An ontology of adverse events associated with Chinese medicines.
Draft version
OCMR: Ontology of Chinese Medicine for Rheumatism
OWL-DL
The Ontology of Chinese Medicine for Rheumatism (OCMR) is a biomedical ontology that represents traditional Chinese medications for treating various rheumatism diseases, their ingredients, and adverse events, and other related information.
Vision Release; 1.0.11
BFO OWL specification label
Really of interest to developers only
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred term~editor preferred label
editor preferred label
editor preferred term
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
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.
example
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
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.
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.
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.
definition editor
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
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
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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
curator note
An administrative note of use for a curator but of no use for a user
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
expand assertion to
elucidation
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
person:Alan Ruttenberg
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Chinese translation
a chinese translation represents a chinese translation of the existing term.
adverse event outcome
The AE 'cough AE' has the 'label of AE outcome' of 'cough'; 'infection AE' has the 'label of AE outcom' of 'infection'.
an annotation property that represents the label of an adverse event
has_meddra_id
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Chris Mungall
tooth SubClassOf 'never in taxon' value 'Aves'
taxonomic class assertion
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
logical macro assertion
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a property
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on an object property
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1
x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
A metadata relation between a class and its taxonomic rank (eg species, family)
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
derived from the union of EHDAA2 and EMAPA - still to be checked
Subset consisting of classes creating for grouping purposes
A grouping class that depends on an assumption of homology between subclasses
classes that have some inconsistency with FMA
somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads
abstract class brought in to group ontology classes but not informative
organs, excluding individual muscles and skeletal elements
Uberon slim - subset that excludes obscure terms and deep compositional terms
abstract upper-level terms not directly useful for analysis
core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
Source
part of
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
a core relation that holds between a part and its whole
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)
part_of
this day is part of this year (occurrent parthood)
has 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.
a core relation that holds between a whole and its part
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)
is bearer of
bearer of
bearer_of
realized in
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
[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])
is realized by
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
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
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
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.
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
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 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
contains process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
[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
site of
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 bisects an organism from head end to opposite end of body or tail: bearer
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects 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 bisects an organism from head end to opposite end of body or tail.
x proximal_to y iff x is closer to the point of attachment with the body than y.
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 bisects 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 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 proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X 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 part_of Y and X is adjacent_to the proximal boundary of Y
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
is evidence of
This represents a relation between two adverse events AE1 and AE2. However, AE1 may be an evidence of another adverse event AE3, and a dfferent adverse event AE4 may also be an evidence of the same AE2.
An electrocardiogram qt prolonged AE is_evidence_of arrhythmia AE; arrhythmia AE is_evidence_of cardiomyopathy AE; fever AE is_evidence_of inflammation AE; fever AE is_evidence_of viral infection AE; plural effusion AE is_evidence_of cardiac disorder AE.
has participant quality
an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality.
An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased.
adverse event occurs in
a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in.
inheres in
A dependent inheres in its bearer at all times for which the dependent exists.
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
inheres_in
this fragility inheres in this vase
this red color inheres in this apple
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
has participant
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.
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has_participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
A 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.
before or simultaneous with
Primitive instance level timing relation between events
simultaneous with
Relation between occurrents, shares start and end boundaries.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
ends after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
immediately preceded by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
starts during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
happens during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
ends during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
overlaps
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
x overlaps y if and only if there exists some z such that x has part z and z part of y
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
relation between an artery and the structure is supplies with blood.
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
x adjacent_to y iff: x and y share a boundary
temporally related to
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.
Relation between occurrents, shares a start boundary with.
starts with
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.
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
Relation between occurrents, shares an end boundary with.
ends with
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.
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
mereotopologically 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
has potential to developmentally contribute to
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
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.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
has...channel tropism
归...经
has..nature
具有...药性
has...flavour
具有...药味
has...toxicity
具有...毒性
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 in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
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.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
has_proper_part
entity
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
continuant
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
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])
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
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])
occurrent
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
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.
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
An entity that has temporal parts and that happens, unfolds or develops through time.
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])
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.
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
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.
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
independent continuant
(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]
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
a heart
a chair
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
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])
the bottom right portion of a human torso
the interior of your mouth
process
(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 that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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)
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
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])
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
disposition
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
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.
(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]
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])
an atom of element X has the disposition to decay to an atom of element Y
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])
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
realizable entity
(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]
(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]
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.
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
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])
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
quality
(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]
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])
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])
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
specifically dependent continuant
(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]
(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]
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.
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
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.
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])
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
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.
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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.
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.
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])
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
object aggregate
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.
(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]
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
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
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)
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])
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.
site
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
object
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
atom
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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.
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])
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.
material entity
(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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
(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]
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])
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.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
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
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
the undetached arm of a human being
immaterial entity
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
A carbazole that has formula C22H24N2O4.
A sesquiterpenoid that has formula C43H49NO19.
A pentacyclic triterpenoid that is ursane which contains a double bond between positions 12 and 13 and in which the hydrogen at the 3beta position is substituted by a hydroxy group.
A triterpenoid that has formula C30H48O3.
A pentacyclic triterpenoid that is oleanane substituted at the 3beta-position by a hydroxy group and containing a double bond between positions 12 and 13. It is one of the most commonly occurring triterpenoids in higher plants.
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.
An oxo steroid that has formula C20H24O3.
A group of fat-soluble retinoids produced via metabolism of provitamin A carotenoids. Vitamin A is involved in immune function, vision, reproduction, and cellular communication.
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
A steroid compound with a structure based on a 27-carbon (cholestane) skeleton.
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor
A DNA polymerase inhibitor that interferes with the action of a DNA-directed DNA polymerase (EC 2.7.7.7).
DNA nucleotidyltransferase (DNA-directed) inhibitor
DNA nucleotidyltransferase (DNA-directed) inhibitors
DNA-directed DNA polymerase (EC 2.7.7.7) inhibitor
DNA-directed DNA polymerase (EC 2.7.7.7) inhibitors
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitors
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitor
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitors
deoxyribonucleate nucleotidyltransferase inhibitor
deoxyribonucleate nucleotidyltransferase inhibitors
deoxyribonucleic acid duplicase inhibitor
deoxyribonucleic acid duplicase inhibitors
deoxyribonucleic acid polymerase inhibitor
deoxyribonucleic acid polymerase inhibitors
deoxyribonucleic polymerase I inhibitors
Any steroid (or derivative) based on a stigmastane skeleton.
Any sterol based on a stigmastane skeleton.
Any monounsaturated fatty acid carrying one or more hydroxy substituents.
Any organic heterobicyclic compound containing two ortho-fused pyran rings.
A pyranopyran in which at least one of the pyran rings in the pyranopyran skeleton is substituted by an oxo group.
dicarboxylic acids and O-substituted derivatives
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
A fatty acid ethyl ester resulting from the formal condensation of the carboxy group of a long-chain fatty acid with the hydroxy group of ethanol.
An organic heteropentacyclic compound and pyridine alkaloid with formula C43H49NO18 originally isolated from the roots of Tripterygium wilfordii.
(3R,4S,5R,5aS,6R,7S,9R,9aS,10R)-6,10-bis(acetyloxy)-7,9-dihydroxy-2,2,5a,9-tetramethyloctahydro-2H-3,9a-methano-1-benzoxepine-4,5-diyl dibenzoate
A dihydroagarofuran sesquiterpenoid that is isolated from Tripterygium wilfordii.
A spermidine alkaloid that is isolated from Maytenus heterophylla and Maytenus senegalensis.
A diterpene triepoxide that is triptobenzene K in which the acylhydroquinone moiety has undergone oxidation to the corresponding triepoxyketone derivative. It has been isolated from the roots of Tripterygium wilfordii.
A tetracyclic diterpenoid that is isolated from Tripterygium wilfordii and exhibits anti-inflammatory properties.
(2R,4aS,6aS,12bR,14aS,14bR)-11-hydroxy-10-methoxy-2,4a,6a,9,12b,14a-hexamethyl-8-oxo-1,2,3,4,4a,5,6,6a,8,12b,13,14,14a,14b-tetradecahydropicene-2-carboxylic acid
(3br,9bs)-9-hydroxy-6-methoxy-9b-methyl-7-(propan-2-yl)-3b,4,5,9b,10,11-hexahydrophenanthro[1,2-c]furan-1(3h)-one Vendors Literature
An abietane diterpenoid that is abieta-8(14),9(11),12-triene substituted at positions 3 and 14 respectively by oxo and hydroxy groups. It is found in Tripterygium wilfordii.
EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitor
An EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor that interferes with the action of procollagen-proline dioxygenase (EC 1.14.11.2).
EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitors
hydroxylase, collagen proline inhibitors
procollagen-L-proline,2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating) inhibitor
procollagen-L-proline,2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating) inhibitors
procollagen-proline 4-dioxygenase inhibitor
procollagen-proline 4-dioxygenase inhibitors
procollagen-proline dioxygenase (EC 1.14.11.2) inhibitor
procollagen-proline dioxygenase (EC 1.14.11.2) inhibitors
procollagen-proline dioxygenase inhibitor
procollagen-proline dioxygenase inhibitors
procollagen-proline,2-oxoglutarate-4-dioxygenase inhibitor
procollagen-proline,2-oxoglutarate-4-dioxygenase inhibitors
proline protocollagen hydroxylase inhibitor
proline protocollagen hydroxylase inhibitors
proline, 2-oxoglutarate dioxygenase inhibitor
proline, 2-oxoglutarate dioxygenase inhibitors
proline,2-oxoglutarate 4-dioxygenase inhibitor
proline,2-oxoglutarate 4-dioxygenase inhibitors
prolyl-glycyl-peptide, 2-oxoglutarate:oxygen oxidoreductase, 4-hydroxylating inhibitor
prolyl-glycyl-peptide, 2-oxoglutarate:oxygen oxidoreductase, 4-hydroxylating inhibitors
prolylprotocollagen dioxygenase inhibitor
prolylprotocollagen dioxygenase inhibitors
prolylprotocollagen hydroxylase inhibitor
prolylprotocollagen hydroxylase inhibitors
protocollagen proline 4-hydroxylase inhibitor
protocollagen proline 4-hydroxylase inhibitors
protocollagen proline dioxygenase inhibitor
protocollagen proline dioxygenase inhibitors
protocollagen proline hydroxylase inhibitor
protocollagen proline hydroxylase inhibitors
protocollagen prolyl hydroxylase inhibitor
protocollagen prolyl hydroxylase inhibitors
From EC 2.4.1.17: This entry denotes a family of enzymes accepting a wide range of substrates, including phenols, alcohols, amines and fatty acids. So R can also 'start' with an N
A sesquiterpene alkaloid that is isolated from Tripterygium wilfordii and Tripterygium hypoglaucum.
A sesquiterpene alkaloid that is isolated from Tripterygium wilfordii and exhibits immunosuppressive and insecticidal properties.
A sesquiterpene alkaloid that is isolated from Tripterygium wilfordii.
A sesquiterpene alkaloid that is isolated from Tripterygium hypoglaucum.
A sesquiterpene alkaloid that is isolated from Euonymus Sieboldiana.
A sesquiterpene alkaloid that is isolated from Tripterygium forrestii, Platanus chiapensis and Maytenus chiapensis.
A sesquiterpene alkaloid that is isolated from Tripterygium hypoglaucum and Tripterygium wilfordii.
(3R,5R,5aS,6S,9S,9aS,10R)-5,6-bis(benzoyloxy)-9-hydroxy-2,2,5a,9-tetramethyloctahydro-2H-3,9a-methano-1-benzoxepin-10-yl pyridine-3-carboxylate
A sesquiterpene alkaloid that is isolated from the stem of Tripterygium regelii.
A member of the class of hydroxypiperidines that is piperidine carrying a hydroxymethyl substituent at position 2 as well as two hydroxy substituents at positions 3 and 4 (the 2R,3R,4S-diastereomer).
2-[(2S)-7-oxo-2,3-dihydro-7H-furo[3,2-9][1]benzopyran-2-yl]propan-2-yl beta-D-glucopyranoside
A member of the class of psoralens that is (-)-marmesin in which the hydroxy hydrogen is replaced by a beta-D-glucosyl residue.
A member of the class of coumarins that is 7-methoxycoumarin in which the hydrogen at position 6 has been replaced by a 1,2,3-trihydroxy-3-methylbutyl group (the 1R,2S stereoisomer). Originally isolated from the roots of Angelica pubescens, angelitriol shows strong inhibitory effects on human platelet aggregation.
A tetracyclic diterpenoid with fromula C20H22O5, originally isolated from the dried root outer bark of Tripterygium hypoglaucum.
An abietane diterpenoid that is abieta-8(14),9(11),12-triene substituted at positions 3, 11 and 14 respectively by oxo, hydroxy and methoxy groups. It is found in Tripterygium wilfordii and Tripterygium hypoglaucum.
EC 3.2.1.23 (beta-galactosidase) inhibitor
An EC 3.2.1.* (glycosidase) inhibitor that interferes with the action of beta-galactosidase (EC 3.2.1.23).
EC 3.2.1.23 (beta-galactosidase) inhibitors
beta-D-galactoside galactohydrolase inhibitor
beta-D-galactoside galactohydrolase inhibitors
exo-(1->4)-beta-D-galactanase inhibitors
(3|A,5xi,18|A,22|A)-3,22-dihydroxyolean-12-en-30-oic acid
(5xi,18|A,22|A)-22-hydroxy-3-oxoolean-12-en-30-oic acid
A sterol that is cholestanol in which the hydrogen at the 6alpha position has been replaced by a hydroxy group.
A monoterpenoid indole alkaloid that is strychnine in which the hydrogen at position 3 has been replaced by a methoxy group. It is a minor alkaloid from Strychnos nux-vomica.
A monoterpenoid indole alkaloid that is strychnine in which the hydrogen at position 2 has been replaced by a methoxy group. It is a minor alkaloid from Strychnos nux-vomica.
An N-oxide resulting from the oxidation of the non-acylated nitrogen of strychnine. It is a metabolite of strychnine.
(E)-ethyl 3-(3,4-dihydroxyphenyl)acrylate
An ethyl ester resulting from the formal condensation of the carboxy group of trans-caffeic acid with ethanol.
ethyl (2E)-3-(3,4-dihydroxyphenyl)acrylate
ethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
A cyclic monoterpene ketone that is bicyclo[3.1.1]heptan-2-one which is substituted at positions 4, 6, and 6 by hydroxymethyl, methyl, and methyl groups (the 1R,4S,5R stereoisomer). It has been found in Japanese Paeoniae Radix, which has been used in various Chinese medicinal preparations as an anodyne, sedative, antispasmodic, and astringent.
5-hydroxy-2-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl beta-D-glucopyranosiduronic acid
A dihydroxyflavanone that is naringenin in which the phenolic hydrogen at position 7 has been replaced by a beta-D-glucuronosyl residue.
A heptadienal in which the two double bonds are located at positions 2 and 4 (the E,E-geoisomer).
A 3-hydroxy fatty acid that is heptanoic acid in which one of the hydrogens at position 3 is replaced by a hydroxy group.
A monoterpenoid that is 2-(2-hydroxypropan-2-yl)oxolane carying additional methyl and vinyl substituents both located at position 5 (the 2R,5S-diastereomer).
A 2-undecenal in which the C=C bond has E configuration.
A carbonate ester that is dimethyl carbonate in which one of the methyl groups has been replaced by a (Z)-hex-3-en-1-yl group. It has a floral scent and is used in the production of fruit or vegetable-like flavour additives.
(4aS,5R,6S)-1-oxo-5-vinyl-4,4a,5,6-tetrahydro-1H,3H-pyrano[3,4-c]pyran-6-yl 2,3,6-tri-O-acetyl-4-O-[3-(beta-D-glucopyranosyloxy)-2-hydroxybenzoyl]-beta-D-glucopyranoside
A secoiridoid glycoside that is (4aS,5R,6R)-6-hydroxy-5-vinyl-4,4a,5,6-tetrahydro-1H,3H-pyrano[3,4-c]pyran-1-one in which the hydroxy group has been converted to the corresponding 2,3,6-tri-O-acetyl-beta-D-glucoside, the 4-hydroxy group of which has been esterified by formal condensation with the carboxy group of 2,3-dihydroxybenzoic acid 3-beta-D-glucoside. It is a component of Gentiana scabra root extract, which is used as an internal remedy in traditional Korean medicine for the treatment of diabetes mellitus.
A member of the class of pterocarpans that is (6aR,11aR)-3,9-dihydroxypterocarpan in which the hydrogen at position 8 has been replaced by a methoxy group.
2-(3,4-dihydroxyphenyl)ethyl 3-O-(6-deoxy-alpha-L-mannopyranosyl)-4-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranoside
2-(3,4-dihydroxyphenyl)ethyl 3-O-(alpha-L-rhamnopyranosyl)-4-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranoside
A glycoside that is the alpha-L-rhamnosyl-(1->3)-beta-D-glucoside of hydroxytyrosol in which the hydroxy group at position 4 of the glucopyranosyl moiety has undergone esterification by formal condensation with trans-caffeic acid.
A hydroxy monounsaturated fatty acid that is undec-10-enoic acid which is substituted by a hydroxy group at position 9. It has been isolated from the leaves of Corchorus olitorius, also known as the medicinal foodstuff moroheiya.
A sesquiterpene lactone containing two epoxide groups and two tertiary hydroxy groups that has been isolated from the roots of Coriaria nepalensis.
An extended flavonoid that is cyclomulberrin in which the hydroxy group at position 10 has undergone oxidative cyclisation to position 3 of the 3-methylbut-2-en-1-yl substituent, with migration of the double bond into conjugation with the aromatic ring. It is a moderate inhibitor of acetylcholinesterase (IC50 = 16.2 - 36.6 muM), and a strong inhibitor of platelet-activating factor (PAF; 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) induced platelet aggregation.
A extended flavonoid that is 6H,7H-chromeno[4,3-b]chromen-7-one which is substituted by a 2-methylprop-1-en-1-yl group at position 6, a 3-methylbut-2-en-1-yl group at position 11, and hydroxy groups at positions 3, 8, and 10. It is found in the bark of Morus species and has been reported to protect human neuronal cells derived from the human neuroblastoma SH-SY5Y cell line.
An organic heterotricyclic compound and sesquiterpenoid that is 11-oxatricyclo[5.3.1.0(2,6)]undecane-1,8-diol which is substituted by methyl groups at positions 5 and 8, and by an isopropyl group at position 5. The absolute stereochemistry is not known; it is either 1R,2S,5R,6R,7R,8R (as shown), or the enantiomer.
An organic heterotricyclic compound and sesquiterpenoid that is 11-oxatricyclo[5.3.1.0(2,6)]undecan-8-ol which is substituted by methyl groups at positions 2 and 8, and by an isopropyl group at position 5. The absolute stereochemistry is not known; it is either 1R,2R,5S,6S,7R,8R (as shown), or the enantiomer.
A bisbenzylisoquinoline alkaloid that is (1beta)- berbaman which has been substituted by methyl groups at the 2 and 2' positions, by methoxy groups at the 6, 6', and 12 positions, and by a hydroxy group at position 7. Isolated from Stephania tetrandra, it has been found to possess neuroprotective and anti-tumour activity.
An oxoaporphine alkaloid that is 7H-dibenzo[de,g]quinolin-7-one which is substituted by methylenedioxy grups at the 1,2 and 9,10 positions. Compared with liriodenine, which lacks the 9,10-methylenedioxy group, cassameridine displays only moderate antifungal activity.
A bisbenzylisoquinoline alkaloid that is 1',2',3',4'-tetradehydroberbaman which has been substituted by a methyl group at position 2, methoxy groups at positions 6, 6', 7, and 12, and an oxo group at the 15' position. Isolated from Stephania tetrandra.
A sesquiterpenoid that is perhydroindane which is substituted by a (2-methylprop-1-en-1-yl) group at position 1, methyl groups at positions 3a and 7, and hydroxy groups at positions 4 and 7 (the 1R,3aR,4R,7S,7aR stereoisomer).
A sesquiterpenoid that is (+)-homalomenol A in which the double bond of the 2-methylpropen-1-yl group has migrated from the 1-2 position to the 2-3 position.
A sesqiterpenoid that is octahydro-1H-indene which is substituted by a 2-hydroxy-2-methylpropyl group at position 1, methyl groups at positions 3a and 7, and hydroxy groups at positions 4 and 7 (the 1R,3aR,4R,7S,7aR stereoisomer). It has been isolated from various Homalomena species.
An octadecenoate in which the double bond is at C-9.
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of any tartaric acid.
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of oxalic acid.
Any benzylisoquinoline alkaloid that has a 7-keto-4H-dibenzo[de,g]quinoline skeleton. They are found in members of the Anonacea, Aracea, Hernandiaceae, Lauraceae, Magnoliaceae, Menispermaceae, Monimiaceae, Papaveraceae, and Ranunculaceae families.
A type of benzylisoquinoline alkaloid whose structures are built up of two benzylisoquinoline units linked by ether bridges. Various structural patterns resulting from additional bridging between the two units by direct carbon-carbon bridging or by methylenedioxy groups are common.
A diterpenoid compound that contains three epoxide groups.
An oxaspiro compound in which a carbon atom of an epoxide ring is the only common member of two rings.
Any organic heteroolycyclic compound whose skeleton two ortho-fused chromene rings, and their derivatives.
A monounsaturated fatty acid aldehyde that is undecanal which has undergone formal dehydrogenation to introduce a double bond at unspecified position.
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid that contains no carbon-carbon double bonds.
Any dicarboxylic acid dianion carrying one or more oxo groups.
A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent.
An amino-acid anion that has formula CH2NO2.
An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group
An enal that consists of 3,7-dimethyl-9-nona-2,4,6,8-tetraenal (double bond geometry unspecified) carrying a 2,6,6-trimethylcyclohex-1-en-1-yl group at the 9-position.
An elemental selenium that has formula Se.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
A glucosiduronic acid resulting from the formal condensation of any substance with beta-D-glucuronic acid to form a glycosidic bond.
3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate}
A thiol comprising a panthothenate unit in phosphoric anhydride linkage with a 3',5'-adenosine diphosphate unit; and an aminoethanethiol unit.
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate
A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function.
Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.
A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3.
A simple monocarboxylic acid containing two carbons.
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
(all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ECL)
A retinoic acid in which all four exocyclic double bonds have E- (trans-) geometry.
A monoterpene that is cyclohex-1-ene substituted by a methyl group at position 1 and a prop-1-en-2-yl group at position 4 respectively.
A member of the cadinene family of sesquiterpenes in which the double bonds are located at the 4-4a and 7-8 positions, and in which the isopropyl group at position 1 is cis to the hydrogen at the adjacent bridgehead carbon (the 1S,8aR-enantiomer).
The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.
A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration.
An oxo fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any 3-oxo-fatty acid..
A C4-dicarboxylate resulting from deprotonation of both carboxy groups of malic acid.
The (+)-enantiomer of catechin and a polyphenolic antioxidant plant metabolite.
A pterocarpan that has formula C15H12O4.
A tetraric acid that is butanedioic acid substituted by hydroxy groups at positions 2 and 3.
Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals.
Any alpha-amino acid having L-configuration at the alpha-carbon.
A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects.
An alpha,omega-dicarboxylic acid resulting from the formal oxidation of each of the terminal methyl groups of butane to the corresponding carboxy group. It is an intermediate metabolite in the citric acid cycle.
A straight-chain, sixteen-carbon, saturated long-chain fatty acid.
1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid methyl ester
An iridoid monoterpenoid isolated from the plant species of the genus Cornus.
methyl (1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
A dicarboxylic acid dianion obtained by the deprotonation of the carboxy groups of malonic acid.
A 3'-hydroxyflavonoid which is thought to play an important role in the human body as an antioxidant, a free radical scavenger, an agent in the prevention of inflammation, a promoter of carbohydrate metabolism, and an immune system modulator.
A 3-hydroxy steroid closely related to cholestan-3-ol.
A pyrimidine obtained by formal addition of hydrogen across the 5,6-position of uracil.
D-Glucopyranose with beta configuration at the anomeric centre.
A fatty acid with a chain length ranging from C13 to C22.
A pyridinemonocarboxylic acid that is pyridine in which the hydrogen at position 3 is replaced by a carboxy group.
An optically active form of lactate having (R)-configuration.
