the Solar system but is outside the system's gravity well. It is therefore not influenced by the gravitational time dilation caused by the Sun and the rest of the system." From: (https://en.wikipedia.org/wiki/Barycentric_Coordinate_Time)
Barycentric Coordinate Time
Minute Measurement Unit
Sierra Leone Leone
Gigahertz Measurement Unit
GHz
Malaysia Ringgit
Azerbaijan Manat
Square Decimeter Measurement Unit
dm^2
Japanese Yen
The Gregorian Calendar was instituted by Pope Gregory XIII via papal bull on 24 February 1582 as a reform of the Julian Calendar to stop the drift of the calendar with respect to the equinoxes and solstices. The Gregorian Calendar is currently the most widely used civil Calendar System in the world and is 13 days ahead of the Julian Calendar Date.
Gregorian Calendar
A Solar Calendar System that has a regular Year of 365 24-Hour Days divided into 12 Months with a leap day added at the end of February every 4 Years except Years that are evenly divisible by 100 but not 400 such that there are 97 leap Years every 400 Years and the average length of a Gregorian Year is 365.2425 Days (365 Days 5 Hours 49 Minutes 12 Seconds).
Slug Foot Per Second Measurement Unit
slug ft/s
Metric Ton Measurement Unit
tonne
Inch Measurement Unit
Cubic Decimeter Measurement Unit
dm^3
St Helena Pound
Miles Per Second Per Second Measurement Unit
mi/s/s
Gallon Per Minute Measurement Unit
gal/min
Kilopond Measurement Unit
Kilogram Force Measurement Unit
Kilogram-Force
kgf
Meter Measurement Unit
Burundi Franc
Second of Arc Measurement Unit
Arcsecond
arcsec
asec
Standard Cubic Centimeter Per Minute Measurement Unit
cm^3/min
Cubic Yard Measurement Unit
yrd^3
Sao Tome Principe Dobra
British Thermal Unit Measurement Unit
BTU
Btu
Turkmenistan Manat
GMT-6
CST
Central Standard Time
Unix Time is a Temporal Reference System for describing a point in time, defined as the number of seconds that have elapsed since 00:00:00 Coordinated Universal Time (UTC) Thursday, 1 January 1970 minus the number of leap seconds that have taken place since then. (See: https://en.wikipedia.org/wiki/Unix_time)
Unix Time
Zulu Time Zone
Pounds Per Square Inch Measurement Unit
psi
UT2 is a variant of Universal Time that smooths UT1 by accounting for both polar motion and variations in Earth's rotation due to seasonal factors, such as changes in vegetation and water or snow distribution.
Universal Time 2
Centigram Measurement Unit
Kilometers Per Second Per Second Measurement Unit
km/s/s
Long Ton Measurement Unit
Displacement Ton
Gross Ton
Imperial Ton
Weight Ton
ton (UK)
Morocco Dirham
Juliet time is used as an indexical to refer to local time without otherwise specifying the time zone.
Juliet Time Zone
GMT-3
AGT
Argentina Standard Time
Indian Standard Time
Sri Lanka Standard Time
Brazilian Real
GMT+3
EAT
Eastern African Time
Chilean Peso
Acre Measurement Unit
acre
Month Measurement Unit
Serbian Dinar
Quartic Meter Measurement Unit
Danish Krone
Dyne Second Measurement Unit
dyne s
dyne second
Offset from Universal Coordinated Time = UTC-5
Romeo Time Zone
Square Millimeter Measurement Unit
mm^2
Foot Measurement Unit
Terahertz Measurement Unit
THz
UT1 is a derivation of UT0 that takes into account distortions caused by polar motion and is proportional to the rotation angle of the Earth with respect to distant quasars, specifically, the International Celestial Reference Frame (ICRF). UT1 is currently the most widely used variant of Universal Time and has the same value everywhere on Earth.
Universal Time 1
Astronomical Time
Croatia Kuna
Honduras Lempira
Kyrgyzstan Som
Guatemala Quetzal
Libyan Dinar
Bhutan Ngultrum
Offset from Universal Coordinated Time = UTC+4
Delta Time Zone
Degree Fahrenheit Measurement Unit
Iceland Krona
Norwegian Krone
Offset from Universal Coordinated Time = UTC+10
Kilo Time Zone
Pound Measurement Unit
Volt Ampere Measurement Unit
Hertz Measurement Unit
cycles per second
Jamaican Dollar
Offset from Universal Coordinated Time = UTC+3
Charlie Time Zone
Slug Per Second Measurement Unit
slug/s
Australian Dollar
third planet from the Sun in the Solar System
Earth
Sol
World Ocean
Radon dosimeters are radiation dosimeters used to measure the presence and concentration of radon gas (Rn-222), a radioactive noble gas that can accumulate in buildings and pose health risks. Different types of radon detectors use various detection methods, based on the radioactive decay products of radon.