An alkylbenzene carrying an ethyl substituent. It is a constituent of coal tar and petroleum.
5-O-(3,4-Dihydroxycinnamoyl)-L-quinic acid
A cinnamate ester obtained by formal condensation of the carboxy group of trans-caffeic acid with the 3-hydroxy group of quinic acid. It is an intermediate metabolite in the biosynthesis of lignin.
[1S-(1alpha,3beta,4alpha,5alpha)]3-[[3-(3,4-dihydroxyphenyl)-1-oxo-2-propenyl]oxy]-1,4,5-trihydroxycyclohexanecarboxylic acid
edit(1S,3R,4R,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4,5-trihydroxycyclohexane-1-carboxylic acid
A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.
(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
3,4,5-Trihydroxy-1-cyclohexenecarboxylic acid
3alpha,4alpha,5beta-trihydroxy-1-cyclohexene-1-carboxylic acid
A cyclohexenecarboxylic acid that is cyclohex-1-ene-1-carboxylic acid substituted by hydroxy groups at positions 3, 4 and 5 (the 3R,4S,5R stereoisomer). It is an intermediate metabolite in plants and microorganisms.
[3R-(3alpha,4alpha,5beta)]-3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A straight-chain alkane with 17 carbon atoms. It is a component of essential oils from plants like Opuntia littoralis and Annona squamosa.
The simplest member of the class of benzoates that is the conjugate base of benzoic acid, comprising a benzoic acid core with a proton missing to give a charge of -1.
A carboxylic ester obtained by formal condensation of the hydroxy group of retinol with the carboxy group of any carboxylic acid.
An octadec-9-enoic acid in which the double bond at C-9 has Z (cis) stereochemistry.
A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
A pentahydroxyflavone having the five hydroxy groups placed at the 3-, 3'-, 4'-, 5- and 7-positions.
A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.
A ribonucleoside composed of a molecule of adenine attached to a ribofuranose moiety via a beta-N(9)-glycosidic bond.
An optically active form of threonine having D-configuration.
(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoic acid
An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2.
An aromatic hydrocarbon comprising two fused benzene rings. It occurs in the essential oils of numerous plant species e.g. magnolia.
A triamine that is the 1,5,10-triaza derivative of decane.
A methoxybenzoate that is the conjugate base of vanillic acid.
3,6-dideoxy-D-xylo-hexosyl-D-mannosyl-rhamnosyl-D-galactose 1-diphospholipid
abequosyl-D-mannosyl-rhamnosyl-D-galactose 1-diphospholipid
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.
An optically active form of lactate having (S)-configuration.
A ribosyl or deoxyribosyl derivative of a pyrimidine or purine base in which C-5 of the ribose ring is mono-, di-, tri- or tetra-phosphorylated.
A ribonucleoside composed of a molecule of uracil attached to a ribofuranose moiety via a beta-N(1)-glycosidic bond.
The parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6.
A six-carbon aromatic annulene in which each carbon atom donates one of its two 2p electrons into a delocalised pi system. A toxic, flammable liquid byproduct of coal distillation, it is used as an industrial solvent. Benzene is a carcinogen that also damages bone marrow and the central nervous system.
A furancarboxylate that is the conjugate base of 2-furoic acid.
A purine ribonucleoside 5'-diphosphate having adenine as the nucleobase.
An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position.
A member of the class of acetamides that is acetamide in which one of the hydrogens attached to the nitrogen atom is replaced by a 2-(5-methoxy-1H-indol-3-yl)ethyl group. It is a hormone secreted by the pineal gland in humans.
An oxo dicarboxylate obtained by deprotonation of both carboxy groups of 2-oxoglutaric acid.
A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4.
alpha-amino-gamma-methylmercaptobutyric acid
An optically active form of threonine having L-configuration.
A gamma-amino acid that is butanoic acid with the amino substituent located at C-4.
A monohydroxybenzoic acid that is benzoic acid with a hydroxy group at the ortho position. It is obtained from the bark of the white willow and wintergreen leaves.
A trihydroxybenzoate that is the conjugate base of gallic acid.
A phytosterol consiting of ergostane having double bonds at the 5,6-, 7,8- and 22,23-positions as well as a 3beta-hydroxy group.
2-hydroxy-1,2,3-propanetricarboxylic acid, ion(3-)
A tricarboxylic acid trianion, obtained by deprotonation of the three carboxy groups of citric acid.
A monoterpenoid that is (2E,6E)-octa-2,6-dienal substituted by methyl groups at positions 3 and 7.
An alpha,omega-dicarboxylic acid that is ethane substituted by carboxyl groups at positions 1 and 2.
The simplest member of the class of propane-1,2-diols, consisting of propane in which a hydrogen at position 1 and a hydrogen at position 2 are substituted by hydroxy groups. A colourless, viscous, hygroscopic, low-melting (-59degreeC) and high-boiling (188degreeC) liquid with low toxicity, it is used as a solvent, emulsifying agent, and antifreeze.
An isoquinoline alkaloid that has formula C19H19NO4.
Cholesterol esterified at the 3-hydroxy group.
An alpha-CH2-containing aldehyde that has formula C18H36O.
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
The meso-diastereomer of butane-1,2,3,4-tetrol.
A short-chain fatty acid anion that is the conjugate base of hexanoic acid (also known as caproic acid).
A fatty alcohol with a chain length of C13 or greater.
An arenecarbaldehyde that consists of benzene bearing a single formyl substituent; the simplest aromatic aldehyde and parent of the class of benzaldehydes.
A primary alcohol comprising an allyl core with a hydroxy substituent at the 1-position and a phenyl substituent at the 3-position (geometry of the C=C bond unspecified).
A morphinane alkaloid from the opium poppy, in which the 5,6,8,14-tetradehydromorphinan-7-one skeleton is substituted at position 4 by a hydroxyl group, positions 3 and 6 by methoxy groups and position N17 by a methyl group. An intermediate in the biosynthesis of narcotic analgesics such as morphine and codeine.
An aldohexose used as a source of energy and metabolic intermediate.
The conjugate base of propionic acid; a key precursor in lipid biosynthesis.
Any mixture of complex, colloidal, macromolecular plant galacturonans containing a large proportion of D-galactopyranosyluronic acid residues in alpha-(1->4) linkage, the carboxy groups of which may be esterified to varying degrees by methyl groups or be partially or completely converted into salts. The structure shown is that of the parent polygalacturonan.
A retinol in which all four exocyclic double bonds have E- (trans-) geometry.
An octadecadienoic acid in which the two double bonds are at positions 9 and 12 and have Z (cis) stereochemistry.
C18:2 9c, 12c omega6 todos cis-9,12-octadienoico
3,3'-disulfanediylbis(2-aminopropanoic acid)
A sulfur-containing amino acid obtained by the oxidation of two cysteine molecules which are then linked via a disulfide bond.
A 5-hydroxyfurocoumarin that has formula C11H6O4.
A monoterpenoid consisting of two prenyl units linked head-to-tail and functionalised with a hydroxy group at its tail end.
A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group.
A hydroxycoumarin that is umbelliferone bearing a methoxy substituent at position 6.
(1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid
1L-1(OH),3,4/5-tetrahydroxycyclohexanecarboxylic acid
A carbohydrate that is an acyclic polyol having the general formula HOCH2[CH(OH)]nCH2OH (formally derivable from an aldose by reduction of the carbonyl group).
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside
A quercetin O-glycoside that is quercetin substituted by a alpha-L-rhamnosyl moiety at position 3 via a glycosidic linkage.
luteolin 6-deoxy-alpha-L-mannopyranoside
A phthalate that is the dianion obtained by the deprotonation of both the carboxy groups of phthalic acid.
A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription.
The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent.
A cyclic carotene obtained by dimerisation of all-trans-retinol. A strongly-coloured red-orange pigment abundant in plants and fruit and the most active and important provitamin A carotenoid.
A monoterpenoid that is octa-1,6-diene substituted by methyl groups at positions 3 and 7 and a hydroxy group at position 3. It has been isolated from plants like Ocimum canum.
Any D-aldose having a chain of six carbon atoms in the molecule.
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoic acid
(E)-3-(4-Hydroxy-3-methoxyphenyl)-2-propenoic acid
3-(4-Hydroxy-3-methoxyphenyl)propenoic acid
A ferulic acid consisting of trans-cinnamic acid bearing methoxy and hydroxy substituents at positions 3 and 4 respectively on the phenyl ring.
A phenylpropanoid that is one of the main monolignols, produced by the reduction of the carboxy functional group in cinnamic acid and the addition of a hydroxy and a methoxy substituent to the aromatic ring.
1-carboxy-N,N,N-trimethylmethanaminium inner salt
The amino acid betaine derived from glycine.
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
An alpha-amino acid that is alanine substituted at position 3 by a hydroxy group.
An alpha,omega-dicarboxylic acid that is a linear five-carbon dicarboxylic acid.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
A retinal in which all four exocyclic double bonds have E- (trans-) geometry.
A piperidinemonocarboxylic acid in which the carboxy group is located at position C-2.
A flavone C-glycoside consisting of luteolin having a beta-D-glucosyl residue at the 6-position.
A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group.
A thioester that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any carboxylic acid.
An aromatic alcohol that consists of benzene bearing a single hydroxymethyl substituent.
3-Ethenyl-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylic acid, methyl ester
An iridoid monoterpenoid that is acetaldehyde in which on of the hydrogens of the methyl group has been replaced by a 2-(beta-D-glucopyranosyloxy)-3,4-dihydro-2H-pyran-4-yl group which is substituted at positions 3 and 5 by a vinyl and a methoxycarbonyl group, respectively (the 2S,3R,4S stereoisomer).
METHYL (2S,3R,4S)-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-(2-OXOETHYL)-3-VINYL-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE
methyl (2S,3R,4S)-3-ethenyl-2-(beta-D-glucopyranosyloxy)-4-(2-oxoethyl)-3,4-dihydro-2H-pyran-5-carboxylate
methyl (2S,3R,4S)-4-(formylmethyl)-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylate
A butenedioic acid in which the C=C double bond has E geometry. It is an intermediate metabolite in the citric acid cycle.
A monocarboxylic acid anion that has formula C16H23O10.
'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.
A member of the class of 7-hydroxyisoflavones that is 7-hydroxyisoflavone substituted by a methoxy group at position 4'.
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 benzenediol comprising of a benzene core carrying two hydroxy substituents ortho to each other.
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.
A simplest member of the class of isoflavones that is 4H-chromen-4-one in which the hydrogen at position 3 is replaced by a phenyl group.
An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2.
An iron group element atom that has atomic number 26.
Any nucleoside where the sugar component is D-ribose.
A medium-chain fatty acid anion that is the conjugate base of dodecanoic acid (lauric acid); major species at pH 7.3.
That part of DNA or RNA that may be involved in pairing.
A manganese group element atom that has formula Mn.
A member of the class of imidazoles that is 1H-imidazole substituted at position C-4 by a 2-aminoethyl group.
An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
A C-glycosyl compound that consists of apigenin substituted by a 1,5-anhydro-D-glucitol moiety at position 6.
A member of the class of benzaldehydes carrying methoxy and hydroxy substituents at positions 3 and 4 respectively.
6-hydroxy-7-methoxy-5-benzofuranacrylic acid delta-lactone
A member of the class of psoralens that is 7H-furo[3,2-g]chromen-7-one in which the 9 position is substituted by a methoxy group. It is a constituent of the fruits of Ammi majus. Like other psoralens, trioxsalen causes photosensitization of the skin. It is administered topically or orally in conjunction with UV-A for phototherapy treatment of vitiligo and severe psoriasis.
A phosphate ion that is the conjugate base of hydrogenphosphate.
A trihydroxyflavone that is flavone substituted by hydroxy groups at positions 4', 5 and 7.
A monocarboxylic acid anion that is the conjugate base of phenylacetic acid.
A phenol substituted at position 4 by a 2-hydroxyethyl group.
A lactone having a six-membered lactone ring.
A hexenal having the double bond at the 2-position.
A hexenal carrying an unsaturation at position 3.
A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics.
Any compound having 6-aminopurine (adenine) as part of its structure.
A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a carbon atom, thus creating a C-C bond.
A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.
A substance used to destroy pests of the subclass Acari (mites and ticks).
Compounds with the general formula RNHC(=O)CH3.
A tricarboxylic acid trianion that is the conjugate base of aconitic acid.
A tricarboxylic acid that is prop-1-ene substituted by carboxy groups at positions 1, 2 and 3.
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.
Dicarboxylic acids formed from aldoses by replacement of both terminal groups (CHO and CH2OH) by carboxy groups.
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 univalent group -CnH2n+1 derived from an alkane by removal of a hydrogen atom from any carbon atom.
A terpineol that is propan-2-ol substituted by a 4-methylcyclohex-3-en-1-yl group at position 2.
Any purine having at least one amino substituent.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A substance that prevents pests from feeding.
A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
A substance that destroys or inhibits replication of viruses.
A monocarboxylic acid amide in which the amide linkage is bonded directly to an arene ring system.
An L-alpha-amino acid which is L-aspartic acid or any of the essential amino acids biosynthesised from it (asparagine, lysine, methionine, threonine and isoleucine). A closed class.
oxaloacetate/aspartate family amino acid
oxaloacetate/aspartate family amino acids
An alpha-amino acid that consists of succinic acid bearing a single alpha-amino substituent
Any of a group of compounds, both naturally occurring and synthetic, that induce cell elongation in plant stems (from Greek alphaupsilonxialphanuomega, "to grow").
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 arenecarbaldehyde that consists of a formyl substituted benzene ring and its substituted derivatives thereof.
Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.
A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid.
Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group.
Compounds containing a phenylmethanol skeleton.
Any isoquinoline alkaloid based on a benzylisoquinoline skeleton.
Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents.
An insecticide compound naturally occurring in plants.
Any amino acid in which the parent hydrocarbon chain has one or more alkyl substituents
Any gamma-lactone having the lactone moiety derived from 4-hydroxybutanoic acid.
A C4-dicarboxylic acid that has formula C4H4O4.
Any sesquiterpene having a cadinane skeleton containing one or more C=C bonds.
An alkaline earth metal atom that has formula Ca.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
Organooxygen compounds that are salts or esters of carbonic acid, H2CO3.
One of a class of tetraterpenoids (C40), formally derived from the acyclic parent, psi,psi-carotene by hydrogenation, dehydrogenation, cyclization, oxidation, or combination of these processes. This class includes carotenes, xanthophylls and certain compounds that arise from rearrangement of the skeleton of psi,psi-carotene or by loss of part of this structure. Retinoids are excluded.
Members of the class of hydroxyflavan that have a flavan-3-ol skeleton and its substituted derivatives.
A quaternary ammonium ion based on the choline ion and its substituted derivatives thereof.
A member of the class of cinnamates that results from the deprotonation of the carboxy group of cinnamic acid.
Any alpha,beta-unsaturated monocarboxylic acid based on the cinnamic acid skeleton and its substituted derivatives.
A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons.
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.
A cyclic terpene ketone in which the terpene specified is monoterpene.
A polyol consisting of a cycloalkane containing at least three hydroxy groups, each attached to a different ring carbon atom.
Saturated monocyclic hydrocarbons (with or without side chains).
An amino acid derivative resulting from reaction of cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of cysteine by a heteroatom. The definition normally excludes peptides containing cysteine residues.
Any C6 deoxy sugar having at least one hydroxy group replaced by hydrogen.
Any sugar having a hydroxy group replaced with a hydrogen atom.
An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring.
Any member of the class of hydroxybenzoic acids carrying two phenolic hydroxy groups on the benzene ring and its derivatives.
A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols.
Any terpenoid derived from a diterpene. The term includes compounds in which the C20 skeleton of the parent diterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups).
A straight-chain saturated fatty acid anion that is the conjugate base of behenic acid, arising from deprotonation of the carboxylic acid group.
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.
Any primary alcohol based on an ethanol skeleton.
Any carboxylic ester resulting from the formal condensation of the carboxy group of a carboxylic acid with ethanol.
Vitamins like A, D, E and K that dissolve in fats and are stored in body tissues. Unlike the water-soluble vitamins, these are stored in the body for long periods of time and generally pose a greater risk for toxicity when consumed in excess.
An aliphatic alcohol consisting of a chain of 8 to 22 carbon atoms. Fatty alcohols may be saturated or unsaturated and may be branched or unbranched.
A member of the class of flavonoid with a 2-aryl-1-benzopyran-4-one (2-arylchromen-4-one) skeleton and its substituted derivatives.
Any furochromene that consists of a furan ring fused with a coumarin. The fusion may occur in different ways in give several isomers.
Compounds containing at least one furan ring.
16-Ethyl-1alpha,6alpha,19beta-trimethoxy-4-(methoxymethyl)-aconitane-3alpha,8,10alpha,11,18alpha-pentol, 8-acetate 10-benzoate
20-ethyl-3alpha,13,15alpha-trihydroxy-1alpha,6alpha,16beta-trimethoxy-4-(methoxymethyl)aconitane-8,14alpha-diyl 8-acetate 14-benzoate
A diterpenoid that is 20-ethyl-3alpha,13,15alpha-trihydroxy-1alpha,6alpha,16beta-trimethoxy-4-(methoxymethyl)aconitane-8,14alpha-diol having acetate and benzoate groups at the 8- and 14-positions respectively.
Any substance produced by linking glucuronic acid to another substance via a glycosidic bond.
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of glutaric acid.
A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
Any phospholipid that contain both phosphate and carbohydrate as integral structural components.
A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively.
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.
Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas.
An alkaloid that has formula C18H22ClNO6.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
A C16 straight-chain monounsaturated fatty acid having one C=C double bond.
A monounsaturated fatty acid aldehyde that is hexene having an oxo group at position 1.
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.
A compound consisting of carbon and hydrogen only.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
Any fatty acid carrying one or more hydroxy substituents.
Any carboxylic acid with at least one hydroxy group.
Any benzoate derivative carrying a single carboxylate group and at least one hydroxy substituent.
Any benzoic acid carrying one or more phenolic hydroxy groups on the benzene ring.
Any compound comprising a butyric acid core carrying at least one hydroxy substituent.
Any member of the class of cinnamic acids carrying one or more hydroxy substituents.
A member of the class of flavanones that consists of flavanone with one or more hydroxy substituents.
Any flavone in which one or more ring hydrogens are replaced by hydroxy groups.
A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.
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 chemical that lures insects to a trap, thereby removing them from crops, animals or stored products.
Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects.
A molecular entity having a net electric charge.
A 2-amino-3-methylpentanoic acid having either (2R,3R)- or (2S,3S)-configuration.
rel-(2R,3R)-2-amino-3-methylpentanoic acid
Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives.
Any alkaloid that has a structure based on an isoquinoline nucleus. They are derived from the amino acids like tyrosine and phenylalanine.
A class of organic heteropolycyclic compound consisting of isoquinoline and its substitution derivatives.
Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
A hydroxy monocarboxylic acid anion that is the conjugate base of lactic acid, arising from deprotonation of the carboxy group.
Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group.
Any phenylpropanoid derived from phenylalanine via dimerization of substituted cinnamic alcohols, known as monolignols, to a dibenzylbutane skeleton. Note that while individual members of the class have names ending ...lignane, ...lignene, ...lignadiene, etc., the class names lignan, neolignan, etc., do not end with an "e".
A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.
An alkaline earth metal atom that has formula Mg.
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of malic acid.
Any secondary alcohol that is one of the eight possible diastereoisomers of 5-methyl-2-(propan-2-yl)cyclohexan-1-ol.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
Compounds containing a benzene skeleton substituted with one methoxy group.
Any benzoic acid carrying one or more methoxy substituents.
A member of the class of flavanones that consists of flavanone with one or more methoxy substituents.
Any member of the class of flavones with at least one methoxy substituent.
Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol.
mitochondrial respiratory-chain inhibitor
mitochondrial electron transport chain inhibitors
mitochondrial electron-transport chain inhibitor
mitochondrial respiratory chain inhibitors
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An oxoacid containing a single carboxy group.
A hydroxybenzoate carrying a single hydroxy substituent at unspecified position.
Any hydroxybenzoic acid having a single phenolic hydroxy substituent on the benzene ring.
A terpene ketone derived from a monoterpene.
Any terpenoid derived from a monoterpene. The term includes compounds in which the C10 skeleton of the parent monoterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups).
Any fatty acid with one double or triple bond in the fatty acid chain and singly bonded carbon atoms in the rest of the chain. MUFAs have positive effects on the cardiovascular system, and in diabetes treatment.
An isoquinoline alkaloid based on a morphinan skeleton and its substituted derivatives.
An agent that increases the frequency of mutations above the normal background level, usually by interacting directly with DNA and causing it damage, including base substitution.
Any benzenoid aromatic compound having a skeleton composed of two ortho-fused benzene rings.
A substance used to destroy pests of the phylum Nematoda (roundworms).
A glycoside containing alpha-L-rhamnopyranosyl-(1->2)-beta-D-glucopyranosyl residue as the sugar unit.
An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.
Any polyprenol composed of at least nine isoprene units.
A nucleobase-containing molecular entity that is a nucleoside in which one or more of the sugar hydroxy groups has been converted into a mono- or poly-phosphate. The term includes both nucleotides and non-nucleotide nucleoside phosphates.
A long-chain, unsaturated fatty acid anion formed by deprotonation of the carboxy group of any octadecadienoic acid; major species at pH 7.3.
Any straight-chain, C18 polyunsaturated fatty acid having two C=C double bonds.
A fatty acid anion 18:0 that is the conjugate base of stearic acid. Stearates have a variety of uses in the pharmaceutical industry.
Any member of the group of C18 monounsaturated fatty acids with the double bond located at any position in the chain.
A primary alcohol that is octanol consisting of two double bonds at unspecified positions.
A straight-chain saturated fatty acid anion that is the conjugate base of octanoic acid (caprylic acid); believed to block adipogenesis.
Any organic ion with a net positive charge.
An organooxygen compound with formula ROR, where R is not hydrogen.
An alcohol derived from an aliphatic compound.
An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters.
A solute used by a cell under water stress to maintain cell volume.
An oxide is a chemical compound of oxygen with other chemical elements.
Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule.
Any fatty acid anion containing at least one C-C unsaturated bond; formed by deprotonation of the carboxylic acid moiety.
A fatty acid ester obtained by condensation of the carboxy group of palmitic acid with a hydroxy group of an alcohol or phenol.
A hydroxyflavone substituted by five hydroxy groups.
A five-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldopentose) or a ketone group at position 2 (ketopentose).
Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.
A 2-hydroxy monocarboxylic acid that is lactic acid in which one of the methyl hydrogens is substituted by a phenyl group.
Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin.
A semiochemical used in olfactory communication between organisms of the same species eliciting a change in sexual or social behaviour.
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 consits of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
A member of the class of benzoic acids in that consists of benzene substituted by two carboxy groups.
Sterols similar to cholesterol which occur in plants and vary only in carbon side chains and/or presence or absence of a double bond.
An endogenous molecular entity that results in a colour of an organism as the consequence of the selective absorption of light.
A chemical, natural or artificial, that can affect the rate of growth of a plant.
Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides.
A compound that contains two or more hydroxy groups.
Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group.
Any member of the class of prenols possessing the general formula H-[CH2C(Me)=CHCH2]nOH in which the carbon skeleton is composed of more than one isoprene units.
Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome.
Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
An alkali metal atom that has formula K.
Any alcohol possessing the general formula H-[CH2C(Me)=CHCH2]nOH in which the carbon skeleton is composed of one or more isoprene units (biogenetic precursors of the isoprenoids).
A flavonoid oligomer obtained by the the condensation of two or more units of hydroxyflavans.
An alpha-amino acid that is pyrrolidine bearing a carboxy substituent at position 2.
A furanocoumarin with a 7H-furo[3,2-g]chromen-7-one skeleton and its substituted derivatives thereof.
Members of the class of benzofurochromene with a 6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromene skeleton and its substituted derivatives. They generally bear structural resemblance to isoflavanoids that possess antibiotic activity and are produced by plant tissues in response to infection. They are the 3,4-dihydroderivatives of coumestans.
Any nucleotide that has a purine nucleobase.
Any ribonucleotide that has a purine nucleobase.
A class of imidazopyrimidines that consists of purine and its substituted derivatives.
A monocarboxylic acid in which the carboxy group is attached to a pyridine (or substituted pyridine) ring.
Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives.
A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen.
A cyclitol carboxylic acid anion that is conjugate base of quinic acid.
3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraenoic acid substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified).
Oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.
A deoxymannose sugar that is the 6-deoxy derivative of hexose.
A glycoside that is a compound containing one or more hydrophilic glycoside moieties combined with a lipophilic triterpenoid or steroid derivative. Found in particular abundance in plant species.
Any organic polycyclic compound that is the aglycon moiety of a saponin; sapogenins may be steroids or triterpenoids.
Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess.
A molecular messenger released by an organism that affects the behaviour within or between species.
An L-alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class.
Any terpenoid derived from a sesquiterpene. The term includes compounds in which the C15 skeleton of the parent sesquiterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups).
An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid.
A nonaprenol that is hexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-ol substituted by 9 methyl groups at positions 3, 7, 11, 15, 19, 23, 27, 31 and 35 (the all-trans0stereoisomer).
A steroid fundamental parent that has formula C29H52.
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of succinic acid.
Any of a group of astringent polyphenolic vegetable principles or compounds, chiefly complex glucosides of catechol and pyrogallol.
(2R,3R)-rel-2,3-dihydroxybutanedioic acid
(R*,R*)-(+-)-2,3-dihydroxybutanedioic acid
rel-(2R,3R)-2,3-dihydroxybutanedioic acid
Any terpenoid which contains a keto group.
Any isoprenoid that is a natural product or related compound formally derived from isoprene units. Terpenoids may contain oxygen in various functional groups. This class is subdivided according to the number of carbon atoms in the parent terpene. The skeleton of terpenoids may differ from strict additivity of isoprene units by the loss or shift of a fragment, generally a methyl group.
A family of monoterpenols that have a p-menthane skeleton containing one double bond and bearing a single hydroxy substituent.
A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it.
Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
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 terpenoid derived from a tetraterpene. The term includes compounds in which the C40 skeleton of the parent tetraterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups).
An ester in which one or both oxygens of an ester group have been replaced by divalent sulfur.
An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms.
An alpha-amino acid in which one of the hydrogens attached to the alpha-carbon of glycine is substituted by a 1-hydroxyethyl group.
Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group.
Poisonous substance produced by a biological organism such as a microbe, animal or plant.
An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
An oxoacid containing three carboxy groups.
Any hydroxyflavone carrying three hydroxy groups at unspecified positions.
A chemical compound containing three hydroxy groups.
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.
Any fatty acid containing at least one C=C or C#C bond.
A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isopropyl group.
A fatty acid which has a chain length greater than C22.
Vitamin D is a group of fat-soluble prohormones, which can be obtained from sun exposure, food and supplements. Vitamin D is biologically inactive and converted to the biologically active calcitriol via double hydroxylation in the body.
Any metabolite that is found naturally as a component of a volatile oil.
A subclass of carotenoids consisting of the oxygenated carotenes.
A zinc group element atom that has formula Zn.
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 monocarboxylic acid that consists of acrylic acid bearing a phenyl substituent at the 3-position. It is found in Cinnamomum cassia.
A xylene with methyl groups at positions 1 and 4.
A hydroxycoumarin that is coumarin substituted by a hydroxy group ay position 7.
A boron group element atom that has formula B.
A saturated organic heteromonocyclic parent that is a three-membered heterocycle of two carbon atoms and one oxygen atom.
2-amino-3-(1H-imidazol-4-yl)propanoic acid
An alpha-amino acid that is propanoic acid bearing an amino substituent at position 2 and a 1H-imidazol-4-yl group at position 3.
alpha-Amino-1H-imidazole-4-propionic acid
A carbon group element atom that has formula Si.
A proanthocyanidin obtained by the condensation of (-)-epicatechin and (+)-catechin units.
A carbon group element atom that has formula C.
3-(6-hydroxy-5-benzofuranyl)-2-propenoic acid delta-lactone
6-hydroxy-5-benzofuranacrylic acid delta-lactone
The simplest member of the class of psoralens that is 7H-furo[3,2-g]chromene having a keto group at position 7. It has been found in plants like Psoralea corylifolia and Ficus salicifolia.
A D-galactopyranose having beta-configuration at the anomeric centre.
A fatty acid anion 10:0 that is the conjugate base of decanoic acid.
A phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3.
Any hydroxyflavone with a hydroxy substituent at position 3'.
(2E)-3-(3-hydroxy-4-methoxyphenyl)prop-2-enoic acid
A ferulic acid consisting of trans-cinnamic acid bearing methoxy and hydroxy substituents at positions 4 and 3 respectively on the phenyl ring.
2-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-4H-chromen-7-yl beta-D-glucopyranoside
A glycosyloxyflavone that is luteolin substituted by a beta-D-glucopyranosyl moiety at position 7 via a glycosidic linkage.
An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group.
A xylene substituted by methyl groups at positions 1 and 3.
A glycosylglucose consisting of two D-glucopyranose units connected by a beta-(1->6)-linkage.
7-Hydroxyisoflavone with additional hydroxy groups at positions 5 and 4'. It is a phytoestrogenic isoflavone with antioxidant properties.
A bornane monoterpenoid that is 1,7,7-trimethylbicyclo[2.2.1]heptane substituted by a hydroxy group at position 2.
An aromatic amide that consists of benzene bearing a single carboxamido substituent. The parent of the class of benzamides.
A member of the class of 7-hydroxyisoflavones that is 7-hydroxyisoflavone substituted by an additional hydroxy group at position 4'.
A trihydroxyflavanone having the three hydroxy gropus located at the 3'-, 5- and 7-positions and an additional methoxy substituent at the 4'-position.
A fenchane monoterpenoid that is 3,5,5-trimethylcyclohex-2-en-1-one substituted by a hydroxy and a (1E)-3-hydroxybut-1-en-1-yl group at position 4.
An aldohexose that is the C-4 epimer of glucose.
A racemate comprising equimolar amounts of (R)- and (S)-lactic acid.
A fatty alcohol 30:0 that has formula C30H62O.
A tetrahydroxyflavanone that is flavanone substituted by hydroxy groups at positions 5, 7, 3' and 4' respectively.
A cyclic carotene with a beta- and an epsilon-ring at opposite ends respectively.
A C5, branched-chain saturated fatty acid.
4H-1-Benzopyran-4-one, 3,5,7-trihydroxy-2-(4-hydroxyphenyl)-5,7,4'-Trihydroxyflavonol
A tetrahydroxyflavone in which the four hydroxy groups are located at positions 3, 5, 7 and 4'.
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-glucopyranoside
A rutinoside that is quercetin with the hydroxy group at position C-3 substituted with glucose and rhamnose sugar groups.
A monomethoxybenzene that consists of phenol with a methoxy substituent at the ortho position.
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 chromium group element atom that has formula Mo.
A copper group element atom that has formula Cu.
A dihydroxyflavanone compound having the two hydroxy substituents at the 4'- and 7-positions. Isolated from the root of Glycyrrhizae uralensis, it is a selective agonist for oestrogen receptor beta.
2-Propenoic acid, 3-(2-hydroxyphenyl)-, d-lactone
2-Propenoic acid, 3-(2-hydroxyphenyl)-, delta-lactone
A chromenone having the keto group located at the 2-position.
Any hydroxyflavone in which is the ring hydrogen at position 3 of the heterocyclic ring is replaced by a hydroxy group.
A primary alcohol, being cinnamyl alcohol hydroxylated at C-4 and methoxylated at C-3 and -5.
A straight-chain alkane with 12 carbon atoms. It has been form the essential oils of various plants including Zingiber officinale (ginger).
(2S)-5-hydroxy-2-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-chromen-7-yl 2-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-glucopyranoside
A disaccharide derivative that is (S)-naringenin substituted by a 2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl moiety at position 7 via a glycosidic linkage.
Naringenin 7-O-[alpha-L-rhamnosyl-(1->2)-beta-D-glucoside]
Naringenin 7-O-alpha-L-rhamnosyl-(1->2)-beta-D-glucoside
A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions.
A straight-chain saturated fatty acid that is heptane in which one of the hydrogens of a terminal methyl group has been replaced by a carboxy group. Octanoic acid is also known as caprylic acid.
A C18 straight-chain saturated fatty acid component of many animal and vegetable lipids. As well as in the diet, it is used in hardening soaps, softening plastics and in making cosmetics, candles and plastics.
A primary alcohol that consists of (3Z)-hex-3-ene substituted by a hydroxy group at position 1.
Members of the class of flavans with a 3,4-dihydro-2-aryl-2H-1-benzopyran-4-one skeleton and its substituted derivatives.
A C24 straight-chain saturated fatty acid.
The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid.
A straight-chain, fourteen-carbon, long-chain saturated fatty acid mostly found in milk fat.
A primary alcohol that is butane in which a hydrogen of one of the methyl groups is substituted by a hydroxy group. It it produced in small amounts in humans by the gut microbes.
A straight-chain alkane with 15 carbon atoms. It is a component of volatile oils isolated from plants species like Scandix balansae.
A fatty alcohol consisting of a hydroxy function at C-1 of an unbranched saturated chain of ten carbon atoms.
An onium cation obtained by protonation of ammonia.
A straight-chain, C22, long-chain saturated fatty acid.
Any sugar having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups.
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid.
A propane-1,2-diol that has formula C3H8O2.
A monoterpenoid indole alkaloid that is strychnidine bearing a keto substituent at the 10-position.
A chalcocarbonic acid that has formula CH2O3.
An alicyclic hydrocarbon comprising a ring of six carbon atoms; the cyclic form of hexane, used as a raw material in the manufacture of nylon.
2-amino-5-(carbamimidamido)pentanoic acid
An alpha-amino acid that is glycine in which the alpha-is substituted by a 3-guanidinopropyl group.
A C9 straight-chain saturated fatty acid which occurs naturally as esters of the oil of pelargonium. Has antifungal properties, and is also used as a herbicide as well as in the preparation of plasticisers and lacquers.
A divalent metal cation in which the metal is manganese.
An ion of copper carrying a double positive charge.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A benzenedicarboxylic acid cosisting of two carboxy groups at ortho positions.
A monoatomic monocation obtained from potassium.
A nitrogen hydride that has formula H2N.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A carboxamide derived from a monocarboxylic acid.
A monocarboxylic acid amide derived from a fatty acid.
The (2Z)-stereoisomer of 3,7-dimethylocta-2,6-dien-1-ol. It has been isolated from the essential oils from plants like lemon grass.
A monocarboxylic acid anion obtained by the deprotonation of the carboxy group of ferulic acid.
A quinate that is the conjugate base of (-)-quinic acid.
A C4-dicarboxylate that is the E-isomer of but-2-enedioate(2-)
A dicarboxylic acid dianion that is the conjugate base of glutamate(1-).
An aspartate(1-) that is the conjugate base of D-aspartic acid.
An aspartate(1-) that is the conjugate base of L-aspartic acid.
An aspartate(2-) that is the conjugate base of L-aspartate(1-).
An aspartate(2-) that is the conjugate base of D-aspartate(1-).
A C4-dicarboxylate that is the dianion obtained by the deprotonation of both the carboxy groups of aspartic acid.
A dicarboxylic acid dianion resulting from the removal of a proton from both of the carboxy groups of succinic acid.
A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid.
4H-1-Benzopyran-4-one, 3-(beta-D-glucopyranosyloxy)-5,7-dihydroxy-2-(4-hydroxyphenyl)-
5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl beta-D-glucopyranoside
A kaempferol O-glucoside in which a glucosyl residue is attached at position 3 of kaempferol via a beta-glycosidic linkage.
A monoatomic phosphorus that has formula P.
A monoatomic fluorine that has formula F.
(9Z,12Z)-9,12-octadecadienoic acid, ion(1-)
(Z,Z)-9,12-octadecadienoic acid, ion(1-)
An octadecadienoate with cis- double bonds at the 9- and 12- positions; the conjugate base of linoleic acid.
An alkane that is propane substituted by a methyl group at position 2.
A copper group element atom that has formula Ag.
An gamma-amino acid anion resulting from the deprotonation of the carboxy group of gamma-aminobutyric acid.
An elemental silicon that has formula Si.
A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of oxalic acid.
A bisbenzylisoquinoline alkaloid that has formula C37H40N2O6.
(1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid
A cyclopentapyran that is 1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid substituted at positions 1, 6 and 7 by beta-D-glucosyloxy, hydroxy and methyl groups respectively
A monocarboxylic acid that is toluene in which one of the hydrogens of the methyl group has been replaced by a carboxy group.
A compound comprising a benzene ring core carrying a carboxylic acid substituent.
The simplest carboxylic acid, containing a single carbon. Occurs naturally in various sources including the venom of bee and ant stings, and is a useful organic synthetic reagent. Principally used as a preservative and antibacterial agent in livestock feed. Induces severe metabolic acidosis and ocular injury in human subjects.
A monohydroxybenzoate that is the conjugate base of salicylic acid.
A short-chain saturated fatty acid comprising ethane attached to the carbon of a carboxy group.
2-Hydroxy-1,2,3-propanetricarboxylic acid
2-hydroxypropane-1,2,3-tricarboxylic acid
3-Carboxy-3-hydroxypentane-1,5-dioic acid
A tricarboxylic acid that is propane-1,2,3-tricarboxylic acid bearing a hydroxy substituent at position 2. It is an important metabolite in the pathway of all aerobic organisms.
A straight-chain saturated fatty acid that is butane in which one of the terminal methyl groups has been oxidised to a carboxy group.
A C6, straight-chain saturated fatty acid.
A trihydroxybenzoic acid in which the hydroxy groups are at positions 3, 4, and 5.
A dicarboxylic acid monoanion resulting from the removal of a proton from one of the carboxy groups of succinic acid.
An alpha,omega-dicarboxylic acid in which the two carboxy groups are separated by a single methylene group.
A dicarboxylic acid monoanion that has formula C3H3O4.
A phthalate that is the conjugate base of phthalic acid.
A straight-chain, twelve-carbon medium-chain saturated fatty acid with strong bactericidal properties; the main fatty acid in coconut oil and palm kernel oil.
A long-chain fatty acid anion that is the conjugate base of myristic acid; major species at pH 7.3.
A C10, straight-chain saturated fatty acid.
A monohydroxybenzoic acid that is 4-hydroxybenzoic acid substituted by a methoxy group at position 3.
A C18, long straight-chain monounsaturated fatty acid anion; and the conjugate base of oleic acid, arising from deprotonation of the carboxylic acid group.
A furoic acid having the carboxylic acid group located at position 2.
A pentacyclic triterpenoid that is lupane having a double bond at position 20(29) as well as 3beta-hydroxy and 28-hydroxymethyl substituents.
A pentacyclic triterpenoid that is lupane having a double bond at position 20(29) as well as 3beta-hydroxy and 28-carboxy substituents. It is found in the bark and other plant parts of several species of plants including Syzygium claviflorum. It exhibits anti-HIV, antimalarial, antineoplastic and anti-inflammatory properties.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
An oxo dicarboxylic acid that consists of glutaric acid bearing an oxo substituent at position 2. It is an intermediate metabolite in Krebs cycle.
A dicarboxylic acid monoanion resulting from selective deprotonation of the 1-carboxy group of 2-oxoglutaric acid.
A dicarboxylic acid dianion obtained by deprotonation of both the carboxy groups of glutaric acid.
A tartaric acid anion that is the conjugate base of 3-carboxy-2,3-dihydroxypropanoate.
A C28, very long straight-chain, saturated fatty acid.
A very long straight-chain saturated fatty acid anion and the conjugate base of octacosanoic acid (montanic acid), arising from deprotonation of the carboxy group.
A C30, very long straight-chain, saturated fatty acid.
A very long straight-chain saturated fatty acid anion that is the conjugate base of melissic acid, arising from deprotonation of the carboxylic acid group.
A 26-carbon, straight-chain, saturated fatty acid.
A straight-chain saturated fatty acid anion that is the conjugate base of lignoceric acid, formed by deprotonation of the carboxy group.
A monoterpenoid that has formula C12H20O2.
A monoterpenoid indole alkaloid that has formula C23H26N2O4.
A fatty alcohol consisting of a hydroxy function at C-1 of an unbranched saturated chain of 18 carbon atoms.
A medium-chain fatty acid anion that is the conjugate base of nonanoic acid that in methyl ester form has significant nematicidal activity.
A medium-chain fatty acid anion that is the conjugate base of heptanoic acid; shown in myocardial ischaemia/reperfusion studies to increase levels of C4 Kreb's cycle intermediates.
A straight-chain, eleven-carbon saturated medium-chain fatty acid found in body fluids; the most fungitoxic of the C7:0 - C18:0 fatty acid series.
A medium-chain fatty acid anion that is the conjugate base of undecanoic acid; used in tandem with testosterone cation in the treatment of male hypogonadism. Major species at pH 7.3.
A phenolate anion that is the conjugate base of catecholate(1-).
An alpha-amino-acid anion that is the conjugate base of alanine, arising from deprotonation of the carboxy group.
An alpha-amino-acid cation that is the conjugate acid of alanine.
A sulfur-containing amino-acid anion that is the conjugate base of cysteine, obtained by deprotonation of the carboxy group.
An alpha-amino-acid anion that has formula C3H5NO2S.
An alpha-amino-acid cation that has formula C3H8NO2S.
An aromatic amino-acid anion that is the conjugate base of phenylalanine, arising from deprotonation of the carboxy group.
An alpha-amino-acid cation that is the conjugate acid of phenylalanine, arising from protonation of the amino group.
An alpha-amino-acid cation that is the conjugate acid of glycine, arising from protonation of the amino.
An alpha-amino-acid anion that is the conjugate base of glycine, arising from deprotonation of the carboxy group.
An alpha-amino-acid anion that has formula C6H8N3O2.
An alpha-amino-acid anion that has formula C6H7N3O2.
An alpha-amino-acid cation that has formula C6H10N3O2.
An alpha-amino-acid cation that has formula C6H11N3O2.
A pyridinemonocarboxylate that is the conjugate base of nicotinic acid, arising from deprotonation of the carboxy group; major species at pH 7.3.
An alkaline earth metal atom that has formula Ba.
An alpha-amino-acid anion that is the conjugate base of leucine, arising from deprotonation of the carboxy group.
An alpha-amino-acid cation that is the conjugate acid of leucine, arising from protonation of the amino group.
A sulfur-containing amino-acid anion that is the conjugate base of methionine, arising from deprotonation of the carboxy group.
A sulfur-containing amino-acid anion that is the conjugate acid of methionine, arising from protonation of the amino group.
An alpha-amino-acid anion that has formula C6H13N4O2.
An alpha-amino-acid cation that has formula C6H15N4O2.
An alpha-amino-acid cation that has formula C6H16N4O2.
An L-alpha-amino acid anion that is the conjugate base of L-threonine, arising from deprotonation of the carboxy group.
An alpha-amino-acid anion that is the conjugate base of serine.
An alpha-amino-acid cation that is the conjugate acid of serine.
A branched-chain amino-acid anion that has formula C5H10NO2.
An alpha-amino-acid cation that has formula C5H12NO2.
An alpha-amino-acid anion that is the conjugate base of proline, arising from deprotonation of the carboxy group.
An alpha-amino-acid cation that is the conjugate acid of proline, arising from protonation of the amino group.
An acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n. Acyclic branched or unbranched hydrocarbons having more than one double bond are alkadienes, alkatrienes, etc.
A straight chain alkane composed of 9 carbon atoms.
A straight-chain alkane carrying 18 carbon atoms.
A straight-chain alkane with 19 carbon atoms. It has been found as a component of essential oils isolated from Artemisia armeniaca.
An alkane that has 21 carbons and a straight-chain structure. It has been isolated from plants like Periploca laevigata and Carthamus tinctorius.
A straight-chain alkane containing 24 carbon atoms.
A straight-chain alkane containing 28 carbon atoms.
Any cyclic ether in which the oxygen atom forms part of a 3-membered ring.
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.
A fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any long-chain (C13 to C22) fatty acid.
The E (trans) stereoisomer of cinnamyl alcohol.
An organic substance that is distributed in foodstuffs, is distinct from the main organic components of food (protein, carbohydrate and fat) and is needed for the normal nutrition of the organism in question. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines.
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 assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
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.
A univalent group formed by removing a hydrogen atom from a hydrocarbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A substance that kills or slows the growth of bacteria.
A nutrient is a chemical element needed by all life forms.
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 substance used to destroy rodent pests.
A substance used to destroy bird pests (class Aves).
An energy-rich substance that can be transformed with release of usable energy.
A molecular entity containing one or more atoms of an alkali metal.
An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
An alkaline earth metal atom that has formula Sr.
Any monosaccharide containing an alcoholic hydroxy group esterified with phosphoric acid.
Arylmethyl groups and derivatives formed by substitution: ArCR2-.
A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.
A molecular entity containing one or more atoms of a transition element.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent.
Any compound containing an o-diphenol component.
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.
Any carboxylic acid having a sulfur substituent.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A cyclic compound having as ring members atoms of the same element only.
A homocyclic compound in which all of the ring members are carbon atoms.
A compound having one atom as the only common member of two rings.
A molecule that features two fused rings.
A polycyclic compound in which two rings have two, and only two, atoms in common. Such compounds have n common faces and 2n common atoms.
Acyclic and cyclic hydrocarbons having one or more carbon-carbon double bonds, apart from the formal ones in aromatic compounds. The class olefins subsumes alkenes and cycloalkenes and the corresponding polyenes.
The inclusive term for any cyclic hydrocarbon having any number of double bonds.
An unsaturated monocyclic hydrocarbon having at least one endocyclic double bond.
Acyclic branched or unbranched hydrocarbons having one or more carbon-carbon double bond.
Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds.
An aliphatic compound having a carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system.
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.
Any monocyclic or polycyclic aromatic hydrocarbon.
A mancude monocyclic hydrocarbon without side chains of the general formula CnHn (n is an even number) or CnHn+1 (n is an odd number). In systematic nomenclature an annulene with seven or more carbon atoms may be named [n]annulene, where n is the number of carbon atoms.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A 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.
A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Alkenols; the term refers specifically to vinylic alcohols, which have the structure HOCR'=CR2. Enols are tautomeric with aldehydes (R' = H) or ketones (R' =/= H).
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).
An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
Any alcohol in which the alcoholic hydroxy group is attached to a carbon which is itself bonded to an aromatic ring.
Any aldehyde in which the carbonyl group is attached to an aromatic moiety.
Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring.
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
A pentose with a (potential) aldehyde group at one end.
A hexose with a (potential) aldehyde group at one end.
Any aldopentose where the open-chain form has all the hydroxy groups on the same side in the Fischer projection. Occurrs in two enantiomeric forms, D- and L-ribose, of which only the former is found in nature.
1,2-Benzenedicarboxylic acid dibutyl ester
A phthalate ester that is the diester obtained by the formal condensation of the carboxy groups of phthalic acid with two molecules of butan-1-ol.
Benzene-o-dicarboxylic acid di-n-butyl ester
o-Benzenedicarboxylic acid dibutyl ester
1,2-Benzenedicarboxylic acid diethyl ester
The diethyl ester of benzene-1,2-dicarboxylic acid.
o-Benzenedicarboxylic acid diethyl ester
An aldehyde that is furan with the hydrogen at position 2 substituted by a formyl group.
A trimethylbenzene carrying methyl substituents at positions 1, 3 and 5.
An ortho-fused bicyclic hydrocarbon that is 1,2,3,4-tetrahydro derivative of naphthalene.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
An alpha-carotene that has formula C40H56.
An azamacrocycle that has formula C23H29N3O2.
A hydrocarbon of biological origin having carbon skeleton formally derived from isoprene [CH2=C(CH3)CH=CH2].
A substance that diminishes the rate of a chemical reaction.
An amino acid zwitterion that has formula C3H7NO2S.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amnio group of serine.
A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups.
Ammonium, NH4(+), and derivatives formed by substitution by univalent groups.
Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom.
Any neutral molecule having charge-separated forms with a quaternary ammonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom.
A choline ester formed from choline and a carboxylic acid.
A retinoate that is the conjugate base of all-trans-retinoic acid.
A polyclic compound in which all of the ring members are carbon atoms.
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, so may be considered as triterpenoids.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax.
An oligomer comprising five monomeric monosaccharide units.
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 alpha-amino-acid anion that is the conjugate base of aspartic acid.