The atomic mass (ma or m) is the mass of an atom. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions. It is measured in Daltons (unit).
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
"A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
"A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST]
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
"A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST]
"An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length." [BIPM:BIPM, NIST:NIST]
"A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST]
"A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12." [BIPM:BIPM, NIST:NIST]
"A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian." [BIPM:BIPM, NIST:NIST]
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
"A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST]
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
"A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST]
A length unit which is equal to one millionth of a meter or 10^[-6] m.
"A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
"A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]
A length unit which is equal to 10 [-10] m.
"A length unit which is equal to 10 [-10] m." [NIST:NIST]
"A length unit which is equal to 10^[-12] m." [NIST:NIST]
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
"A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST]
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
"A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG]
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
"A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
"A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]
A mass unit which is equal to 10^[-12] g.
"A mass unit which is equal to 10^[-12] g." [UOC:GVG]
"A mass unit which is equal to 10^[-15] g." [NIST:NIST]
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
"A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST]
"A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST]
"A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST]
"A time unit which is equal to 10^[-12] s." [NIST:NIST]
A time unit which is equal to 60 seconds.
"A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia]
A time unit which is equal to 3600 seconds or 60 minutes.
"A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia]
"A time unit which is equal to 24 hours." [Wikipedia:Wikipedia]
"A time unit which is equal to 7 days." [Wikipedia:Wikipedia]
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
"A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia]
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
"A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia]
"An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A." [UOC:GVG]
"An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A." [UOC:GVG]
A substance unit equal to a millionth of a mol or 10^[-6] mol.
"A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST]
"A substance unit equal to a thousandth of a mol or 10^[-3] mol." [NIST:NIST]
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
"A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [NIST:NIST]
"A substance unit equal to 10^[-12] mol." [NIST:NIST]
"A substance unit equal to 10^[-15] mol." [NIST:NIST]
"A substance unit equal to 10^[-18] mol." [NIST:NIST]
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
"A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG]
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
"A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG]
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
"A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG]
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
"A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG]
A unit of molarity which is equal to 10^[-12] M.
"A unit of molarity which is equal to 10^[-12] M." [UOC:GVG]
"A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG]
"A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG]
"A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG]
"A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG]
"A molality unit which is equal to 10^[-12] m." [UOC:GVG]
"A unit of molarity which is equal to 10^[-15] M." [UOC:GVG]
"A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia]
"A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia]
"An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second." [NIST:NIST]
"An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second." [NIST:NIST]
"An angular unit velocity which is equal to about 9.54930 rpm (revolutions per minute)." [NIST:NIST]
"An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST]
"An area unit which is equal to one ten thousandth of a square meter or 10^[-4] m^[2]." [NIST:NIST]
"An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2]." [NIST:NIST]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG]
"A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter." [NIST:NIST]
"An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared." [NIST:NIST]
"A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A momentum unit which is equal to the momentum of a one kilogram mass object with a speed of one meter per second." [NIST:NIST]
"A rotational frequency unit which is equal to the number complete turn in a period of time that equals to 1 second." [NIST:NIST]
"A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST]
"A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST]
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
"A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST]
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
"A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST]
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
"A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST]
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
"A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST]
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
"A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST]
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
"A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST]
A volume unit which is equal to 10^[-12] L.