A 3-carboxy-2,3-dihydroxypropanoate that is the conjugate base of tartaric acid.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A substance used in the prophylaxis or therapy of infectious diseases.
A substance used to treat or prevent parasitic infections.
A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.
A substance that reduces or suppresses inflammation.
An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms.
A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors.
A loosely defined group of drugs that tend to reduce the activity of the central nervous system.
Compounds of structure RSSR in which R and R' are organic groups.
An amino acid zwitterion that is the tautomer of cystine.
A drug that prevents or reduces fever by lowering the body temperature from a raised state. An antipyretic will not affect the normal body temperature if one does not have fever. Antipyretics cause the hypothalamus to override an interleukin-induced increase in temperature. The body will then work to lower the temperature and the result is a reduction in fever.
A steroid fundamental parent that has formula C28H50.
A steroid fundamental parent that has formula C27H48.
A drug which lowers the blood glucose level.
EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitor
(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate,hydrogen-donor:oxygen oxidoreductase inhibitor
(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate,hydrogen-donor:oxygen oxidoreductase inhibitors
A compound or agent that combines with cyclooxygenases (EC 1.14.99.1) and thereby prevents its substrate-enzyme combination with arachidonic acid and the formation of icosanoids, prostaglandins, and thromboxanes.
EC 1.14.99.1 (cyclooxygenase) inhibitors
EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitors
cyclooxygenase (EC 1.14.99.1) inhibitors
prostaglandin endoperoxide synthetase inhibitor
prostaglandin endoperoxide synthetase inhibitors
heterocyclic organic fundamental parents
organic heterocyclic fundamental parents
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
mancude organic heteromonocyclic parents
mancude-ring organic heteromonocyclic parents
A monocyclic heteroarene with a structure consisting of a 5-membered ring containing four carbons and one oxygen, with formula C4H4O. It is a toxic, flammable, low-boiling (31degreeC) colourless liquid.
Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds.
mancude-ring organic heterobicyclic parents
mancude-ring organic heterocyclic parents
A heterobicyclic aromatic organic compound comprising a pyrimidine ring fused to an imidazole ring; the parent compound of the purines.
A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n.
A substance that inhibits or prevents the proliferation of neoplasms.
A food additive that is used to added improve the taste or odour of a food.
Any ether in which the oxygen is attached to at least one aryl substituent.
A drug used to cause dilation of the blood vessels.
A drug used to prevent seizures or reduce their severity.
An isoquinoline alkaloid fundamental parent that has formula C16H21N.
Any drug used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism.
A substance used to treat hyperlipidemia (an excess of lipids in the blood).
A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it.
Any carboxylic acid containing two carboxy groups.
Any dicarboxylic acid anion that is a monoanion obtained by the deprotonation of only one of the carboxy groups of the dicarboxylic acid.
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.
An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response.
A monoterpene that is bicyclo[3.1.1]heptane substituted by methyl groups at positions 2, 6 and 6.
An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce.
An aldehyde formally arising from reduction of the carboxylic acid group of its corresponding fatty acid, having a carbonyl group at one end of the carbon chain.
A carboxylic ester in which the carboxylic acid component can be any fatty acid.
Any anion of a tricarboxylic acid formed by deprotonation of at least one carboxy group.
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 tricarboxylic acid monoanion that is the conjugate base of citric acid, obtained by deprotonation of one of the three carboxy groups.
A tricarboxylic acid dianion obtained by deprotonation of two of the three carboxy groups of citric acid.
Any fatty acid in which the parent hydrocarbon chain has one or more alkyl substituents; a common component in animal and bacterial lipids. The fatty acyl chain is usually saturated and the substituent a methyl group; however, unsaturated BCFAs are found in marine animals, and branches other than methyl are found in microbial lipids.
Any antimicrobial drug which is used to treat or prevent protozoal infections.
A substance used to lower plasma cholesterol levels.
A compound or agent that combines with lipoxygenase and thereby prevents its substrate-enzyme combination with arachidonic acid and the formation of the icosanoid products hydroxyicosatetraenoic acid and various leukotrienes.
A dicarboxylic acid monoanion that is the conjugate base of glutaric acid.
A terpene alkaloid fundamental parent that has formula C18H27N.
A pyridine alkaloid fundamental parent that has formula C36H43NO17.
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 hydroxy monocarboxylic acid that has a hydroxy group beta to the carboxy group.
Any hydroxy monocarboxylic acid carrying at least two hydroxy groups.
A fatty alcohol consisting of a hydroxy function at C-1 of an unbranched saturated chain of nine carbon atoms. It has been isolated as a component of volatile oils from plants like Hordeum vulgare.
A polycyclic compound in which two rings have two or more atoms in common.
A straight chain alkane containing 13 carbon atoms. It forms a component of the essential oils isolated from plants such as Abelmoschus esculentus.
A family of polyunsaturated fatty acids that have in common a final carbon-carbon double bond in the n-6 position, i.e., the sixth bond from the methyl end of the fatty acid.
An octadecenoic acid with a double bond at C-9.
A drug used to treat or prevent microbial infections.
Esters of benzoic acid or substituted benzoic acids.
A monocarboxylic acid that consists of a furan ring having a single carboxylic acid group on any ring position and derivatives thereof.
Any monocarboxylic acid anion carrying at least one hydroxy substituent.
A dihydroxybenzoic acid in which the hydroxy groups are located at positions 3 and 4.
A hydroxybenzoate that is the conjugate base of dihydroxybenzoic acid.
A piperidinecarboxylate that is the conjugate base of pipecolic acid.
(1R,3S,4R,5S)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid
1D-1(OH),3,4/5-tetrahydroxycyclohexanecarboxylic acid
An alicyclic ketone in which the carbocyclic ring structure forms part of a terpene skeleton.
A cyclic ketone in which the carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system.
Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included).
Any dicarboxylic acid carrying one or more oxo groups.
A C4-dicarboxylate that has formula C4H2O4.
A cyclohexenecarboxylate that is the conjugate base of shikimic acid.
A compound in which two monosaccharides are joined by a glycosidic bond.
A dihydroxybenzoate having the two hydroxy groups located at the 3- and 4-positions.
3-(3,4-dihydroxyphenyl)prop-2-enoic acid
A hydroxycinnamic acid that is cinnamic acid in which the phenyl ring is substituted by hydroxy groups at positions 3 and 4. It exists in cis and trans forms; the latter is the more common.
A drug used to treat or prevent infections caused by protozoal organisms belonging to the suborder Trypanosomatida.
A quinoline alkaloid fundamental parent that has formula C21H24N2O.
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.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
saturated organic heteromonocyclic parent
saturated heteromonocyclic parent hydride
saturated heteromonocyclic parent hydrides
saturated organic heteromonocyclic parents
A monocyclic hydrocarbon having any number of double bonds.
A terpenoid fundamental parent that has formula C15H30.
A sesquiterpene consisting of decalin having two methyl substituents at the 1- and 6-positions, an isopropyl substituent at the 4-position and (1S,4S,4aS,6S,8aS)-configuration.
A terpenoid fundamental parent that has formula C15H28.
A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table.
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.
A monoterpene that is bicyclo[2.2.1]heptane substituted by methy groups at positions 1, 3 and 3.
Any terpenoid derived from a triterpene. The term includes compounds in which the C30 skeleton of the parent triterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups).
A pinene that is bicyclo[3.1.1]hept-2-ene substituted by methyl groups at positions 2, 6 and 6 respectively.
A sesquiterpene that is dodecane substituted by methyl groups at positions 2, 6 and 10.
A diterpenoid based on an abietane skeleton.
A cyclic monoterpene ketone that is bornane bearing an oxo substituent at position 2. A naturally occurring monoterpenoid.
A bicyclic compound in which all the ring atoms are carbon.
Compounds containing a tetralin skeleton.
Any hydroxy steroid carrying a hydroxy group at position 3.
A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A nucleotide is a nucleoside phosphate. It is a phosphate ester that has a nucleoside moiety and has at least one phosphate moiety attached to the C-5 carbon of the ribose or deoxyribose moiety.
A hydroxy fatty acid anion that is the conjugate base of 3-hydroxybutyric acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.
A barium cation that has formula 137.32700.
A hydrogen butenedioate obtained by deprotonation of one of the carboxy groups of fumaric acid.
A dicarboxylic acid monoanion that has formula C4H3O4.
A polyol that contains 6 hydroxy groups.
Any ether in which the oxygen atom forms part of a ring.
An anthraquinone substituted with one or more hydroxy groups.
A member of the class of hydroxyanthraquinones carrying three hydroxy substituents.
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).
An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any fatty acid.
A molecular entity consisting of two or more chemical elements.
A lactone having a five-membered lactone ring.
An octadec-9-ene that has formula C18H36.
An alkene that is octadecane containing one double bond at unspecified position.
A L-galactopyranose with a beta-configuration at the anomeric position.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
A L-glucopyranose with a beta-configuration at the anomeric position.
A pentacyclic triterpenoid that is olean-12-en-28-oic acid substituted by a beta-hydroxy group at position 3.
Any member of a diverse class of complex, multicyclic phytochemicals showing a variety of skeleton arrangements and bioactivities, and having in common a sesquiterpenoid structure including a lactone ring.
An EC 2.7.* (P-containing group transferase) inhibitor that interferes with the action of protein kinases.
A straight chain alkane composed of 4 carbon atoms.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
A plant growth regulator that modulates the formation of stems, leaves and flowers, as well as the development and ripening of fruit. The term includes endogenous and non-endogenous compounds (e.g. active compounds produced by bacteria on the leaf surface) as well as semi-synthetic and fully synthetic compounds.
Any coumarin carrying at least one hydroxy substituent.
A spiro compound in which at least one of the cyclic components is an oxygen heterocyle.
Any of a class of cyclic chemical compounds that contain an unsaturated six-membered ring with one ring oxygen atom and an oxo substituent.
A carbopolyclic compound comprising of three carbocyclic rings.
A drug used in the treatment of malaria. Antimalarials are usually classified on the basis of their action against Plasmodia at different stages in their life cycle in the human.
A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres.
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 organic heterocyclic compound containing at least one ring oxygen atom.
Cyclic hemiacetals formed by intramolecular addition of a hydroxy group to an aldehydic or ketonic carbonyl group. They are thus 1-oxacycloalkan-2-ols or unsaturated analogues.
A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate.
A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of a pyridinemonocarboxylic acid. A 'closed class'.
Any of a class of heterocyclic amines having a saturated five-membered ring.
An alpha-amino acid that is butanoic acid substituted by an amino group at position 2 and a hydroxy group at position 3.
A branched chain amino acid that consists of 3-methylpentanoic acid bearing an amino substituent at position 2.
A monoterpene with a bicyclic skeleton that is bicyclo[2.2.1]heptane substituted by geminal methyl groups at position 2 and a methylidene group at position 3. It is a widespread natural product found in many essential oils.
Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure).
Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons.
Any drug that binds to and activates cholinergic receptors.
Any drug that binds to and activates a muscarinic cholinergic receptor.
muscarinic acetylcholine receptor agonist
A pyrimidine carrying one or more oxo substituents.
EC 3.1.1.7 (acetylcholinesterase) inhibitor
An EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that interferes with the action of enzyme acetylcholinesterase (EC 3.1.1.7), which helps breaking down of acetylcholine into choline and acetic acid.
EC 3.1.1.7 (acetylcholinesterase) inhibitors
acetyl.beta-methylcholinesterase inhibitor
acetyl.beta-methylcholinesterase inhibitors
acetylcholine acetylhydrolase inhibitors
acetylcholinesterase (EC 3.1.1.7) inhibitor
acetylcholinesterase (EC 3.1.1.7) inhibitors
respiratory electron-transport chain inhibitor
isoquinoline alkaloid fundamental parent
isoquinoline alkaloid fundamental parents
Any agent that affects the transport of molecular entities across a biological membrane.
Any protein kinase inhibitor that interferes with the action of tyrosine kinase.
A methyl-branched fatty acid comprising a butyric acid core carrying a single methyl substituent.
Any flavonoid with a 3,4-dihydro-2-aryl-2H-1-benzopyran skeleton and its substituted derivatives.
Any hydroxyflavone carrying four hydroxy substituents.
Any dianion containing at least one carboxy group.
A trianion containing at least one carboxy group.
Any methoxyflavanone that is flavanone substituted by a methoxy group.
A hydroxyflavanone carrying three hydroxy substituents.
A hydroxyflavanone with atleast four hydroxy substituents.
Any hydroxyflavanone carrying two hydroxy substituents.
Any polyamine that contained three amino groups.
Member of the class of isoflavones bearing at least one hydroxy group.
Members of the class of isoflavones with at least one methoxy substituent.
Any isoflavonoid with a 3-aryl-1-benzopyran-4-one (3-aryl-4H-chromen-4-one) skeleton and its substituted derivatives.
A gamma-lactone that has formula C15H18O5.
An organic heteropolycyclic compound whose skeleton consists of a chromene ring fused onto a 1-benzofuran ring, together with their substituted derivatives.
An alkaloid containing an indole skeleton.
Any alkylbenzene that is benzene substituted with one or more methyl groups.
A monocyclic arene that is benzene substituted with one or more alkyl groups.
Any magnesium ion that is positively charged.
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 farnesene that is 1,3,6,10-tetraene substituted by methyl groups at positions 3, 7 and 11 respectively.
A sesquiterpene that is any of the four possible isomers of 3,7,11-trimethyl-1,3,6,10-dodecatetraene (alpha-farnesene) or of the two possible isomers of 7,11-dimethyl-3-methylene-1,6,10-dodecatriene.
Any chemical substance that inhibits the life-cycle of an organism.
Any saturated fatty acid with a carbon side-chain or isopropyl termination.
Any saturated fatty acid lacking a side-chain.
A role played by a fluorescent molecular entity used to study the microscopic environment by fluorescence spectroscopy.
Any compound having a pyrimidine as part of its structure.
Any azaalkane in which two or more carbons in the chain are replaced by nitrogen.
A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.
A quaternary ammonium ion in which the substituents on nitrogen are methyl (three) and carboxymethyl.
A member of the class of furans that is furan which is substituted at positions 2 and 5 by formyl and hydroxymethyl substituents, respectively. Virtually absent from fresh foods, it is naturally generated in sugar-containing foods during storage, and especially by drying or cooking. It is the causative component in honey that affects the presystemic metabolism and pharmacokinetics of GZ in-vivo.
A galactopyranose having D-configuration.
A carbon oxoanion that has formula 60.00890.
A straight-chain alkane with 10 carbon atoms.
A hexose that has D-configuration at position 5.
An optically active form of lactic acid having (R)-configuration.
An optically active form of lactic acid having (S)-configuration.
A trihydroxyanthraquinone that is 9,10-anthraquinone which is substituted by hydroxy groups at positions 1, 3, and 8 and by a methyl group at position 6. It is present in the roots and barks of numerous plants (particularly rhubarb and buckthorn), moulds, and lichens. It is an active ingredient of various Chinese herbs.
A flavan-3,3',4',5,5',7-hexol having (2R,3R)-configuration.
A very long-chain fatty acid that is tricosane in which one of the methyl groups has been oxidised to the corresponding carboxylic acid.
The simplest member of the class of flavones that consists of 4H-chromen-4-one bearing a phenyl substituent at position 2.
A straight-chain, fifteen-carbon carboxylic acid with no heteroatoms; a long-chain of mainly ruminant origin.
An alkylbenzene that is benzene having one of its aromatic hydrogens substituted by a propyl group.
A butan-4-olide that is tetrahydrofuran substituted by an oxo group at position 2.
A phosphate ion that is the conjugate base of dihydrogenphosphate.
A pyranone that is 4H-pyran substituted by a hydroxy group at position 5, a hydroxymethyl group at position 2 and an oxo group at position 4. It has been isolated from the fungus Aspergillus oryzae.
A straight chain alkane composed of 20 carbon atoms. It has been isolated from the leaves of Agave attenuata.
A diterpenoid that has formula C24H39NO7.
A diterpenoid that has formula C33H45NO9.
An optically active form of 2-(hydroxymethyl)piperidine-3,4,5-triol having 2R,3R,4R,5S-configuration.
A straight-chain alkane with 16 carbon atoms. It is a component of essential oil isolated from long pepper.
A C7, straight-chain fatty acid that contributes to the odour of some rancid oils. Used in the preparation of esters for the fragrance industry, and as an additive in cigarettes.
An organophosphate oxoanion that is the trianion of adenosine 5'-diphosphate arising from deprotonation of all three OH groups of the diphosphate; major species present at pH 7.3.
A straight-chain alkane with 11 carbon atoms.
Any carbonate that is carbonic acid in which the hydrogens have been replaced by organyl groups.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
A dicarboxylic acid monoanion that is the conjugate base of oxalic acid.
Compounds containing an anthracene skeleton.
The (7alpha,7'alpha,8alpha,8'alpha)-stereoisomer of syringaresinol.
Any oxolane having an oxo- substituent at any position on the tetrahydrofuran ring.
Any carboxylic ester where the carboxylic acid component is acetic acid.
Any oxo steroid carrying an oxo group at position 16.
Any oxo steroid where an oxo substituent is located at position 3.
Organic heterobicyclic compounds containing a two furan rings ortho-fused to each other.
Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
A chemical compound that can be excited by light of a specific wavelength and subsequently transfer energy to a chosen reactant. This is commonly molecular oxygen within a cancer tissue, which is converted to (highly rective) singlet state oxygen. This rapidly reacts with any nearby biomolecules, ultimately killing the cancer cells.
A 3-oxo steroid conjugated to a C=C double bond at the alpha,beta position.
Any member of the 'superclass' flavonoids whose skeleton is based on 1-benzopyran with an aryl substituent at position 2. The term was originally restricted to natural products, but is now also used to describe semi-synthetic and fully synthetic compounds.
Any hydroxyflavanone with a hydroxy substituent at position 3' of the phenyl ring.
An olefin that contains more than one carbon-carbon double bond.
A substance used locally on humans and other animals to destroy harmful microorganisms or to inhibit their activity (cf. disinfectants, which destroy microorganisms found on non-living objects, and antibiotics, which can be transported through the lymphatic system to destroy bacteria within the body).
An antimicrobial agent that is applied to non-living objects to destroy harmful microorganisms or to inhibit their activity.
A tetritol that is butane substituted by hydroxy groups at positions 1, 2, 3 and 4.
A substance, extract, or preparation for diffusing or imparting an agreeable or attractive smell.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
An agent and endogenous substances that antagonize or inhibit the development of new blood vessels.
EC 1.1.1.21 (aldehyde reductase) inhibitor
An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of aldehyde reductase (EC 1.1.1.21).
EC 1.1.1.21 (aldehyde reductase) inhibitors
aldehyde reductase (EC 1.1.1.21) inhibitor
aldehyde reductase (EC 1.1.1.21) inhibitors
alditol:NAD(P)(+) 1-oxidoreductase inhibitor
alditol:NAD(P)(+) 1-oxidoreductase inhibitors
alditol:NADP(+) 1-oxidoreductase inhibitor
alditol:NADP(+) 1-oxidoreductase inhibitors
polyol dehydrogenase (NADP(+)) inhibitor
polyol dehydrogenase (NADP(+)) inhibitors
A role played by a substance that can react readily with, and thereby eliminate, radicals.
An olefinic compound that has formula C10H12O.
BENZENE,1-ALLYL,4-METHOXY METHYLCHAVICOL
Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own.
Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances.
One of a pair of phellandrene cyclic monoterpene double-bond isomers in which one double bond is exocyclic (cf. alpha-phellandrene, where both of them are endoocyclic).
Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists.
A tartaric acid anion that is the conjugate base of 2,3-dihydroxybutanedioic acid.
A branched-chain saturated fatty acid anion that is the conjugate base of isovaleric acid; reported to improve ruminal fermentation and feed digestion in cattle.
A bisbenzylisoquinoline alkaloid that has formula C38H42N2O6.
A primary alcohol that is ethanol substituted by a phenyl group at position 2.
A (6R)-vomifoliol that has formula C13H20O3.
A (6S)-vomifoliol with a R configuration for the hydroxy group at position 9.
A phenylpropanoid formally derived from guaiacol with an allyl chain substituted para to the hydroxy group.
One of various classes of drugs with different action mechanisms used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract.
A lignan that is 7,9':7',9-diepoxylignane substituted by hydroxy groups at positions 4 and 4' and methoxy groups at positions 3, 3', 5 and 5' respectively.
The (7beta,7'beta,8beta,8'beta)-stereoisomer of syringaresinol.
A bisabolene that is cyclohexene substituted by a methyl group at position 1 and a 6-methylhepta-1,5-dien-2-yl group at position 4.
A molybdenum cation that has formula 95.94000.
A s-block element atom that has formula 1.00794.
An ion of nickel carrying a double positive charge.
A fatty acid ester that is the carboxylic ester obtained by the formal condensation of a fatty acid with methanol.
A member of the class of flavones having one or more glycosyl residues attached at unspecified positions.
An isomer of pinene with an exocyclic double bond. It is a component of essential oils from many plants.
A thujene that is a bicyclic monoterpene isolated from the essential oils of various plant species.
A monoterpene based on a thujane skeleton.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
A monoterpene that consists of an unsaturated p-menthane skeleton having two double bonds.
An agent that binds to and activates excitatory amino acid receptors.
Any hormone that is responsible for controlling sexual characteristics and reproductive function.
A hormone that stimulates or controls the development and maintenance of female sex characteristics in mammals by binding to oestrogen receptors. The oestrogens are named for their importance in the oestrous cycle. The oestrogens that occur naturally in the body, notably estrone, estradiol, estriol, and estetrol are steroids. Other compounds with oestrogenic activity are produced by plants (phytoestrogens) and fungi (mycoestrogens); synthetic compounds with oestrogenic activity are known as xenoestrogens.
A flavonoid oligomer that is obtained by the oxidative coupling of at least two units of aryl-substituted benzopyran rings or its substituted derivatives, resulting in the two ring systems being joined together by a single atom or bond.
A drug that softens, separates, and causes desquamation of the cornified epithelium or horny layer of skin. Keratolytic drugs are used to expose mycelia of infecting fungi or to treat corns, warts, and certain other skin diseases.
A drug used to treat or prevent skin disorders or for the routine care of skin.
An enzyme inhibitor that interferes with the activity of cytochrome P450 involved in catalysis of organic substances.
A substance that can be converted into a vitamin by animal tissues.
A trihydroxyflavanone that is flavanone substituted by hydroxy groups at positions 5, 6 and 4'.
A dihydroxybenzaldehyde that has formula C7H6O3.
A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraen-1-ol substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified).
EC 3.1.4.* (phosphoric diester hydrolase) inhibitor
An EC 3.1.* (ester hydrolase) inhibitor that interferes with the action of a phosphoric diester hydrolase (EC 3.1.4.*).
EC 3.1.4.* (phosphoric diester hydrolase) inhibitors
phosphoric diester hydrolase (EC 3.1.4.*) inhibitor
phosphoric diester hydrolase (EC 3.1.4.*) inhibitors
Any protective agent counteracting or neutralizing the action of poisons.
Drug that acts on blood and blood-forming organs and those that affect the hemostatic system.
Any dicarboxylic acid carrying a hydroxy group on the carbon atom at position alpha to the carboxy group.
A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active drug for which it is a prodrug.
Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent.
A substance that does not act as agonist or antagonist but does affect the gamma-aminobutyric acid receptor-ionophore complex. GABA-A receptors appear to have at least three allosteric sites at which modulators act: a site at which benzodiazepines act by increasing the opening frequency of gamma-aminobutyric acid-activated chloride channels; a site at which barbiturates act to prolong the duration of channel opening; and a site at which some steroids may act.
EC 5.99.1.2 (DNA topoisomerase) inhibitor
A topoisomerase inhibitor that inhibits the bacterial enzymes of the DNA topoisomerases, Type I class (EC 5.99.1.2) that catalyze ATP-independent breakage of one of the two strands of DNA, passage of the unbroken strand through the break, and rejoining of the broken strand. These bacterial enzymes reduce the topological stress in the DNA structure by relaxing negatively, but not positively, supercoiled DNA.
EC 5.99.1.2 (DNA topoisomerase) inhibitors
EC 5.99.1.2 (topoisomerase I) inhibitors
topoisomerase I (EC 5.99.1.2) inhibitors
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
proteinogenic amino-acid side-chain group
A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid.
proteinogenic amino-acid side-chain groups
Any steroid based on a cholestane skeleton and its derivatives.
A role played by a molecular entity used to study the microscopic environment.
A drug or agent which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system.
An agent that produces a soft formed stool, and relaxes and loosens the bowels, typically used over a protracted period, to relieve constipation. Compare with cathartic, which is a substance that accelerates defecation. A substances can be both a laxative and a cathartic.
A gamma-lactone that consists of a 2-furanone skeleton and its substituted derivatives.
A phenolate anion that is the conjugate base of catechol.
An organic anion arising from deprotonation of the OH function of a phenol compound.
One of a class of monoterpenoids biosynthesized from isoprene and often intermediates in the biosynthesis of alkaloids. Iridoids usually consist of a cyclopentane ring fused to a six-membered oxygen heterocycle.
Any aliphatic alcohol in which the carbon chain contains one or more olefinic bonds.
An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
A cyclooxygenase inhibitor that interferes with the action of cyclooxygenase 2.
prostaglandin-endoperoxide synthase 2 inhibitor
prostaglandin-endoperoxide synthase 2 inhibitors
A cyclooxygenase inhibitor that interferes with the action of cyclooxygenase 1.
prostaglandin-endoperoxide synthase 1 inhibitor
prostaglandin-endoperoxide synthase 1 inhibitors
A reagent with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between macromolecules, principally side chains of amino acids in proteins, allowing the locations of naturally reactive areas within the proteins to be identified.
A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues.
A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance.
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor
A topoisomerase inhibitor that inhibits DNA topoisomerase (ATP-hydrolysing), EC 5.99.1.3 (topoisomerase II), which catalyses ATP-dependent breakage of both strands of DNA, passage of the unbroken strands through the breaks, and rejoining of the broken strands.
DNA topoisomerase (ATP-hydrolysing) (EC 5.99.1.3) inhibitor
DNA topoisomerase (ATP-hydrolysing) (EC 5.99.1.3) inhibitors
DNA topoisomerase (ATP-hydrolysing) inhibitor
DNA topoisomerase (ATP-hydrolysing) inhibitors
EC 5.99.1.3 (DNA topoisomerase (ATP-hydrolysing)) inhibitor
EC 5.99.1.3 (DNA topoisomerase (ATP-hydrolysing)) inhibitors
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitors
Any 1-benzopyran with an aryl substituent at position 3. The term was originally restricted to natural products, but is now also used to describe semi-synthetic and fully synthetic compounds.
Biologically active substance whose activity affects or plays a role in the functioning of the immune system.
A substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity.
Any carboxylic ester where the carboxylic acid component is 2-furoic acid.
Any molecular entity that contains carbon.
A role played by a chemical compound to induce direct or indirect DNA damage. Such damage can potentially lead to the formation of a malignant tumour, but DNA damage does not lead inevitably to the creation of cancerous cells.
A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities.
A chemical compound which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy.
A role played by a chemical compound in biological systems with adverse consequences in embryo developments, leading to birth defects, embryo death or altered development, growth retardation and functional defect.
A role played by a chemical compound exihibiting itself through the ability to induce damage to the liver in animals.
A poison that interferes with the functions of the nervous system.
An agent that modulates the physiologic angiogenesis process. This is accomplished by endogenous angiogenic proteins and a variety of other chemicals and pharmaceutical agents.
A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups.
A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups.
A cyclic compound containing nine or more atoms as part of the cyclic system.
A chemical substance which binds to specific hormone receptors activating the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites.
A drug that modulates the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites.
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.
Polycyclic aromatic hydrocarbons consisting of fused benzene rings in a rectilinear arrangement and their substitution derivatives.
A compound of general formula RC(=O)SR'. Compare with thionoester, RC(=S)OR'.
Quinones containing an acene fused ring system.
A diester is a compound containing two ester groups.
A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
Any methoxybenzene that consists of a benzene skeleton substituted with two methoxy groups and its derivatives.
Any aromatic ether that consists of a benzene skeleton substituted with one or more methoxy groups.
An alpha,beta-unsaturated aldehyde of general formula R(1)R(2)C=CR(3)-CH=O in which the aldehydic C=O function is conjugated to a C=C double bond at the alpha,beta position.
An alpha,beta-unsaturated ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) in which the C=O function is conjugated to a C=C double bond at the alpha,beta position.
An alpha,beta-unsaturated carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) in which the ester C=O function is conjugated to a C=C double bond at the alpha,beta position.
A pentacyclic triterpenoid that is perhydropicene which is substituted by an oxo group at position 3 and by methyl groups at the 4, 4a, 6b, 8a, 11, 11, 12b, and 14a-positions (the 4R,4aS,6aS,6bR,8aR,12aR,12bS,14aS,14bS-enantiomer). It is the major triterpenoid constituent of cork.
An aldehyde of general formula R(1)R(2)C=CR(3)-CH=O or RC#C-CH=O in which the aldehydic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
A ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) or R(1)C#C-C(=O)R(2) (R(2) =/= H) in which the ketonic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
A carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) or R(1)C#C-C(=O)OR(2) (R(2) =/= H) in which the ester C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
alpha,beta-unsaturated carboxylic esters
alpha,beta-unsaturated carboxylic acid amide
A monocarboxylic amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) or R(1)C#C-C(=O)NR(2)R(3) in which the amide C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position.
alpha,beta-unsaturated monocarboxylic acid amide
alpha,beta-unsaturated monocarboxylic acid amides
An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position.
An seven carbon-enal containing one extra C=C double bond, which may or may not be conjugated with the aldehydic C=O and alpha,beta-double bond systems.
A monoterpenoid that has formula C21H22O5.
A furanocoumarin which bears a hydroxy group at position 5.
An organic anion that is the conjugate base of methanol.
An organic anion that is the conjugate base of ethanol.
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 molecule or ion capable of binding to a central metal atom to form coordination complexes.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
Any flavonol carrying a 7-hydroxy substituent.
An EC 2.1.1.* (methyltransferases) inhibitor that interferes with the action of sterol methyltransferase.
An EC 3.2.* (glycosylase) inhibitor that interferes with the action of any glycosidase (i.e. enzymes hydrolysing O- and S-glycosyl compounds, EC 3.2.1.*).
A glycolipid and which the glyco component is specified as galactosyl.
A diterpenoid with a tetracyclic skeleton.
EC 3.1.26.13 (retroviral ribonuclease H) inhibitor
An inhibitor of ribonuclease H (EC 3.1.26.13), an enzyme required for specific hydrolysis of the RNA strand of an RNA/DNA hybrid.
EC 3.1.26.13 (retroviral ribonuclease H) inhibitors
retroviral reverse transcriptase RNaseH inhibitor
retroviral reverse transcriptase RNaseH inhibitors
retroviral ribonuclease H (EC 3.1.26.13) inhibitor
retroviral ribonuclease H (EC 3.1.26.13) inhibitors
An organic group that consists of a closed ring. It may be a substituent or a skeleton.
A cyclic macromolecule containing one or more nitrogen atoms in place of carbon either as the divalent group NH for the group CH2 or a single trivalent nitrogen atom for the group CH.
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.
Any fatty acid containing at least one C=C double bond.
A macromolecule containing ionic groups.
A diterpenoid compound having a kaurane skeleton.
An entity which inhibits the activity of HIV-1 reverse transcriptase.
Any drug found useful in the symptomatic treatment of diarrhoea.
A drug used for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion.
A hydroxyisoflavone compound having a hydroxy group at the 7-position.
A compound having the general formula RR'C(OH)OR'' (R'' =/= H).
A cyclic compound having as ring members atoms of at least two different elements.
3'-phosphonatoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] diphosphate}
An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine.
An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate groups of any 3-oxo-fatty acyl-CoA.
2-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-4H-chromen-7-olate luteolin-7-olate(1-)
A flavonoid oxoanion that is the conjugate base of luteolin, arising from selective deprotonation of the 7-hydroxy group.
A fatty acid anion with a chain length of C13 or greater.
A monocarboxylic acid anion that is the conjugate base of chlorogenic acid; major species at pH 7.3.
Conjugate base of quercetin arising from selective deprotonation of the 7-hydroxy group; major species at pH 7.3.
A D-alpha-amino acid zwitterion that is D-threonine in which a proton has been transferred from the carboxy group to the amino group. It is the major species at pH 7.3.
The conjugate base of trans-caffeic acid; major species at pH 7.3.
An ammonium ion that is the trication of spermidine, formed by protonation at all three nitrogens.
The conjugate base of a nucleoside 5'-phosphate.
An ammonium ion that is the conjugate acid of tryptamine arising from protonation of the primary amino group; major species at pH 7.3.
Zwitterionic form of L-threonine arising from transfer of a proton from the carboxy to the amino group; major species at pH 7.3.
Trianion of nucleoside diiphosphate arising from deprotonation of all three free OH groups of the diphosphate; major species at pH 7.3.
The dianion of a nucleoside monophosphate: major species at pH 7.3.
The conjugate acid of salutaridine; major species at pH 7.3.
Conjugate base of quercitrin arising from selective deprotonation of the 7-hydroxy group; major species at pH 7.3.
A flavonoid oxoanion that is the conjugate base of (S)-naringenin, arising from selective deprotonation of the 7-hydroxy group; major species at pH 7.3.
A diterpenoid that has formula C33H45NO10.
A flavonoid oxoanion that is the conjugate base of isoorientin, arising from selective deprotonation of the 7-hydroxy group; major species at pH 7.3.
An acyl-CoA oxoanion arising from deprotonation of the phosphate and diphosphate OH groups of any acyl-CoA; major species at pH 7.3.
An ammonium ion that is the conjugate acid of histamine protonated on the side-chain nitrogen.
The conjugate base of a flavonol compound.
The conjugate base of a 2-hydroxy carboxylic acid.
An organic phosphoric acid derivative in which one or more oxygen atoms of the phosphate group(s) has been deprotonated.
Any acyl coenzyme A thioester in which one or more of the phosphate and/or diphosphate groups has been deprotonated.
Any fatty acid anion with a chain length greater than C22.
Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6).
Any fatty acid anion in which there is no C-C unsaturation.
straight-chain saturated fatty acid anion
Any saturated fatty acid anion lacking a carbon side-chain.
straight-chain saturated fatty acid anions
Any fatty acid anion with a carbon side-chain or isopropyl termination.
branched-chain saturated fatty acid anion
Any saturated fatty acid anion with a carbon side-chain or isopropyl termination.
branched-chain saturated fatty acid anions
(2S)-5-hydroxy-2-(3-hydroxy-4-methoxyphenyl)-4-oxo-3,4-dihydro-2H-chromen-7-yl 2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranoside
A flavanone glycoside that is hesperitin having an 2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl moiety attached to the 7-hydroxy group.
A substance used as an indicator of a biological state.
Any fatty acid whose skeletal carbon atoms form an unbranched open chain.
A fatty acid anion formed by deprotonation of the carboxylic acid functional group of a straight-chain fatty acid.
Any member of the sub-set of polyunsaturated fatty acid for which there is an absolute dietary requirement.
Any fatty acid with a chain length of between C6 and C12.
A fatty acid anion resulting from the deprotonation of the carboxylic acid moiety of a medium-chain fatty acid.
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.
An aldehyde derived from an aliphatic compound
An organooxygen compound having the structure RR'C(OR'')(OR''') (R'', R''' =/= H). Mixed acetals have R'' and R''' groups which differ.
An acetal in the molecule of which the acetal carbon and one or both oxygen atoms thereon are members of a ring.
Conjugate base of an L-alpha-amino acid arising from deprotonation of the C-1 carboxy group.
The conjugate base of any hydroxy fatty acid, formed by deprotonation of the carboxylic acid moiety.
Any fatty acid with a hydroxy functional group in the beta- or 3-position. beta-Hydroxy fatty acids accumulate during cardiac hypoxia, and can also be used as chemical markers of bacterial endotoxins.
Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group and a protonated amino group.
Zwitterionic form of a D-alpha-amino acid having an anionic carboxy group and a protonated amino group.
Zwitterionic form of gamma-aminobutyric acid having an anionic carboxy group and a protonated amino group.
The angular furanocoumarin analogue of the linear furanocoumarin marmesin.
Any EC 1.14.18.* (oxidoreductase acting on paired donors, miscellaneous compound as one donor, incorporating 1 atom of oxygen) inhibitor that interferes with the action of tyrosinase (monophenol monooxygenase), EC 1.14.18.1, an enzyme that catalyses the oxidation of phenols (such as tyrosine) and is widespread in plants and animals.
L-tyrosine,L-dopa:oxygen oxidoreductase inhibitor
L-tyrosine,L-dopa:oxygen oxidoreductase inhibitors
NN-acetyl-6-hydroxytryptophan oxidase inhibitor
NN-acetyl-6-hydroxytryptophan oxidase inhibitors
monophenol dihydroxyphenylalanine:oxygen oxidoreductase inhibitor
monophenol dihydroxyphenylalanine:oxygen oxidoreductase inhibitors
monophenol, dihydroxy-L-phenylalanine oxygen oxidoreductase inhibitor
monophenol, dihydroxy-L-phenylalanine oxygen oxidoreductase inhibitors
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..
Any anion arising from deprotonation of at least one OH group in a flavonoid compound.
Conjugate base of a 7-hydroxyflavonol compound arising from selective deprotonation of the 3-hydroxy group; major species at pH 7.3.
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.
A silver atom having a net electric charge.
A nickel atom having a net electric charge.
Any cation arising from protonation of at least one of the amino functions in an indole alkaloid.
Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs.
N-methyl-D-aspartate receptor antagonist
N-methyl-D-aspartate receptor antagonists
Any substance which inhibits the action of receptors for excitatory amino acids.
excitatory amino acid receptor antagonist
excitatory amino acid receptor antagonists
Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself.
Any alpha-amino acid anion in which the parent amino acid has D-configuration.
A racemate is an equimolar mixture of a pair of enantiomers.
Any amino sugar that is a monosaccharide in which one alcoholic hydroxy group is replaced by an amino group.
A glucoside in which the anomeric carbon of the glycosidic bond is in a beta configuration
A nucleoside bisphosphate that has a purine nucleobase.
A nucleoside bisphosphate where sugar of the nucleoside is ribose.
EC 3.5.1.98 (histone deacetylase) inhibitor
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the function of histone deacetylase (EC 3.5.1.98).
EC 3.5.1.98 (histone deacetylase) inhibitors
histone deacetylase (EC 3.5.1.98) inhibitor
histone deacetylase (EC 3.5.1.98) inhibitors
Any compound that has a nucleobase as a part.
nucleobase-containing molecular entities
Aconitane-1,8,14-triol, 20-ethyl-16-methoxy-4-methyl-, (1-alpha,14-alpha,16-beta)-
An organonitrogen heterocyclic compound that is aconitane bearing hydroxy groups at the 1alpha, 8, and 14alpha positions and substituted at on the nitrogen and at positions 4 and 16beta by ethyl, methyl, and methoxy groups, respectively.
A flavonoid oxoanion that is the conjugate base of hesperetin arising from selective deprtotonation of the 7-hydroxy group.
A nucleotide having adenine as the base.
A purine riboncleotide where adenine is the purine.
A dicarboxylate that contains four carbon atoms.
Any hydroxy carboxylic acid which contains a hydroxy group located beta- to the carboxylic acid group.
A polymer, composed of polyanion macromolecules.
Any saponin derived from a hydroxysteroid.
Any organic molecular entity derived from a fatty acid.
A carbotricyclic compound and sesquiterpene that is 1a,2,3,4,4a,5,6,7b-octahydro-1H-cyclopropa[e]azulene which is substituted by methyl groups at positions 1, 1, 4 and 7 (the 1aR,4R,4aR,7bS- diastereoisomer). It has been isolated from plant species like Anaphalis nubigena and Jatropha ribifolia.
A terpenoid in which one or more hydroxy functions are glycosylated.
A terpene glycoside in which the terpene moiety is a triterpenoid.
Any fatty aldehyde with one double or triple bond located at any position in the aliphatic chain.
A fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any oxo-fatty acid.
A fatty acyl-CoA in which the fatty acyl group has a chain length greater than C22.
Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group.
Any donor that can transfer acyl groups between molecular entities.
A class of secondary metabolites developed by many plants to influence the behaviour, growth or survival of herbivores, and thus acting as a defence against herbivory.
A molecular messenger in which the molecule is specifically involved in transmitting information between cells. Such molecules are released from the cell sending the signal, cross over the gap between cells by diffusion, and interact with specific receptors in another cell, triggering a response in that cell by activating a series of enzyme controlled reactions which lead to changes inside the cell.
Any branched-chain fatty acid containing methyl branches only.
Any sesquiterpenoid having a eudesmane skeleton.
A eudesmane sesquiterpenoid in which the eudesmane skeleton carries a hydroxy substituent at C-11 and has a double bond between C-4 and C-5.
Any organophosphate oxoanion that is a negatively charged phospholipid, e.g. phosphatidylserine(1-), phosphatidate(2-), phosphatidylglycerol(1-).
An ester where the ester linkage is bonded directly to an aromatic system.
An amide in which the amide linkage is bonded directly to an aromatic system.
Any additive that enhances the efficiency of fuel.
A sesquiterpene that consists of cyclohexane bearing methyl and vinyl substituents at position 1 as well as two isopropenyl substituents at positions 2 and 4.
Any compound that is able to prevent damage to the liver.
An agonist that selectively binds to and activates an odorant receptor.
The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability.
A food additive used to form or maintain a uniform emulsion of two (or more) phases in a food.
Any zinc ion that is positively charged.
A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity.
An organophosphate oxoanion resulting from deprotonation of at least one of the acidic hydroxy groups from the phosphate moiety of a ribonucleoside monophosphate.
A sesquiterpene with a [7.2.0]-bicyclic structure comprising fused 9- and 4-membered rings, with a trans-ring junction, a trans-double bond between the 4- and 5-positions of the 9-membered ring, a methylidene group at position 9, and methyl groups at positions 3, 11, and 11. The most commonly occurring form is the (1R,9S)-(-)-enantiomer, which is found in many essential oils, particularly clove oil.
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 disaccharide.
A carbohydrate derivative that is formally obtained from a monosaccharide.
A monosaccharide derivative that is formally obtained from a pentose.
A retintinyl ester in which all double bonds of the retinyl side-chain have trans-configuration.
A carbohydrate derivative that is formally obtained from a carbohydrate acid.
A sulfur-containing amino acid whose alpha-carboxylic acid group is ionized (not protonated).
A branched-chain amino acid whose alpha-carboxylic acid group is ionized (not protonated).
An aromatic amino acid whose alpha-carboxylic acid group is ionized (non-protonated).
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative.
A carbohydrate derivative that is formally obtained from an oligosaccharide.
An oligosaccharide derivative that is formally obtained from a pentasaccharide.
A member of the cadinene family of sesquiterpenes in which the double bonds are located at the 4-4a and 7-8 positions, and in which the isopropyl group at position 1 is cis to the hydrogen at the adjacent bridgehead carbon (the 1R,8aS-enantiomer).
Any compound that can be used for the treatment of neurodegenerative disorders.
An agonist that selectively binds to and activates a retinoid X receptor.
A monohydroxybenzoate that is the conjugate base of 3-hydroxy-4-methoxybenzoic acid, arising from deprotonation of the carboxy group.
A methoxybenzoic acid that is 4-methoxybenzoic acid bearing a hydroxy substituent at position 3.
A primary alcohol that is ethanol in which one of the methyl hydrogens is replaced by a butoxy group. A high-boiling (171degreeC) colourless liquid, it is used as a solvent for paints and inks, as well as in some dry cleaning solutions.
Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule.
3-hydroxy-9beta,13alpha-dimethyl-2-oxo-24,25,26-trinoroleana-1(10),3,5,7-tetraen-29-oic acid
A pentacyclic triterpenoid that is 24,25,26-trinoroleana-1(10),3,5,7-tetraen-29-oic acid bearing an oxo substituent at position 2, a hydroxy substituent at position 3 and two methyl groups at positions 9 and 13. An antioxidant and anti-inflammatory agent. Potently inhibits lipid peroxidation in mitochondria and inhibits TNF-alpha-induced NFkappaB activation. Also shown to inhibit topoisomerase II activity in vitro (IC50 = 7.41 muM).
D:A-Friedo-24-noroleana-1(10),3,5,7-tetraen-29-oic acid, 3-hydroxy-2-oxo-, (20alpha)-
An EC 3.6.4.10 (non-chaperonin molecular chaperone ATPase) inhibitor that blocks the action of heat shock protein 90.
An agonist that selectively binds to and activates a protein kinase C receptor
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents.
An agonist that selectively binds to and activates a protein kinase receptor.
'matrix-assisted laser desorption/ionization' matrix material
'matrix-assisted laser desorption/ionization' matrix materials
A compound used to form the matrix for MALDI (matrix-assisted laser desorption/ionization) mass spectrometry. MALDI matrix materials are crystalline compounds with a fairly low molecular weight, so as to allow facile vaporization, have strong absorption at UV or IR wavelengths (to rapidly and efficiently absorb laser irradiation), generally contain polar groups (enabling them to be used in aqueous solutions) and are frequently acidic (so assisting ionisation of the compound being studied, which is contained within the matrix material).
An organic amino compound in which an aminoalkyl group is linked to an arene.
A metabolite of plant origin (phytochemical) which acts as a source material for biosynthesis of both lignans and lignin.
Sinapyl alcohol in which the configuration of the propenyl double bond is E. It is one of the main monolignols.
An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of methionine; major species at pH 7.3.
EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor
5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor
5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors
An EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor that interferes with the action of glycine hydroxymethyltransferase (EC 2.1.2.1).
EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors
L-serine hydroxymethyltransferase inhibitor
L-serine hydroxymethyltransferase inhibitors
glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor
glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors
glycine hydroxymethyltransferase inhibitor
glycine hydroxymethyltransferase inhibitors
serine hydroxymethyltransferase inhibitor
serine hydroxymethyltransferase inhibitors
An excitatory amino acid agonist which binds to NMDA receptors and triggers a response.
A quercetin O-glycoside that is an O-glucosylated derivative of quercetin.
A glycosyloxyflavone that is an O-glucosylated derivative of kaempferol.
An inorganic cation with a valency of two.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
EC 3.1.4.11 (phosphoinositide phospholipase C) inhibitor
1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase inhibitor
1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase inhibitors
1-phosphatidyl-D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase inhibitor
1-phosphatidyl-D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase inhibitors
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase inhibitor
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase inhibitors
An EC 3.1.4.* (phosphoric diester hydrolase) inhibitor that interferes with the action of phosphatidylinositol-specific phospholipase C (EC 3.1.4.11).
EC 3.1.4.11 (phosphoinositide phospholipase C) inhibitors
monophosphatidylinositol phosphodiesterase inhibitor
monophosphatidylinositol phosphodiesterase inhibitors
phosphatidylinositol phospholipase C inhibitor
phosphatidylinositol phospholipase C inhibitors
phosphatidylinositol-specific phospholipase C inhibitor
phosphatidylinositol-specific phospholipase C inhibitors
phosphoinositide phospholipase C (EC 3.1.4.11) inhibitor
phosphoinositide phospholipase C (EC 3.1.4.11) inhibitors
phosphoinositide phospholipase C inhibitor
phosphoinositide phospholipase C inhibitors
triphosphoinositide phosphodiesterase inhibitor
triphosphoinositide phosphodiesterase inhibitors
The role played by a substance in enhancing the appearance or odour of the human body; a name given to the substance itself or to a component of it.
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.
An antiparasitic drug which is effective against Apicomplexan parasites in the genus Plasmodium. The genus contains over 200 species and includes those responsible for malaria.
An antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus.
An anti-HIV agent that destroys or inhibits the replication of HIV-1, the more infective and more virulent of the two types of HIV virus.
An antiviral agent that destroys or inhibits the replication of the hepatitis B virus.
EC 1.13.11.34 (arachidonate 5-lipoxygenase) inhibitor
A lipoxygenase inhibitor that interferes with the action of arachidonate 5-lipoxygenase (EC 1.13.11.34).
EC 1.13.11.34 (arachidonate 5-lipoxygenase) inhibitors
arachidonate 5-lipoxygenase (EC 1.13.11.34) inhibitor
arachidonate 5-lipoxygenase (EC 1.13.11.34) inhibitors
arachidonic acid 5-lipoxygenase inhibitor
arachidonic acid 5-lipoxygenase inhibitors
EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitor
A lipoxygenase inhibitor that interferes with the action of arachidonate 15-lipoxygenase (EC 1.13.11.33).
EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitors
arachidonate 15-lipoxygenase (EC 1.13.11.33) inhibitor
arachidonate 15-lipoxygenase (EC 1.13.11.33) inhibitors
arachidonate:oxygen 15-oxidoreductase inhibitor
arachidonate:oxygen 15-oxidoreductase inhibitors
linoleic acid omega(6)-lipoxygenase inhibitor
linoleic acid omega(6)-lipoxygenase inhibitors
EC 3.1.1.3 (triacylglycerol lipase) inhibitor
Any EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that inhibits the action of triacylglycerol lipase (EC 3.1.1.3).
EC 3.1.1.3 (triacylglycerol lipase) inhibitors
heparin releasable hepatic lipase inhibitor
heparin releasable hepatic lipase inhibitors
hepatic monoacylglycerol acyltransferase inhibitor
hepatic monoacylglycerol acyltransferase inhibitors
pancreatic triacylglycerol lipase inhibitor
pancreatic triacylglycerol lipase inhibitors
post-heparin plasma protamine-resistant lipase inhibitor
post-heparin plasma protamine-resistant lipase inhibitors
salt-resistant post-heparin lipase inhibitor
salt-resistant post-heparin lipase inhibitors
triacylglycerol ester hydrolase inhibitor
triacylglycerol ester hydrolase inhibitors
triacylglycerol lipase (EC 3.1.1.3) inhibitor
triacylglycerol lipase (EC 3.1.1.3) inhibitors
Any compound that has anti-asthmatic effects.
Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.
A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299).
An indole alkaloid which is biosynthesised from L-tryptophan and isoprenoid building blocks.
A terpenoid indole alkaloid which is biosynthesised from L-tryptophan and diisoprenoid (usually secolaganin) building blocks.
A cinnamate ester obtained by formal condensation of caffeic acid with any alkyl alcohol.
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl alpha-L-arabinofuranoside
A quercetin O-glycoside in which an alpha-L-arabinofuranosyl residue is attached at position 3 of quercetin via a glycosidic linkage. It is isolated particularly from Juglans regia and Foeniculum vulgare.
A pentacyclic triterpenoid that is lupane in which the hydrogen at the 3beta position is substituted by a hydroxy group. It occurs in the skin of lupin seeds, as well as in the latex of fig trees and of rubber plants. It is also found in many edible fruits and vegetables.
1,5,7,8,11-pentaacetoxy-2-furanoyl-4-hydroxy-3,15[2'-hydroxy-2',3'-dimethyl-3'-(3''-carboxy-4''-pyridyl)-propanoic acid]dicarbolactone-dihydroagarofuran
A sesquiterpene alkaloid that is a macrolide incorporating a substituted pyridine and dihydroagarofuran moieties. Isolated from root barks of Tripterygium hypoglaucum, it exhibits anti-HIV activity.
(3S,5aR,7aS,7bR,9aS,12R,13aR,13bS,15aR,15bS,16R)-3-hydroxy-7b,9a,12,13b,15a,16-hexamethylicosahydro-3,5a-methanochryseno[2,1-c]oxepine-12(5H)-carboxylic acid
(3beta,20alpha)-3,24-epoxy-3-hydroxy-D:A-friedooleanan-29-oic acid
A hexacyclic triterpenoid that is D:A-friedooleanan-29-oic acid substituted by a hydroxy group at position 3 and an epoxy group across positions 3 and 24 (the (3beta,20alpha stereoisomer). Isolated from Salacia macrosperma and Tripterygium wilfordii, it exhibits anti-HIV activity.
A kaurane diterpenoid that is (5beta,8alpha,13alpha)-18,20-epoxykauran-18-one substituted by a hydroxy group at position 16. Isolated from the roots of Tripterygium wilfordii, it exhibits anti-HIV activity.
Kauran-18-oic acid, 16,20-dihydroxy-, delta-lactone,(4alpha)-
A sesquiterpene alkaloid with anti-HIV activity isolated from Tripterygium hypoglaucum.
An isoquinoline alkaloid that has formula C20H24NO4.
A triterpenoid saponin isolated from Scilla scilloides and has been shown to exhibit anti-tumour activity.
A lignan that consists of tetrahydro-1H,3H-furo[3,4-c]furan substituted by 1,3-benzodioxole groups at positions 1 and 4 (the 1S,3aR,4S,6aR stereoisomer). Isolated from Cinnamomum camphora, it exhibits cytotoxic activity.
A 2-hydroxydicarboxylic acid that is succinic acid in which one of the hydrogens attached to a carbon is replaced by a hydroxy group.
(2alpha,3beta)-2,3-dihydroxyolean-12-en-28-oic acid
A pentacyclic triterpenoid that is olean-12-ene substituted by hydroxy groups at positions 2 and 3 and a carboxy group at position 28 (the 2alpha,3beta stereoisomer). It is isolated from Olea europaea and Salvia canariensis and exhibits anti-inflammatory, antioxidant and antineoplastic activity.
Any dicarboxylic acid that contains four carbon atoms.
An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of alanine; major species at pH 7.3.
A lignan that is gamma-butyrolactone in which the 3 and 4 positions are substituted by 4-hydroxy-3-methoxybenzyl groups (the 3R,4R-diastereomer).
Any branched-chain fatty acid anion containing methyl branches only.
Any compound that has anti-inflammatory effects.
gap junctional intercellular communication inhibitor
An inhibitor that interferes with the process of gap junctional intercellular communication.
gap junctional intercellular communication inhibitors
An agonist that selectively binds to and activates a retinoic acid receptor.
An antogonist that interferes with the action of activator protein 1 (AP-1).
A provitamin that can be converted into vitamin A by enzymes from animal tissues.
EC 3.2.1.10 (oligo-1,6-glucosidase) inhibitor
An EC 3.2.1.* (glycosidase) inhibitor that inhibits the action of sucrose oligo-1,6-glucosidase (EC 3.2.1.10).
EC 3.2.1.10 (oligo-1,6-glucosidase) inhibitors
dextrin 6alpha-glucanohydrolase inhibitor
dextrin 6alpha-glucanohydrolase inhibitors
oligo-1,6-glucosidase (EC 3.2.1.10) inhibitor
oligo-1,6-glucosidase (EC 3.2.1.10) inhibitors
oligosaccharide alpha-1,6-glucohydrolase inhibitor
oligosaccharide alpha-1,6-glucohydrolase inhibitors
EC 3.2.1.20 (alpha-glucosidase) inhibitor
An EC 3.2.1.* (glycosidase) inhibitor that interferes with the action of alpha-glucosidase (EC 3.2.1.20).
EC 3.2.1.20 (alpha-glucosidase) inhibitors
alpha-glucosidase (EC 3.2.1.20) inhibitor
alpha-glucosidase (EC 3.2.1.20) inhibitors
A lignan that is tetrahydrofuran substituted at positions 2, 3 and 4 by 4-hydroxy-3-methoxyphenyl, hydroxymethyl and 4-hydroxy-3-methoxybenzyl groups respectively (the 2R,3S,4S-diastereomer).
A lignan that is tetrahydrofuran substituted at positions 2, 3 and 4 by 4-hydroxy-3-methoxyphenyl, hydroxymethyl and 4-hydroxy-3-methoxybenzyl groups respectively (the 2S,3R,4R-diastereomer).
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl beta-D-galactopyranoside
A quercetin O-glycoside that is quercetin with a beta-D-galactosyl residue attached at position 3. Isolated from Artemisia capillaris, it exhibits hepatoprotective activity.
(3beta)-stigmast-5-en-3-yl beta-D-glucopyranoside
A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa.
beta-sitosterol 3-O-beta-D-glucopyranoside
A diterpenoid that has formula C33H45NO11.
A triterpenoid that has formula C30H50O2.
A pentacyclic triterpenoid that is beta-amyrin in which one of the hydrogens of the methyl group at position 28 has been replaced by a hydroxy group. It is a plant metabolite found in olive oil as well as in Rhododendron ferrugineum and other Rhododendron species.
3beta-(acetyloxy)olean-18-en-28-oic acid
A pentacyclic triterpenoid that is olean-18-ene substituted by an acetyloxy group at position 3 and a carboxy group at position 28. It has been isolated from Juglans sinensis.
A pentacyclic triterpenoid that is urs-12-ene substituted by an oxo group at position 3, a carboxy group at position 28 and a hydroxy group at position 23. It has been isolated from Juglans sinensis.
(3alpha)-3-hydroxyolean-12-en-28-oic acid
(2R*,3S*)- 3,4-dihydro-2-(3,4,5-trihydroxyphenyl)-2H-1-benzopyran-3,5,7-triol
A catechin that is a flavan substituted by hydroxy groups at positions 3, 3', 4', 5, 5' and 7 (the trans isomaer). It is isolated from Acacia mearnsii.
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
Any substance that inhibits the process of apoptosis (programmed cell death) in multi-celled organisms.
Any substance that induces the process of apoptosis (programmed cell death) in multi-celled organisms.
An polyanionic polymer obtained by global deprotonation of the carboxy groups of pectin.
A member of the class of catechols that is benzene-1,2-diol substituted by a 2-hydroxyethyl group at position 4. Isolated from Olea europaea, it exhibits antioxidant and antineoplastic activities.
2(3H)-Furanone, 4-((3,4-dimethoxyphenyl)methyl)-3-((4-(beta-D-glucopyranosyloxy)-3-methoxyphenyl)methyl)dihydro-3-hydroxy-, (3S-cis)-
6a-alpha-Aporphine, 1,2-dimethoxy-9,10-(methylenedioxy)-
An isoquinoline alkaloid that has formula C20H21NO4.
A fatty acid methyl ester of linoleic acid. It has been isolated from Neolitsea daibuensis.
A fatty acid methyl ester that has formula C17H34O2.
An ergostanoid that is (22E)-ergosta-4,6,8(14),22-tetraene substituted by an oxo group at position 3. It has been isolated from the mycelia of Cordyceps sinensis.
A lignan that is 5,6,7,8-tetrahydronaphthalen-2-ol substituted by hydroxymethyl groups at positions 6 and 7, a methoxy group at position 3 and a 4-hydroxy-3-methoxyphenyl group at position 8. It has been isolated from the roots of Rubia yunnanensis.
(3beta)-3,23-dihydroxyolean-12-en-28-oic acid
A sapogenin that is olean-12-en-28-oic acid substituted by hydroxy groups at positions 3 and 23 (the 3beta stereoisomer).
A methoxybenzene that has formula C9H10O3.
A benzoate ester that has formula C17H18O6.
A terpene glycoside that has formula C30H32O12.
18-Norandrosta-11,13(17)-diene-15,16-dione, 3,17-dihydroxy-4,4,8,14-tetramethyl-, (3beta,5alpha)-
A 16-oxo steroid that has formula C22H30O4.
5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 6-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-glucopyranoside
A kaempferol O-glucoside that is kaempferol attached to a rutinosyl [6-deoxy-alpha-L-mannosyl-(1->6)-beta-D-glucosyl] residue at position 3 via a glycosidic linkage. It has been isolated from the leaves of Solanum campaniforme.
kaempferol 3-O-(6''-O-alpha-L-rhamnopyranosyl)-beta-D-glucopyranoside
A fatty amide that has formula C14H25NO.
A terpene lactone that has formula C38H47NO18.
2H-1-Benzopyran-2-one, 7-methoxy-8-(3-methyl-2-butenyl)-
A botanical anti-fungal agent that has formula C15H16O3.
Coumarin, 7-methoxy-8-(3-methyl-2-butenyl)-
A sesquiterpenoid that has formula C15H26O2.
An extended flavonoid that is flavone substituted by hydroxy groups at positions 5, 2' and 4', a prenyl group at position 3 and a 2,2-dimethyl pyran group across positions 7 and 8.
(2alpha,3beta)-2,3,19-Trihydroxyurs-12-en-28-oic acid
A triterpenoid that has formula C30H48O5.
An EC 5.99.1.* (miscellaneous isomerase) inhibitor that interferes with the action of any of the topoisomerases (enzymes that regulate the overwinding or underwinding of DNA).
An antiprotozoal drug used to treat or prevent infections caused by protozoan parasites that belong to the genus Leishmania.
A triterpenoid that consists of a hexacyclic ring system.
Any flavonoid with one or more rings fused on to the phenyl substituted benzopyran framework.
A hydroxyflavan that is 3,4-dihydro-2H-chromene which is substituted at positions 3, 5, and 7 by hydroxy groups, and at position 2 by a 3,4,5-trihydroxyphenyl group.
A flavan-3,3',4',5,5',7-hexol that has (2S,3S)-configuration.
An enzyme inhibitor that inhibits the action of a transferase (EC 2.*)
A long-chain unsaturated fatty acid anion that is the conjugate base of hexadec-9-enoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.
EC 2.3.1.85 (fatty acid synthase) inhibitor
An EC 2.3.1.* (acyltransferase transferring other than amino-acyl group) inhibitor that interferes with the action of fatty acid synthase (EC 2.3.1.85), a multi-enzyme protein involved in fatty acid synthesis.
EC 2.3.1.85 (fatty acid synthase) inhibitors
acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing and thioester-hydrolysing) inhibitor
acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing and thioester-hydrolysing) inhibitors
fatty acid synthase (EC 2.3.1.85) inhibitor
fatty acid synthase (EC 2.3.1.85) inhibitors
A eudesmane sesquiterpenoid that is octahydro-2H-3,9a-methano-1-benzoxepine substituted by methyl groups at positions 2, 2, 5a and 9 (the 3R,5aS,9R,9aS stereoisomer).
Any sesquiterpenoid with a dihydroagarofuran skeleton.
A triterpene that is docosahydropicene substituted by 8 methyl groups at positions 2, 2, 4a, 6a, 8a, 9, 12b and 14a.
An amino-acid anion in which the amino group is situated gamma- to the carboxylate group.
A hexadecenoic acid in which the double bond is located at position 9.
A member of the class of flavans in which one or more ring hydrogens are replaced by hydroxy groups.
A hydroxypiperidine that has three hydroxy groups located at positions 3, 4 and 5 as well as a hydroxymethyl substituent at position 2.
Any organic molecular entity whose stucture is based on derivatives of a phenyl-substituted 1-phenylpropane possessing a C15 or C16 skeleton, or such a structure which is condensed with a C6-C3 lignan precursors. The term is a 'superclass' comprising all members of the classes of flavonoid, isoflavonoid, neoflavonoid, chalcones, dihydrochalcones, aurones, pterocarpan, coumestans, rotenoid, flavonolignan, homoflavonoid and flavonoid oligomers. Originally restricted to natural products, the term is also applied to synthetic compounds related to them.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A phenylpropanoid obtained by the coupling of two or more units of aryl-substituted benzopyran units and their substituted derivatives.
A member of the class of flavanones having one or more glycosyl residues attached at unspecified positions.
EC 1.1.1.184 [carbonyl reductase (NADPH)] inhibitor
An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of carbonyl reductase (NADPH), EC 1.1.1.184.
EC 1.1.1.184 (carbonyl reductase (NADPH)) inhibitor
EC 1.1.1.184 (carbonyl reductase (NADPH)) inhibitors
EC 1.1.1.184 [carbonyl reductase (NADPH)] inhibitors
NADPH2-dependent carbonyl reductase inhibitor
NADPH2-dependent carbonyl reductase inhibitors
carbonyl reductase (NADPH) (EC 1.1.1.184) inhibitor
carbonyl reductase (NADPH) (EC 1.1.1.184) inhibitors
nonspecific NADPH-dependent carbonyl reductase inhibitor
nonspecific NADPH-dependent carbonyl reductase inhibitors
prostaglandin 9-ketoreductase inhibitors
secondary-alcohol:NADP+ oxidoreductase inhibitor
secondary-alcohol:NADP+ oxidoreductase inhibitors
EC 1.11.1.11 (L-ascorbate peroxidase) inhibitors
An EC 1.11.1.* (peroxidases) inhibitor that inhibits the action of L-ascorbate peroxidase (EC 1.11.1.11).
L-ascorbate peroxidase (EC 1.11.1.11) inhibitor
L-ascorbate peroxidase (EC 1.11.1.11) inhibitors
L-ascorbate:hydrogen-peroxide oxidoreductase inhibitor
L-ascorbate:hydrogen-peroxide oxidoreductase inhibitors
L-ascorbic acid-specific peroxidase inhibitor
L-ascorbic acid-specific peroxidase inhibitors
EC 3.6.* (hydrolases acting on acid anhydrides) inhibitor
Any hydrolase inhibitor that interferes with the action of a hydrolase which acts on acid anhydrides (EC 3.6.*.*).
EC 3.6.* (hydrolases acting on acid anhydrides) inhibitors
inhibitor of hydrolase acting on acid anhydride (EC 3.6.*)
inhibitors of hydrolase acting on acid anhydride (EC 3.6.*)
An inhibitor of NF-kappaB (nuclear factor kappa-light-chain-enhancer of activated B cells), a protein complex involved in the transcription of DNA.
nuclear factor kappa-light-chain-enhancer of activated B cells inhibitor
nuclear factor kappa-light-chain-enhancer of activated B cells inhibitors
An aldehyde of general formula R-CH2-CH=O in which the aldehydic C=O function is attached to a CH2 group at the alpha-position.
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.
A disaccharide consisting of alpha-L-rhamnose and beta-D-glucose linked via a 1->2 glycosidic bond.
An organic anion that is the conjugate base of genistein, obtained by selective deprotonation of the 7-hydroxy group.
Any substance which is used to reduce or control weight.
A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions.
A trihydroxyflavanone that consists of 3'-methoxyflavanone in which the three hydroxy substituents are located at positions 4', 5, and 7.
A pentahydroxyflavone that is 7-hydroxyflavonol bearing three additional hydroxy substituents at positions 2' 4' and 5.
An EC 1.11.* (oxidoreductase acting on peroxide as donors) inhibitor that interferes with the action of any of the peroxidases (EC 1.11.1.*).
An enzyme inhibitor that inhibits the action of an isomerase (EC 5.*.*.*).
Any enzyme inhibitor that interferes with the action of a ligase (EC 6.*.*.*). Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
EC 6.4.* (C-C bond-forming ligase) inhibitor
A ligase inhibitor that interferes with the action of a C-C bond-forming ligase (EC 6.4.*.*).
C-C bond-forming ligase (EC 6.4.*) inhibitor
C-C bond-forming ligase (EC 6.4.*) inhibitorS
EC 6.4.* (C-C bond-forming ligase) inhibitorS
A proanthocyanidin consisting of two molecules of (+)-catechin joined by a bond between positions 4 and 8' in alpha-configuration. It can be found in red wine, in barley, in beer, in peach or in Jatropha macrantha, the Huanarpo Macho.
A proanthocyanidin consisting of two molecules of (-)-epicatechin joined by a bond between positions 4 and 8' in a beta-configuration. Procyanidin B2 can be found in Cinchona pubescens (Chinchona, in the rind, bark and cortex), in Cinnamomum verum (Ceylon cinnamon, in the rind, bark and cortex), in Crataegus monogyna (Common hawthorn, in the flower and blossom), in Uncaria guianensis (Cat's claw, in the root), in Vitis vinifera (Common grape vine, in the leaf), in Litchi chinensis (litchi, in the pericarp), in the apple, in Ecdysanthera utilis and in red wine.
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 of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises vitamin B1, B2, B3, B5, B6, B7, B9, and B12. (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such.)
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.
A methoxyflavone that is flavone substituted by methoxy groups at positions 5, 6, 7, 8, 3' and 4' respectively.
A very long-chain fatty acid anion that is the conjugate base of lacceroic acid, obtained by deprotonation of the carboxy group.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any aromatic amino-acid.
A catechin that is flavan carrying five hydroxy substituents at positions 3, 3', 4', 5 and 7 (the 2S,3S-stereoisomer).
Any metabolite produced by metabolism of a xenobiotic compound.
A straight-chain saturated fatty acid that is dotriacontane in which one of the methyl groups has been oxidised to the corresponding carboxylic acid.
EC 2.3.1.48 (histone acetyltransferase) inhibitor
An EC 2.3.1.* (acyltransferase transferring other than amino-acyl group) inhibitor that interferes with the function of histone acetyltransferase (EC 2.3.1.48).
EC 2.3.1.48 (histone acetyltransferase) inhibitors
acetyl-CoA:histone acetyltransferase inhibitor
acetyl-CoA:histone acetyltransferase inhibitors
histone acetyltransferase (EC 2.3.1.48) inhibitor
histone acetyltransferase (EC 2.3.1.48) inhibitors
nucleosome-histone acetyltransferase inhibitor
nucleosome-histone acetyltransferase inhibitors
A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans.
Any glycosyloxyflavone that is an O-glycosylated derivative of quercetin.
Any unsaturated fatty acid anion containing more than one C-C unsaturated bond. Major species at pH 7.3.
A transferase inhibitor inhibiting the action of transferase of a one-carbon-containing group (EC 2.1.*.*).
one-carbon-containing group transferase inhibitor
one-carbon-containing group transferase inhibitors
A transferase inhibitor that interferes with the action of an acyltransferase (EC 2.3.*.*).
EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitor
A transferase inhibitor that inhibits the transfer of an alkyl (other than methyl) or aryl group (EC 2.5.1.*).
EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitors
alkyl/aryl (non-methyl) transferase inhibitor
alkyl/aryl (non-methyl) transferase inhibitors
non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitor
non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitors
non-methyl alkyl/aryl transferase inhibitor
non-methyl alkyl/aryl transferase inhibitors
non-methyl-alkyl or aryl transferase inhibitor
non-methyl-alkyl or aryl transferase inhibitors
EC 2.7.* (P-containing group transferase) inhibitor
A transferase inhibitor that inhibits the action of a phosphorus-containing group transferase (EC 2.7.*.*).
EC 2.7.* (P-containing group transferase) inhibitors
EC 2.7.* (phosphorus-containing group transferase) inhibitor
EC 2.7.* (phosphorus-containing group transferase) inhibitors
phosphorus-containing group transferase (EC 2.7.*) inhibitor
phosphorus-containing group transferase (EC 2.7.*) inhibitors
phosphorus-containing group transferase inhibitor
phosphorus-containing group transferase inhibitors
An isomerase inhibitor that interferes with the action of any member of the group of 'other isomerases' (EC 5.99.*.*).
EC 5.99.* (miscellaneous isomerases) inhibitor
EC 5.99.* (miscellaneous isomerases) inhibitors
An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-OH group of donors (EC 1.1.*.*).
EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitors
inhibitor of oxidoreductase acting on CH-OH group of donor
inhibitor of oxidoreductase acting on CH-OH group of donors
inhibitors of oxidoreductase acting on CH-OH group of donor
inhibitors of oxidoreductase acting on CH-OH group of donors
oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitor
oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitors
oxidoreductase acting on donor CH-OH group inhibitor
oxidoreductase acting on donor CH-OH group inhibitors
EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-NH2 group of donors (EC 1.4.*.*).
EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitors
inhibitor of oxidoreductase acting on CH-NH2 group of donor
inhibitor of oxidoreductase acting on CH-NH2 group of donors
inhibitors of oxidoreductase acting on CH-NH2 group of donor
inhibitors of oxidoreductase acting on CH-NH2 group of donors
oxidoreductase acting on CH-NH2 group of donor inhibitor
oxidoreductase acting on CH-NH2 group of donor inhibitors
oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitor
oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitors
EC 1.10.* (oxidoreductase acting on diphenols and related substances as donors) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on diphenols and related substances as donors (EC 1.10.*.*).
EC 1.10.* (oxidoreductase acting on diphenols and related substances as donors) inhibitors
EC 1.10.* (oxidoreductases acting on diphenols and related substances as donors) inhibitor
EC 1.10.* (oxidoreductases acting on diphenols and related substances as donors) inhibitors
inhibitor of an oxidoreductase acting on diphenols and related substances as donor
inhibitor of an oxidoreductase acting on diphenols and related substances as donor (EC 1.10.*)
inhibitor of an oxidoreductase acting on diphenols and related substances as donors
inhibitors of an oxidoreductase acting on diphenols and related substances as donor
inhibitors of an oxidoreductase acting on diphenols and related substances as donor (EC 1.10.*)
inhibitors of an oxidoreductase acting on diphenols and related substances as donors
EC 1.11.* (oxidoreductase acting on peroxide as donors) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on peroxide as donors (EC 1.11.*.*).