"A volume unit which is equal to 10^[-12] L." [NIST:NIST]
"A volume unit which is equal to 10^[-15] L." [NIST:NIST]
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
"A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST]
"A force unit which is equal to the force required to cause an acceleration of 1m/s2 of a mass of 1 Kg in the direction of the force." [NIST:NIST]
"A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST]
"An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST]
"A power unit which is equal to the power used when work is done at the rate of 1 joule per second." [NIST:NIST]
"An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 m^[2]." [NIST:NIST]
"A luminous flux unit which is equal to the luminous flux emitted into 1 steradian by a point source of 1 candela." [NIST:NIST]
"A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second." [NIST:NIST]
"A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST]
"A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps)." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps)." [ORCBS:ORCBS]
"An absorbed dose unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST]
"An absorbed dose unit which is equal to 0.01 gray (Gy)." [Wikipedia:Wikipedia]
"An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs." [Wikipedia:Wikipedia]
"A dose equivalent unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST]
"A dose equivalent unit which is equal to one thousandth of a sievert or 10^[-3] Sv." [NIST:NIST]
"A dose equivalent unit which is equal to one millionth of a sievert or 10^[-6] Sv." [NIST:NIST]
"A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem." [Wikipedia:Wikipedia]
"An absorbed dose unit which is equal to one millionth of a gray or 10^[-6] Gy." [NIST:NIST]
"An absorbed dose unit which is equal to one thousandth of a gray or 10^[-3] Gy." [NIST:NIST]
"An absorbed dose unit which is equal to one thousandth of a millionth of a gray or 10^[-9] Gy." [NIST:NIST]
"A dose equivalent unit which is equal to one thousandth of a millionth of a sievert or 10^[-9] Sv." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to one thousandth of a curie or 10^[-3] Ci." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to one millionth of a curie or 10^[-6] Ci." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute." [ORCBS:ORCBS]
"A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST]
"A time unit which is equal to 100 years." [Wikipedia:Wikipedia]
"A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED]
"An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux." [Wikipedia:Wikipedia]
"An irradiance unit which is equal to 1 watt of radiant power incident per one square meter surface area." [NIST:NIST]
mole per second and square meter mol/sm^2
"An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number." [Wikipedia:Wikipedia]
"A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction." [NIST:NIST]
microeinstein per second and square meter
microeinstein per square metre per second
micromole per second and square meter mmol/sm^2
"An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2]." [Wikipedia:Wikipedia]
microeinstein per square meter per second
"A radiant intensity unit which is equal to one kilogram meter squared per second cubed per steradian." [NIST:NIST]
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
"A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia]
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
"A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG]
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
"A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15]." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG]
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
"A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG]
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG]
"A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia]
"A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute." [Wikipedia:Wikipedia]
"An area density unit which is equal to the mass of an object in kilograms divided by one meter." [NIST:NIST]
"A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia]
"A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia]
"A dimensionless count unit which denotes the number of molecules." [MGED:MGED]
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]
"A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED]
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
"A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia]
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
"A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]
"A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST]
"A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST]
"A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST]
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
"A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG]
"A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST]
"A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia]
"A dimensionless count unit which a measure of plaque forming units in a given volume." [Wikipedia:Wikipedia]
A concentration unit which a measure of viable bacterial numbers in a given volume.
"A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia]
"A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia]
"A concentration unit which a measure of plaque forming units in one milliliter." [UOC:GVG]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second." [ORCBS:ORCBS]
"An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia]
"An electrical charge unit which is equal to the amount of charge transferred by a current of 1 ampere in 1 second." [WordNet:WordNet]
"An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia]
"A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia]
"An energy unit which is equal to the amount of electrical energy equivalent to a one-watt load drawing power for one hour." [Wikipedia:Wikipedia]
"An energy unit which is equal to 1,000 watt-hours." [Wikipedia:Wikipedia]
"A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt." [ScienceLobby:ScienceLobby]
"A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet]
"A magnetic flux unit which is equal to 3600 Wb." [UOC:GVG]
"A magnetic flux unit which is equal to one thousand volt-hours." [UOC:GVG]
"An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1)." [Wikipedia:Wikipedia]
"An information unit which is equal to 8 bits." [Wikipedia:Wikipedia]
"An information unit which is equal to 1000 bytes." [Wikipedia:Wikipedia]
"An information unit which is equal to 1000 kB." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the amount of spatial detail in an image." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the amount of contrast available in a pixel." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space." [Wikipedia:Wikipedia]
"A spatial resolution unit which is equal to a pixel size of one micrometer." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image." [Wikipedia:Wikipedia]
"A count unit which contains one nucleotide." [UO:GVG]
"An information unit which is equal to 1024 B." [NIST:NIST]
"An information unit which is equal to 1024 KiB." [NIST:NIST]
"An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG]
"An electric potential difference unit which is equal to one thousand volts or 10^[3] V." [UOC:GVG]
"An electric potential difference unit which is equal to one millionth of a volt or 10^[-6] V." [UOC:GVG]
"An electric potential difference unit which is equal to one billionth of a volt or 10^[-12] V." [UOC:GVG]
"An electric potential difference unit which is equal to one trillionth of a volt or 10^[-12] V." [UOC:GVG]
"An electric potential difference unit which is equal to one million volts or 10^[6] V." [UOC:GVG]
"A surface tension unit which is equal to one newton per meter." [NIST:NIST]
"A surface tension unit which is equal to one dyne per centimeter." [Wikipedia:Wikipedia]
"A viscosity unit which is equal to one pascale per second." [NIST:NIST]
"A viscosity unit which is equal to one dyne second per square centimeter." [Wikipedia:Wikipedia]
"A ratio unit which is an indicator of sound power per unit area." [techtarget:techtarget]
"A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human." [Wikipedia:Wikipedia]
"An electrical conduction unit which is equal to A/V." [NIST:NIST]
"An heat conduction unit which is equal to one watt divided by meter kelvin." [NIST:NIST]
"A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia]
"The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
"A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance]
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
"A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG]
"A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth." [url:en.wiktionary.org/wiki/mmHg]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG]
mcg/mL
µg/mL
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG]
"A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG]
A rate unit which is equal to one over one nanomolar second.
"A rate unit which is equal to one over one nanomolar second." [UOC:GVG]
A rate unit which is equal to one over one molar second.
"A rate unit which is equal to one over one molar second." [UOC:GVG]
"An area density unit which is equal to the mass of an object in kilograms divided by the surface area in hectares." [UO:GVG]
A rate unit which is equal to one over one nanomolar.
"A rate unit which is equal to one over one nanomolar." [UO:GVG]
A rate unit which is equal to one over one molar.
"A rate unit which is equal to one over one molar." [UO:GVG]
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
"A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A derived unit which is a measure of relative light intensity, as typically measured by a luminometer, spectrophotometer, or fluorimeter in biological research applications." [UO:PC]
"A relative light unit which is a measure of relative luminescence intensity." [UO:PC]
"A relative light unit which is a measure of relative fluorescence intensity." [UO:PC]
"A frequency unit which is equal to one million hertz or 10^[6] V." [UOC:GVG]
"A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit equal to one million base pairs" [UOC:GVG]
"A unit equal to one billion base pairs." [UOC:GVG]
"An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long." [NIST:NIST]
"An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR]
"A speed/velocity unit which is equal to the speed of an object traveling 1 millimeter distance in one day." [UOB:LKSR]
"A speed/velocity unit which is equal to the speed of an object traveling 1 kilometer distance in one hour." [NIST:NIST]
"A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia]
"An area unit which is equal to an area of 10,000 square meters. Equivalent to 2.471 acres." [Wikipedia:Wikipedia]
"A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia]
"A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia]
"A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia]
"A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia]
"An area unit which is equal to an area of 25.292,852,64 square meters, or 1 square rod." [Wikipedia:Wikipedia]
"An area unit which is equivalent to 1 furlong x 1 rod. This is equal to an area of 1,011.714,1056 square meters, or 40 square rods." [Wikipedia:Wikipedia]
"An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia]
"An imperial gravitational unit which is equivalent to a mass that accelerates by 1ft/s² when a force of one pound (lbf) is exerted on it." [Wikipedia:Wikipedia]
"A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon]
"DEPRECATED: Duplicate of http://purl.obolibrary.org/obo/UO_0000039. A substance unit which is equal to one millionth of a mole." [UOB:LTS]
"An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST]
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS]
"A unit of energy widely used in nutrition, equivalent to the amount of heat needed to cause one kilogram of water to rise in temperature by one degree Celsius." [Wikipedia:Wikipedia]
"A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS]
"An electric current unit current which is equal to one trillionth of an ampere or 10^[-12] A." [UOB:LTS]
"An absorbed dose unit which is equal to 0.01 gray (Gy)" [NIST:NIST]
"A unit of energy that is equal to one thousand million electronvolts." []
"Derived unit which is equal to the total kinetic energy of an atomic nucleus in GeV divided by the number of nucleons in the nucleus" []
"Derived unit which is equal to the total kinetic energy of an atomic nucleus in MeV divided by the number of nucleons in the nucleus" []
"A derived unit equal to the energy deposited by ionizing radiation per micron of path length in matter" []
"A derived absorbed dose unit which is equal to one gray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one centigray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per day." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per hour." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per second." [NIST:NIST]
"A length unit which is equal to one thousand meters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in deciliters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in deciliters." [UOB:LKSR]
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).