EC 1.11.* (oxidoreductase acting on peroxide as donors) inhibitors
EC 1.11.* (oxidoreductases acting on peroxide as donors) inhibitor
EC 1.11.* (oxidoreductases acting on peroxide as donors) inhibitors
oxidoreductase acting on peroxide as donors (EC 1.11.*) inhibitor
oxidoreductase acting on peroxide as donors (EC 1.11.*) inhibitors
oxidoreductases acting on peroxide as donors (EC 1.11.*) inhibitor
oxidoreductases acting on peroxide as donors (EC 1.11.*) inhibitors
EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases), EC 1.13.*.*.
EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitors
oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitor
oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitors
oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitor
oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitors
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on hydrogen as donors (EC 1.14.*.*).
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors
inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
A hydrolase inhibitor that interferes with the action of any ester hydrolase (EC 3.1.*.*).
A hydrolase inhibitor that interferes with the action of any glycosylase (EC 3.2.*.*).
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
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 3.1.1.* (carboxylic ester hydrolase) inhibitor
An EC 3.1.* (ester hydrolase) inhibitor that interferes with the action of a carboxylic ester hydrolase (EC 3.1.1.*).
EC 3.1.1.* (carboxylic ester hydrolase) inhibitors
carboxylic ester hydrolase (EC 3.1.1.*) inhibitor
carboxylic ester hydrolase (EC 3.1.1.*) inhibitors
EC 3.1.26.* (endoribonucleases producing 5'-phosphomonoesters) inhibitor
An EC 3.1.* (ester hydrolase) inhibitor that interferes with the action of any endoribonuclease producing 5'-phosphomonoesters (EC 3.1.26.*).
EC 3.1.26.* (endoribonucleases producing 5'-phosphomonoesters) inhibitors
endoribonuclease producing 5'-phosphomonoesters (EC 3.1.26.*) inhibitor
endoribonuclease producing 5'-phosphomonoesters (EC 3.1.26.*) inhibitors
endoribonuclease producing 5'-phosphomonoesters inhibitor
endoribonuclease producing 5'-phosphomonoesters inhibitors
EC 2.5.1.18 (glutathione transferase) inhibitor
An EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitor that interferes with the action of a glutathione transferase (EC 2.5.1.18).
EC 2.5.1.18 (glutathione transferase) inhibitors
S-(hydroxyalkyl)glutathione lyase inhibitor
S-(hydroxyalkyl)glutathione lyase inhibitors
glutathione S-alkyl transferase inhibitor
glutathione S-alkyl transferase inhibitors
glutathione S-alkyltransferase inhibitor
glutathione S-alkyltransferase inhibitors
glutathione S-aralkyltransferase inhibitor
glutathione S-aralkyltransferase inhibitors
glutathione S-aryltransferase inhibitors
glutathione transferase (EC 2.5.1.18) inhibitor
glutathione transferase (EC 2.5.1.18) inhibitors
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) 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 2.7.7.* (nucleotidyltransferase) inhibitor
An EC 2.7.* (P-containing group transferase) inhibitor that interferes with the action of any nucleotidyltransferase (EC 2.7.7.*).
EC 2.7.7.* (nucleotidyltransferase) inhibitors
inhibitor of nucleotidyltransferases (EC 2.7.7.*)
inhibitors of nucleotidyltransferases (EC 2.7.7.*)
nucleotidyltransferase (EC 2.7.7.*) inhibitor
nucleotidyltransferase (EC 2.7.7.*) inhibitors
An EC 6.4.* (C-C bond-forming ligase) inhibitor that interferes with the action of a carboxylating enzyme (EC 6.4.1.*).
EC 6.4.1.* (C-C bond forming ligase) inhibitor
EC 6.4.1.* (C-C bond forming ligase) inhibitors
EC 6.4.1.* (C-C bond-forming ligase) inhibitors
inhibitor of ligases forming C-C bonds (EC 6.4.1.*)
inhibitors of ligases forming C-C bonds (EC 6.4.1.*)
EC 5.99.1.* (miscellaneous isomerase) inhibitor
An EC 5.99.* (other isomerases) inhibitor that interferes with the activity of any enzyme in the EC 5.99.1.* class.
EC 5.99.1.* (miscellaneous isomerase) inhibitors
EC 2.5.* (non-methyl-alkyl or aryl transferase) inhibitor
An EC 2.5.* (transferase) inhibitor that inhibits the action of any transferase that transfers an alkyl (other than methyl) or aryl group (EC 2.5.*).
EC 2.5.* (non-methyl-alkyl or aryl transferase) inhibitors
non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitor
non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitors
EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor
An EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor that uses NAD(+) or NADP(+) as acceptor (EC 1.1.1.*).
EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+)acceptor) inhibitors
oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitor
oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitors
EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitor
An EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitor that inhibits the action of any oxidoreductase incorporating 2 atoms of oxygen (EC 1.13.11.*).
EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitors
EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitor
EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitors
oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitor
oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitors
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any such enzyme incorporating one atom of oxygen and using reduced flavin or flavoprotein as donor (EC 1.14.14.*).
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors
EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors
oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor
oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors
EC 1.14.99.* (miscellaneous oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor
An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any enzyme in the EC 1.14.99.* (miscellaneous) category.
EC 1.14.99.* (miscellaneous oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors
miscellaneous oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.99.*) inhibitor
miscellaneous oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.99.*) inhibitors
EC 1.14.18.* (oxidoreductase acting on paired donors, miscellaneous compound as one donor, incorporating 1 atom of oxygen) inhibitor
An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any such enzyme using a miscellaneous compound as one donor and incorporating one atom of oxygen (EC 1.14.18.*).
EC 1.14.18.* (oxidoreductase acting on paired donors, miscellaneous compound as one donor, incorporating 1 atom of oxygen) inhibitors
oxidoreductase acting on paired donors, miscellaneous compound as one donor, incorporating 1 atom of oxygen (EC 1.14.18.*) inhibitor
oxidoreductase acting on paired donors, miscellaneous compound as one donor, incorporating 1 atom of oxygen (EC 1.14.18.*) inhibitors
EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor
An EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.4.3.*).
EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitors
oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitor
oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitors
EC 2.1.1.* (methyltransferases) inhibitor
An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any methyltransferase (EC 2.1.1.*).
EC 2.1.1.* (methyltransferase) inhibitor
EC 2.1.1.* (methyltransferase) inhibitors
EC 2.1.1.* (methyltransferases) inhibitors
methyltransferase (EC 2.1.1.*) inhibitor
methyltransferase (EC 2.1.1.*) inhibitors
EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor
An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any hydroxymethyl-, formyl- and related transferase (EC 2.1.2.*).
EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors
hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor
hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors
EC 2.3.1.* (acyltransferase transferring other than amino-acyl group) inhibitor
An EC 2.3.* (acyltransferase) inhibitor that inhibits the action of any acyltransferase transferring groups other than amino-acyl groups (EC 2.3.1.*).
EC 2.3.1.* (acyltransferase transferring other than amino-acyl group) inhibitors
acyltransferase transferring other than amino-acyl group EC 2.3.1.* inhibitor
acyltransferase transferring other than amino-acyl group EC 2.3.1.* inhibitors
EC 1.14.14.1 (unspecific monooxygenase) inhibitor
An EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor that interferes with the action of an unspecified monooxygenase (EC 1.14.14.1).
EC 1.14.14.1 (unspecific monooxygenase) inhibitors
flavoprotein-linked monooxygenase inhibitor
flavoprotein-linked monooxygenase inhibitors
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitor
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitors
unspecific monooxygenase (EC 1.14.14.1) inhibitor
unspecific monooxygenase (EC 1.14.14.1) inhibitors
EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor
An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the function of any such enzyme using 2-oxoglutarate as one donor and incorporating one atom each of oxygen into both donors (EC 1.14.11.*).
EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitors
EC 1.14.11.* (oxidoreductase acting on paired donors, with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors) inhibitor
EC 1.14.11.* (oxidoreductase acting on paired donors, with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors) inhibitors
oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors (EC 1.14.11.*) inhibitor
oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors (EC 1.14.11.*) inhibitors
oxidoreductase acting on paired donors, with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (EC 1.14.11.*) inhibitor
oxidoreductase acting on paired donors, with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (EC 1.14.11.*) inhibitors
Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms.
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
EC 3.6.4.* (hydrolases acting on ATP; involved in cellular and subcellular movement) inhibitor
An EC 3.6.* (hydrolases acting on acid anhydrides) inhibitor that interferes with the action of any such enzyme acting on ATP and involved in cellular and subcellular movement (EC 3.6.4.*).
EC 3.6.4.* (hydrolase acting on ATP; involved in cellular and subcellular movement) inhibitor
EC 3.6.4.* (hydrolase acting on ATP; involved in cellular and subcellular movement) inhibitors
EC 3.6.4.* (hydrolases acting on ATP; involved in cellular and subcellular movement) inhibitors
hydrolases acting on ATP; involved in cellular and subcellular movement (EC 3.6.4.*) inhibitor
hydrolases acting on ATP; involved in cellular and subcellular movement (EC 3.6.4.*) inhibitors
EC 3.6.4.10 (non-chaperonin molecular chaperone ATPase) inhibitor
ATP phosphohydrolase (polypeptide-polymerising) inhibitor
ATP phosphohydrolase (polypeptide-polymerising) inhibitors
ATP phosphohydrolase (polypeptide-polymerizing) inhibitor
ATP phosphohydrolase (polypeptide-polymerizing) inhibitors
An EC 3.6.4.* (hydrolases acting on ATP; involved in cellular and subcellular movement) inhibitor that interferes with the action of a non-chaperonin molecular chaperone ATPase (EC 3.6.4.10).
EC 3.6.4.10 (non-chaperonin molecular chaperone ATPase) inhibitors
molecular chaperone Hsc70 ATPase inhibitor
molecular chaperone Hsc70 ATPase inhibitors
non-chaperonin molecular chaperone ATPase (EC 3.6.4.10) inhibitor
non-chaperonin molecular chaperone ATPase (EC 3.6.4.10) inhibitors
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any fungal metabolite produced during a metabolic reaction in the mould, Aspergillus.
Any human metabolite produced by metabolism of a xenobiotic compound in humans.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any bacterial metabolite produced by metabolism of a xenobiotic compound in bacteria.
Any compound produced by a plant that happens to have estrogenic activity.
EC 1.10.99.* (oxidoreductases acting on diphenols and related substances as donors, other acceptors) inhibitor
An EC 1.10.* (oxidoreductase acting on diphenols and related substances as donors) inhibitor that interferes with the action of any such enzyme in the EC 1.10.99.* category.
EC 1.10.99.* (oxidoreductases acting on diphenols and related substances as donors, other acceptors) inhibitors
oxidoreductases acting on diphenols and related substances as donors, other acceptors (EC 1.10.99.*) inhibitor
oxidoreductases acting on diphenols and related substances as donors, other acceptors (EC 1.10.99.*) inhibitors
EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor
1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase inhibitor
1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase inhibitors
An EC 1.10.99.* (oxidoreductases acting on diphenols and related substances as donors, other acceptors) inhibitor that interferes with the action of ribosyldihydronicotinamide dehydrogenase (quinone), EC 1.10.99.2.
EC 1.10.99.2 (ribosyldihydronicotinamide dehydrogenase (quinone)) inhibitor
EC 1.10.99.2 (ribosyldihydronicotinamide dehydrogenase (quinone)) inhibitors
EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitors
N-ribosyldihydronicotinamide dehydrogenase (quinone) inhibitor
N-ribosyldihydronicotinamide dehydrogenase (quinone) inhibitors
NAD(P)H:quinone oxidoreductase-2 inhibitor
NAD(P)H:quinone oxidoreductase-2 inhibitors
NAD(P)H:quinone oxidoreductase2 inhibitor
NAD(P)H:quinone oxidoreductase2 inhibitors
ribosyldihydronicotinamide dehydrogenase (quinone) (EC 1.10.99.2) inhibitor
ribosyldihydronicotinamide dehydrogenase (quinone) (EC 1.10.99.2) inhibitors
Compounds that are considered to increase the volume of secretions in the respiratory tract, so facilitating their removal by ciliary action and coughing. Compare with mucolytics, which decrease the viscosity of mucus, facilitating its removal by ciliary action and expectoration, and antitussives, which suppress the cough reflex.
EC 3.5.5.* (hydrolase acting on C-N bonds in nitriles) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any such enzyme acting on the C-N bond of nitriles (EC 3.5.5.*).
EC 3.5.5.* (hydrolase acting on C-N bonds in nitriles) inhibitors
hydrolase acting on C-N bonds in nitriles (EC 3.5.5.*) inhibitor
hydrolase acting on C-N bonds in nitriles (EC 3.5.5.*) inhibitors
inhibitor of hydrolases acting on C-N bonds in nitriles
inhibitors of hydrolases acting on C-N bonds in nitriles
An EC 3.5.5.* (hydrolase acting on C-N bonds in nitriles) inhibitor that interferes with the action of nitrilase (EC 3.5.5.1).
EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitor
(5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitor
(5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitors
9-keto-prostaglandin E2 reductase inhibitor
9-keto-prostaglandin E2 reductase inhibitors
9-ketoprostaglandin reductase inhibitors
An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of prostaglandin-E2 9-reductase (EC 1.1.1.189).
EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitors
prostaglandin E 9-ketoreductase inhibitor
prostaglandin E 9-ketoreductase inhibitors
prostaglandin E2-9-oxoreductase inhibitor
prostaglandin E2-9-oxoreductase inhibitors
prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitor
prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitors
reductase, 15-hydroxy-9-oxoprostaglandin inhibitor
reductase, 15-hydroxy-9-oxoprostaglandin inhibitors
3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-enoic acid
A monohydroxycinnamic acid that is cinnamic acid in which the phenyl hydrogens at positions 3, 4, and 5 are replaced by methoxy, hydroxy, and methoxy groups, respectively.
A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199).
Any protective agent that is able to prevent damage to the heart.
A long-chain fatty alcohol in which the hydroxy group is attached to a methylene (CH2) group.
alpha-methylene long chain fatty alcohol
A long-chain primary fatty alcohol that is tetracosane in which a hydrogen attached to one of the terminal carbons is replaced by a hydroxy group. It has been isolated from a variety of plants, including grape seeds, evening primrose (Oenothera biennis), pitaya fruits (Hylocereus polyrhizus and Hylocereus undatus), and the flowers of Arabian jasmine (Jasminum sambac).
A long-chain fatty alcohol that is heptadecane in which one of the terminal methyl hydrogens is replaced by a hydroxy group.
EC 1.1.1.25 (shikimate dehydrogenase) inhibitor
An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of shikimate dehydrogenase (EC 1.1.1.25).
EC 1.1.1.25 (shikimate dehydrogenase) inhibitors
shikimate dehydrogenase (EC 1.1.1.25) inhibitor
shikimate dehydrogenase (EC 1.1.1.25) inhibitors
shikimate:NADP(+) 3-oxidoreductase inhibitor
shikimate:NADP(+) 3-oxidoreductase inhibitors
shikimate:NADP(+) 5-oxidoreductase inhibitor
shikimate:NADP(+) 5-oxidoreductase inhibitors
shikimate:NADP(+) oxidoreductase inhibitor
shikimate:NADP(+) oxidoreductase inhibitors
Any product obtained as a result of thermally induced non-enzymatic degradation.
Any thermal degradation product obtained as a result of a chemical reaction between an amino acid and a reducing sugar (Maillard reaction, a non-enzymatic browning procedure that usually imparts flavour to starch-based food products).
An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of any fatty acyl-CoA; major species at pH 7.3.
A phenolate anion that is the conjugate base of emodin, obtained by deprotonation of the phenolic hydroxy group at position 2; major species at pH 7.3 (according to Marvin v 6.2.0.).
A flavonoid oxoanion that is the conjugate base of formononetin, obtained by deprotonation of the 7-hydroxy group. Major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
A phenolate anion that is the conjugate base of bergaptol, obtained by deprotonation of the phenolic hydroxy substituent. Major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
A flavonoid oxoanion obtained by deprotonation of the 7-hydroxy group of daidzein. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
A flavonoid oxoanion obtained by deprotonation of the 5-hydroxy group of luteolin 7-O-beta-D-glucoside. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
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 used to preserve the structure of food.
A food additive that is used to increase the viscosity of foodstuffs.
A food additive that enhances the texture of a foodstuff by gel formation.
A propellant that is used to expel foods from an aerosol container.
A fatty acid anion containing 18 carbons and one double bond. Formed by deprotonation of the carboxylic acid group. Major species at pH 7.3.
A long-chain unsaturated fatty acid anion that is the conjugate base of hexadecenoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.
Any saturated fatty acid anion containing 3 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 6 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 8 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 10 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 12 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 14 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 15 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 16 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 18 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 22 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 24 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 26 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 28 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any saturated fatty acid anion containing 30 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any fatty alcohol containing 18 carbons.
Any fatty alcohol containing 24 carbons.
Any fatty alcohol containing 30 carbons.
A fatty acid ester that is the carboxylic ester obtained by the formal condensation of a fatty acid with ethanol.
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.
Any minor or unwanted substance introduced into the environment that can have undesired effects.
A phenylpropanoid that is benzene substituted by methoxy groups at positions 1, 2 and 4 and a propen-1-yl group at position 5. It has been isolated from Acorus.
A carbobicyclic compound that is bicyclo[3.1.1]heptane which is substituted by an oxo group at position 2 and by methyl groups at positions 4, 6 and 6, and which contains a double bond between positions 3 and 4.
A 4,6,6-trimethylbicyclo[3.1.1]hept-3-en-2-one in which both chiral centres have S configuration.
A 2-hydroxy monocarboxylic acid that is propanoic acid in which one of the alpha-hydrogens is replaced by a hydroxy group.
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.
Any EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that inhibits the action of carboxylesterase (EC 3.1.1.1 ).
EC 3.1.1.1 (carboxylesterase) inhibitors
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.
carbohydrates and carbohydrate derivatives
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.
Any metabolite produced by all living cells.
A straight-chain, saturated fatty acid anion resulting from the deprotonation of the carboxy group of pentadecanoic acid. It is the major species at pH 7.3.
Any organic molecular entity that contains at least one C=C bond.
A terpineol that is 1-menthene carrying a hydroxy substituent at position 4.
A terpene glycoside that has formula C23H28O11.
A hydroxy fatty acid that is a straight-chain fatty acid in which one of the hydrogens attached to the carbon adjacent to the terminal methyl group (i.e. at the (omega-1) position) is replaced by a hydroxy group.
A long-chain fatty acid anion that is the conjugate base of hexadecanoic acid (palmitic acid); major species at pH 7.3.
A very long-chain fatty acid anion that is the conjugate base of tricosanoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.
alpha,beta-unsaturated monocarboxylic acid
A monocarboxylic acid in which the carbon of the carboxy group is directly attached to a C=C or C#C bond.
alpha,beta-unsaturated monocarboxylic acids
Any compound that is used as an additive to increase the plasticity or fluidity of a substance, particularly but not exclusively to synthetic polymers.
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 carbotricyclic compound and sesquiterpenoid tertiary alcohol that is tricyclo[5.3.1.0(3,8)]undecan-3-ol which is substituted at positions 2, 2, 6 and 8 by methyl groups (the 1R,3R,6S,7S,8S-diastereoisomer).
An alkaloid that has formula C19H24ClNO6.
A morphinane alkaloid that has formula C38H44N2O8.
An isoquinoline alkaloid that has formula C18H19NO3.
A 2-hydroxy carboxylate that results from the removal of a proton from the carboxylic acid group of 3-phenyllactic acid.
A morphinane alkaloid that has formula C19H23NO4.
A triterpenoid that has formula C30H50O.
A lignan that is tetrahydro-1H,3H-furo[3,4-c]furan substituted at positions 1 and 4 by 4-hydroxy-3-methoxyphenyl groups.
A fatty aldehyde that has formula C6H8O.
An elemental molecular entity in which all of the atoms have atomic number 26.
Any unsaturated fatty acid anion with one double or triple bond in the fatty acid chain.
A monocarboxylic acid anion that is the conjugate base of oleanolic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.
A Daphnia metabolite produced by the species Daphnia galeata.
An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill.
A Daphnia metabolite produced by the species Daphnia magna.
A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia
A fatty acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of any long-chain fatty acyl-CoA; major species at pH 7.3.
A Daphnia metabolite produced by the species Daphnia tenebrosa.
Any C-glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a flavone skeleton, thus creating a C-C bond.
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy group of any beta-D-glucosiduronic acid; major species at pH 7.3.
Any alkane having a chain length of at least 13 carbon atoms.
A 3-oxo-fatty acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of 3-oxolacceroyl-CoA; major species at pH 7.3.
Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom.
Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration.
Any amino-acid that is not naturally encoded in the genetic code of any organism.
Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues.
Any alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids.
A methyl-branched fatty acid anion obtained by deprotonation of the carboxy group of any 3-methyl fatty acid; major species at pH 7.3.
Any phospho sugar that is the phosphate derivative of pentose.
Any metabolite (endogenous or exogenous) found in human urine samples.
A hydroxy fatty acid anion obtained by deprotonation of the carboxy group of any 3-hydroxy fatty acid.
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of nicotinamidase (EC 3.5.1.19).
A fatty aldehyde formally arising from reduction of nonanoic acis. Metabolite observed in cancer metabolism.
(3beta)-cholest-5-en-3-yl tetradecanoate
A cholesterol ester obtained by the formal condensation of the hydroxy group of cholesterol with the carboxy group of myristic acid.
A hydroxy fatty acid anion obtained by deprotonation of the carboxy group of any (omega-1)-hydroxy fatty acid; major species at pH 7.3.
3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-({2-[(3-oxodotriacontanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}butyl] dihydrogen diphosphate}
A 3-oxo-fatty acyl-CoA obtained from the formal condensation of the thiol group of coenzyme A with the carboxy group of 3-oxolacceroic acid.
A fatty aldehyde with a trans-double bond at carbon 2.
Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.
A long-chain fatty acid ethyl ester resulting from the formal condensation of the carboxy group of palmitic acid with the hydroxy group of ethanol.
A long-chain fatty acid ethyl ester resulting from the formal condensation of the carboxy group of oleic acid with the hydroxy group of ethanol.
Any fatty acyl-CoA(4-) in which the 11-12 bond of the fatty acyl group is saturated. This is needed for a reaction together with CHEBI:84947
Any cosmetic used to lighten the colour of skin by reducing the concentration of melanin.
EC 1.10.3.* (oxidoreductase acting on diphenols and related substances as donors with oxygen as acceptor) inhibitor
An EC 1.10.* (oxidoreductase acting on diphenols and related substances as donors) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.10.3.*).
EC 1.10.3.* (oxidoreductase acting on diphenols and related substances as donors with oxygen as acceptor) inhibitors
EC 1.10.3.1 (catechol oxidase) inhibitor
1,2-benzenediol:oxygen oxidoreductase inhibitor
1,2-benzenediol:oxygen oxidoreductase inhibitors
Any EC 1.10.3.* (oxidoreductase acting on diphenols and related substances as donors with oxygen as acceptor) inhibitor that interferes with the action of catechol oxidase (EC 1.10.3.1).
EC 1.10.3.1 (catechol oxidase) inhibitors
catechol oxidase (EC 1.10.3.1) inhibitor
catechol oxidase (EC 1.10.3.1) inhibitors
o-diphenol:oxygen oxidoreductase inhibitor
o-diphenol:oxygen oxidoreductase inhibitors
Any EC 1.10.3.* (oxidoreductase acting on diphenols and related substances as donors with oxygen as acceptor) inhibitor that interferes with the action of laccase (EC 1.10.3.2).
benzenediol:oxygen oxidoreductase inhibitor
benzenediol:oxygen oxidoreductase inhibitors
EC 1.13.11.24 (quercetin 2,3-dioxygenase) inhibitor
Any EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitor that interferes with the action of quercetin 2,3-dioxygenase (EC 1.13.1.24).
EC 1.13.11.24 (quercetin 2,3-dioxygenase) inhibitors
quercetin 2,3-dioxygenase (EC 1.13.11.24) inhibitor
quercetin 2,3-dioxygenase (EC 1.13.11.24) inhibitors
quercetin:oxygen 2,3-oxidoreductase (decyclising) inhibitor
quercetin:oxygen 2,3-oxidoreductase (decyclising) inhibitors
quercetin:oxygen 2,3-oxidoreductase (decyclizing) inhibitor
quercetin:oxygen 2,3-oxidoreductase (decyclizing) inhibitors
quercetin:oxygen 2,3-oxidoreductase (ring-opening) inhibitor
quercetin:oxygen 2,3-oxidoreductase (ring-opening) inhibitors
EC 1.4.3.3 (D-amino-acid oxidase) inhibitor
Any EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor that interferes with the action of D-amino-acid oxidase (EC 1.4.3.3).
D-amino-acid oxidase (EC 1.4.3.3) inhibitor
D-amino-acid oxidase (EC 1.4.3.3) inhibitors
D-amino-acid:oxygen oxidoreductase (deaminating) inhibitor
D-amino-acid:oxygen oxidoreductase (deaminating) inhibitors
EC 1.4.3.3 (D-amino-acid oxidase) inhibitors
L-amino acid:O2 oxidoreductase inhibitor
L-amino acid:O2 oxidoreductase inhibitors
Any metabolite (endogenous or exogenous) found in human blood serum samples.
Any fatty acyl-CoA in which the 11-12 bond of the fatty acyl group is saturated.
Any antifungal agent used to prevent or treat fungal infections in humans or animals.
Heteroorganic entities that are plant metabolites which have significant antifungal properties.
An organophosphate oxoanion obtained by deprotonation of two of the three diphosphate OH groups of adenosine 5'-diphosphate.
A monoterpenoid that is oct-7-en-2-ol substituted by a methyl group at position 2 and a methylidene group at position 6 respectively.
A member of the class of tetralins that is tetralin substituted by methyl groups at positions 1, 1 and 6 respectively.
An aldehyde that is furan substituted by a formyl group at position 3.
Any organic amino compound that contains two or more amino groups.
Any saturated fatty acid anion containing 23 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3.
Any metal cation which causes the onset of an allergic reaction.
Any drug which causes the onset of an allergic reaction.
5-Ethenyltetrahydro-a,a,5-trimethyl-2-furanmethanol, 9CI
alpha,alpha,5-Trimethyl-5-vinyltetrahydrofurfuryl alcohol
1,2,3,4,5,6,7,8-Octahydro-1,4-dimethyl-7-(1-methylethylidene)azulene, 9CI
A sesquiterpene that has formula C15H24.
p-Hydroxyphenethyl alcohol 1-O-beta-D-glucoside
A sesquiterpene lactone of the eudesmanolide group.
EC 6.4.1.1 (pyruvate carboxylase) inhibitor
An EC 6.4.1.* (carboxylase) inhibitor that interferes with the action of pyruvate carboxylase (EC 6.4.1.1).
EC 6.4.1.1 (pyruvate carboxylase) inhibitors
pyruvate carboxylase (EC 6.4.1.1) inhibitor
pyruvate carboxylase (EC 6.4.1.1) inhibitors
pyruvate:carbon-dioxide ligase (ADP-forming) inhibitor
pyruvate:carbon-dioxide ligase (ADP-forming) inhibitors
An indole alkaloid cation obtained by protonation of the tertiary amino group of strychnine.
A nuclear receptor modulator that affects the retinoic acid receptor
Any receptor modulator acting on nuclear receptors
A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors.
An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of any 3-oxoacyl-CoA; major species at pH 7.3.
A carboxylic acic anion obtained by deprotonation of the carboxy group of any aromatic carboxylic acid. Major species at pH 7.3.
4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenyl beta-D-glucopyranoside
A monosaccharide derivative that is trans-sinapyl alcohol attached to a beta-D-glucopyranosyl residue at position 1 via a glycosidic linkage.
A diterpenoid that has formula C24H39NO5.
A methoxyisoflavone that is isoflavone substituted by a methoxy group at position 6 and hydroxy groups at positions 5, 7 and 4' respectively.
Oliver He and Jiahao Wang on 4/18/2017: Triptolide was not classified by ChEBI as diterpene triepoxide as it should be (Ref: https://www.ncbi.nlm.nih.gov/pubmed/5072337). Therefore, we modified the definition here.
Oliver He and Jiahao Wang on 4/18/2017: Triptolide was not classified by ChEBI as diterpene triepoxide as it should be (Ref: https://www.ncbi.nlm.nih.gov/pubmed/17097618). Therefore, we modified the definition here.
A gamma-lactone that has formula C15H18O6.
A pentacyclic triterpenoid that is urs-12-en-28-oic acid substituted by a beta-hydroxy group at position 3.
A 4,6,6-trimethylbicyclo[3.1.1]hept-3-en-2-one in which both chiral centres have R configuration. It is a component of Spanish verbena oil, from Verbena triphylla.
clinical drug role
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
drug product
William Hogan
a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
active ingredient
William R. Hogan
a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism
active ingredient role
role of scattered molecular aggregate
a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes
role of a scattered molecular aggregate
drug administration
a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism
administration of a drug product to an organism
data item
information content entity
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
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.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
Vincetoxicum paniculatum (Bunge) Kitag., non. (R.Br.) Kuntze, 1891
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
WEB: http://en.wikipedia.org/wiki/Adverse_event
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
a skin discoloration AE which has an outcome of flushing, a sudden reddening of the face, neck, or upper chest
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003241.htm
an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue.
WEB: http://www.cdc.gov/niosh/programs/msd/
musculoskeletal and connective tissue disorder AE
A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture
an injury and procedural complication AE which has an outcome of injury
an adverse event that occurs systematically throughout the systemic circulation. This is different from local adverse event that is limited or a certain location.
URL: https://en.wikipedia.org/wiki/Adverse_drug_reaction
a sensory capability AE that resuls in an uncomfortable feeling.
a reproductive system AE that occurs on the female side.
a reproductive system AE that occurs on the male side.
a cardiovascular disorder AE that has a cardiac disorder outcome.
WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/heart+disease Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23091623
a role that is intrinsic to a patient and is associated with an adverse event. No causal effect between this factor and the adverse event is assumed. Examples include: age, race, organ dysfunction, disease, pregrancy, lactation, gender, and genetics.
an intrinsic factor of adverse event that is the lactation of a patient.
a peripheral neuropathy AE which has an outcome of sensory neuropathy that involves damage to nerves of the peripheral nervous system.
WEB: http://www.nlm.nih.gov/medlineplus/tremor.html
Tremor AE is a behavior and neurological AE that has an outcome of an involuntary trembling or quivering, and muscle contraction and relaxation.
a cardiovascular disorder AE that is a result of insufficient blood flow throughout the body. Shock often accompanies severe injury or illness.
WEB: https://www.nlm.nih.gov/medlineplus/ency/article/000039.htm
WEB: http://en.wikipedia.org/wiki/Shock_%28circulatory%29
Circulatory shock is not related to the emotional state of shock.
an adverse event that occurs in hair, skin, or nail.
a hair, skin, and nail AE that occurs in hair.
a hair, skin, and nail AE that occurs in nail.
a sensory capability AE that results in a sensation of elevated abdominal pressure and volume
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003609/
a hematopoietic system AE that has an outcome of acute leukopenia, or lowered white blood cell count, most commonly of neutrophils causing neutropenia in circulating blood
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/001295.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/21942684
a female reproductive system AE that is characterized by the absence of menstrual period in a woman of reproductive age
Aplastic anaemia AE is an anemia AE that occurs when the bone marrow, and the blood stem cells that reside there are damaged. This causes a deficiency of all three blood cell types (pancytopenia): red blood cells (anemia), white blood cells (leukopenia), and platelets (thrombocytopenia).
WEB: http://www.ncbi.nlm.nih.gov/pubmed/23292240
a behavior and neurological AE that has an outcome of a disturbance that causes an individual to feel unsteady, giddy, woozy, or have a sensation of movement, spinning, or floating.
WEB: http://en.wikipedia.org/wiki/Balance_disorder
convulsion AE is a muscle adverse event that results in a medical condition where body muscles contract and relax rapidly and repeatedly, resulting in an uncontrolled shaking of the body
WEB: http://en.wikipedia.org/wiki/Convulsion
a movement disorder AE that has an outcome of difficulty in walking properly
WEB: http://en.wikipedia.org/wiki/Dyspnoea
MedDRA: 10013968 is for "dyspnoea"; MedDRA: 10013963 is for "dyspnea".
dyspnoea AE is an abnormal respiration AE debilitating symptom that is the experience of unpleasant or uncomfortable respiratory sensations, shortness of breath, air hunger
a cardiac disorder AE of the electrical conduction system that controls the heart rate, generates and conducts electrical impulses throughout the muscle of the heart, stimulating the heart to contract and pump blood.
WEB: http://www.medterms.com/script/main/art.asp?articlekey=8407
a muscle AE that has an outcome of muscular weakness AE (i.e., lack of muscle strength).
WEB: http://en.wikipedia.org/wiki/Muscular_weakness
WEB: http://en.wikipedia.org/wiki/Rhinitis
WEB: http://medical-dictionary.thefreedictionary.com/rhinitis
rhinitis AE is a respiratory system inflammation characterized by runny nose,irritation and inflammation of some internal areas of the nose
Axelrod YK1, Diringer MN. Temperature management in acute neurologic disorders. Neurol Clin. 2008 May;26(2):585-603, xi. doi: 10.1016/j.ncl.2008.02.005. PMID: 18514828.
WEB: http://en.wikipedia.org/wiki/Pyrexia
an abnormal body temperature AE which has an outcome of fever
Fever is a frequent medical sign that describes an increase in internal body temperature to levels above normal. Fever is characterized as a temporary elevation in the body's thermoregulatory set-point, usually by about 1-2 °F).
Drug-induced rash is the most commonly reported drug reaction.
URL: http://www.webmd.com/skin-problems-and-treatments/guide/common-rashes
Wick JY. Drug-induced rash: nuisance or threat? Consult Pharm. 2013 Mar;28(3):160-6. PMID: 23462025.
a skin AE that shows the symptom of rash, i.e., an abnormal change in skin color, appearance, or texture. A rash may cause the skin to change color, itch, become warm, bumpy, dry, cracked or blistered, swell and may be painful.
change of name from 'infection adverse event' to 'infectious adverse event' on 09/23/13 for a better clinical relevance, move 'infection adverse event' as an alternative term - SS
an adverse event that has an outcome of a pathogen infection, i.e., an infection caused by a pathogen such as a virus, bacterium, or parasite.
WEB: http://medical-dictionary.thefreedictionary.com/infection
An AE that has an outcome of syndrome. Syndrome is the association of several clinically recognizable features, signs (observed by a physician), symptoms (reported by the patient), phenomena or characteristics that often occur together, so that the presence of one feature alerts the physician to the presence of the others.
WEB: http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh&cmd=DetailsSearch&term=pruritus+generalised&log$=activity
Pruritus is an itch (Latin: pruritus), i.e., an unpleasant sensation that evokes the desire or reflex to scratch.
a skin adverse event that has an outcome of pruritus
a sensory capability AE that has an outcome of pain in a patient
a pain AE that has outcome of myalgia. Myalgia means "muscle pain" and is a symptom of many diseases and disorders.
Urticaria AE is a rash AE notable for dark red, raised, itchy bumps.
a pain AE that has an outcome of headache
I created this term and make it to be an umbrella term for different disorder terms related to respiratory system. --Oliver He
an AE that occurs in respiratory system.
WEB: http://en.wikipedia.org/wiki/Leukocytosis
According to the Vaccine Adverse Event Reporting System (VAERS), 'leukocytosis' is an adverse event that was mentioned in 1,021 VAERS reports (0.8%) during1991-2001 (Reference: PMID: 12825543).
a leukocyte cell number abnormal AE that has an outcome of greater than normal number of leukocytes, or nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue
a cardiovascular disorder AE that has an outcome of abnormal blood pressure, representing altered tension of the blood within the systemic arteries
a sensory capability AE that has an outcome of dizziness
Dizziness describes a number of subjective symptoms, which the patient may describe as feelings of lightheadedness, floating, wooziness, giddiness, confusion, disorientation or loss of balance. Medical terms include vertigo, disequilibrium, pre-syncope or syncoptic episode. Causes may stem from a variety of failures of equilibrioception, hypotension, cerebral hypoxia or a reaction to environmental chemicals or drugs.
a behavior and neurological AE that has an outcome of somnolence
Somnolence (or "drowsiness") is a state of near-sleep, a strong desire for sleep, or sleeping for unusually long periods (c.f. hypersomnia).
a sensory neuropathy AE that shows a sensation of tingling, pricking, or numbness of a person's skin with no apparent long-term physical effect.
Paresthesia is more generally known as the feeling of "pins and needles" or of a limb being "asleep" (although this is not directly related to the phenomenon of sleep). The manifestation of paresthesia may be transient or chronic.
WEB: http://en.wikipedia.org/wiki/Paraesthesia
a gustatory system AE which demonstrates a decreased sensation of appetite.
WEB: http://www.mayoclinic.org/diseases-conditions/anorexia/basics/definition/con-20033002
厌食症
WEB: http://medical-dictionary.thefreedictionary.com/cough
WEB: http://www.nlm.nih.gov/medlineplus/cough.html
an abnormal respiration AE that shows a sudden and often repetitively occurring reflex to keep the throat and airways clear
a skin adverse event that has an outcome of sweating
According to the Vaccine Adverse Event Reporting System (VAERS), 'sweating' is an adverse event that was mentioned in 2,301 VAERS reports (1.8%) during1991-2001 (Reference: PMID: 12825543).
WEB: http://en.wikipedia.org/wiki/Abdominal_pain
According to the Vaccine Adverse Event Reporting System (VAERS), 'abdominal pain' is an adverse event that was mentioned in 2,254 VAERS reports (1.8%) during1991-2001 (Reference: PMID: 12825543).
a pain AE that is observed in abdominal cavity
WEB: http://www.ncbi.nlm.nih.gov/pubmed/21722707
an abnormal blood pressure AE that has an outcome of sustained high blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states
Asthma is a common chronic lung disease. It has been defined by the National Heart, Lung and Blood Institute as a common chronic disorder of the airways that is complex and characterized by variable and recurring symptoms, airflow obstruction, bronchial hyperresponsiveness (bronchospasm), and an underlying inflammation.
a respiratory system AE which has an outcome of asthma
According to the Vaccine Adverse Event Reporting System (VAERS), 'back pain' was mentioned in 1,277 VAERS reports (1.0%) during1991-2001 (Reference: PMID: 12825543).
a pain AE that has an outcome of back pain
a hemorrhage AE that has an outcome of gastrointestinal hemorrhage
WEB: http://medical-dictionary.thefreedictionary.com/gastrointestinal+hemorrhage
bleeding in the stomach and/or the intestines
a nervous system AE that shows a damage to or disease affecting the nerves.
WEB: http://www.medicalnewstoday.com/articles/147963.php
WEB: http://www.emedicinehealth.com/neuropathy/article_em.htm#types_of_neuropathy
WEB: http://www.emedicinehealth.com/neuropathy/article_em.htm
Neuropathy is often classified according to the types or location of nerves that are affected. Neuropathy can also be classified according to the disease causing it. (For example, neuropathy from the effects of diabetes is called diabetic neuropathy. Ref: http://www.emedicinehealth.com/neuropathy/article_em.htm#types_of_neuropathy.
skin discoloration AE is a skin adverse event that results in change in color of skin or mucus membranes
According to the Vaccine Adverse Event Reporting System (VAERS), 'skin discoloration' is an adverse event that was mentioned in 909 VAERS reports (0.7%) during1991-2001 (Reference: PMID: 12825543).
a behavior and neurological AE that has an outcome of disorder in speech
WEB: http://medical-dictionary.thefreedictionary.com/hemorrhage
a cardiovascular disorder AE that has an outcome of hemorrhage
loss of blood from the vascular compartment to the exterior or into nonvascular body space as a result of rupture or severance of the blood vessels
This term will most likely removed since it is just a combination of nausea and vomiting.
an abnormal digestion AE which has an outcome of nausea and vomiting
According to the Vaccine Adverse Event Reporting System (VAERS), 'nausea and vomiting' is an adverse event that was mentioned in 812 VAERS reports (0.6%) during1991-2001 (Reference: PMID: 12825543).
a musculoskeletal system AE that occurs in muscle.
an adverse event that occurs in liver, biliary, and pancreatic areas.
WEB: http://www.uchospitals.edu/online-library/content=P00670
liver, biliary, and pancreatic disorder AE
a paralysis AE that has an outcome of paralysis in face
According to the Vaccine Adverse Event Reporting System (VAERS), 'facial paralysis' was mentioned in 580 VAERS reports (0.5%) during1991-2001 (Reference: PMID: 12825543).
a rash AE which shows red, target-shaped or "bulls-eye" patches or sores on the skin.
WEB: https://en.wikipedia.org/wiki/Erythema_multiforme
The erythema multiforme rash usually begins on the arms, hands, legs, and feet, but you might also find it on the face, neck, and body. It also can affect the lips and inside the mouth. It usuallys follows an infection or drug exposure.
WEB: http://kidshealth.org/parent/infections/skin/erythema_multiforme.html
According to the Vaccine Adverse Event Reporting System (VAERS), 'gastrointestinal disorder' is an adverse event that was mentioned in 449 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543).
a digestive system AE which has an outcome of a gastrointestinal disorder
WEB: http://medical-dictionary.thefreedictionary.com/cardiac+arrest
a cardiac disorder AE that has an outcome of heartarrest, the abrupt cessation of normal circulation of the blood due to failure of the heart to contract effectively during systole.
WEB: http://en.wikipedia.org/wiki/Myocardial_infarction
WEB: http://medical-dictionary.thefreedictionary.com/hepatic+function
According to the Vaccine Adverse Event Reporting System (VAERS), 'liver function tests abnormal' was mentioned in 717 VAERS reports (0.6%) during1991-2001 (Reference: PMID: 12825543).
a liver related investigation result abnormal AE which shows an abnormal test result in a liver function test, indicating aberrant function of liver.
an infection AE that results in detrimental colonization of a host organism by virus
WEB: http://en.wikipedia.org/wiki/Viral_infection
WEB: http://en.wikipedia.org/wiki/Jaundice
According to the Vaccine Adverse Event Reporting System (VAERS), 'jaundice' is an adverse event that was mentioned in 317 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
a liver/biliary system AE which has an outcome of jaundice, which is the clinical manifestation of hyperbilirubinemia, with deposition of bile pigments in the skin, resulting in yellowish staining of the skin and mucous membranes
WEB: http://en.wikipedia.org/wiki/Palpitations
a sensory capability AE that has an outcome of palpitation
A palpitation is an abnormal awareness of the beating of the heart, whether it is too slow, too fast, irregular, or at its normal frequency.
According to the Vaccine Adverse Event Reporting System (VAERS), 'immune system disorder' was mentioned in 292 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
According to the Vaccine Adverse Event Reporting System (VAERS), 'thrombocytopenic purpura'; is an adverse event that was mentioned in 267 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
Thrombocytopenic purpura AE are purpura AE associated with a reduction in circulating blood platelets which can result from a variety of causes.
a behavior and neurological AE that has an outcome of amnesia in a patient
Amnesia is a short term memory condition in which memory is disturbed. In simple terms it is the loss of memory.
Purpura is the appearance of red or purple discolorations on the skin that do not blanch on applying pressure. They are caused by bleeding underneath the skin. This is common with typhus and can be present with meningitis caused by meningococcal meningitis or septicaemia. Reference: http://en.wikipedia.org/wiki/Purpura.
According to the Vaccine Adverse Event Reporting System (VAERS), 'purpura'; is an adverse event that was mentioned in 251 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
a skin discoloration AE which has an outcome of purpura
Coma is a profound state of unconsciousness. A comatose person cannot be awakened, fails to respond normally to pain or light, does not have sleep-wake cycles, and does not take voluntary actions.
a sensory capability AE that has an outcome of coma
an AE that occurs in cardiovascular system.
a urinary system AE that has an outcome of urine abnormality AE
According to the Vaccine Adverse Event Reporting System (VAERS), 'increased salivation' is an adverse event that was mentioned in 336 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543).
an abnormal salivary gland physiology AE which has an outcome of increased salivation, meaning greater than normal amounts of flowing saliva
a muscle spasm AE which has an outcome of generalized spasm, which is an involuntary contraction of a muscle or group of muscles. Spasms may involve skeletal muscle (MUSCLE, SKELETAL) or smooth muscle (MUSCLE, SMOOTH).
a digestive system AE which has an outcome of dry mouth, which is dryness of the mouth resulting from reduced salivary secretion
According to the Vaccine Adverse Event Reporting System (VAERS), 'dry mouth'; is an adverse event that was mentioned in 171 VAERS reports (0.1%) during1991-2001 (Reference: PMID: 12825543).
Epistaxis is the relatively common occurrence of hemorrhage from the nose, usually noticed when the blood drains out through the nostrils.
a hemorrhage AE that has an outcome of epistaxis
a digestive system AE which has an outcome of abnormal salivary gland physiology, which is any functional anomaly of any of the glands in the mouth that secrete saliva
a musculoskeletal system AE that occurs in the bone
a muscle adverse event which has an outcome of muscle spasm, which is an involuntary and often painful muscle contraction or cramps having a number of causes ranging from nutritional deficiency to serious nervous system conditions
According to the Vaccine Adverse Event Reporting System (VAERS), 'abnormal stools' was mentioned in 111 VAERS reports (<0.1%) during1991-2001 (Reference: PMID: 12825543).
a digestive system AE which has an outcome of abnormal stool
a movement disorder AE that results in the loss of power of voluntary movement in a muscle through injury or disease of its nerve supply
WEB: https://www.nlm.nih.gov/medlineplus/paralysis.html
According to the Vaccine Adverse Event Reporting System (VAERS), 'paralysis' is an adverse event that was mentioned in 574 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543).
a movement disorder AE that has an outcome of ataxia, inability to coordinate voluntary muscular movements
According to the Vaccine Adverse Event Reporting System (VAERS), 'ataxia' is an adverse event that was mentioned in 555 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543).
WEB: http://www.thefreedictionary.com/skin+disorder
a hair, skin, and nail AE that occurs in skin.
WEB: http://www.ncbi.nlm.nih.gov/pubmed/21224774
According to the Vaccine Adverse Event Reporting System (VAERS), 'abnormal gait' is an adverse event that was mentioned in 998 VAERS reports (0.8%) during1991-2001 (Reference: PMID: 12825543).
a movement disorder AE that has an outcome of unusual or distinctive way of walking
a homeostasis AE which has an outcome of abnormal fluid regulation, which is any anomaly in the control of intracellular and/or extracellular fluid
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001586/
a hematopoietic system AE which has an outcome of anemia, which is less than normal levels of red blood cells and/or hemoglobin within red blood cells, or volume of packed red blood cells in the bloodstream, resulting in insufficient oxygenation of tissues and organs
blood pressure decreased, low blood pressure
an abnormal blood pressure AE that has an outcome of sustained low blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states
a digestive system AE which has an outcome of abnormal digestion, which is an altered ability of the mechanical, chemical, and enzymatic processes of the body to convert ingested food into material suitable for assimilation for synthesis of tissues or liberation of energy
an AE that occurs in the homeostasis system.
anomaly in the processes involved in the maintenance of an internal equilibrium of various functions and chemical or protein composition of the fluids and tissues
WEB: http://en.wikipedia.org/wiki/Oedema
an abnormal fluid regulation AE which has an outcome of edema, which is an accumulation of an excessive amount of watery fluid in cells or intercellular tissues
WEB: http://en.wikipedia.org/wiki/Swelling_(medical)
WEB: http://en.wikipedia.org/wiki/Inflammation
an immune system disorder AE that results in complex biological response of vascular tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. Inflammation is a protective attempt by the organism to remove the injurious stimuli as well as initiate the healing process for the tissue greater than expected response to injury, infection, or insult.
an inflammation AE which occurs in the respiratory system, which is reflected with the local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system
an inflammation AE that has an outcome of vasculitis, which is an inflammation of a blood or lymph vessel
WEB: http://en.wikipedia.org/wiki/Allergy
a hypersensitivity AE which results in an allergic response showing a marked increase in reactivity to an antigen upon subsequent exposure.
URL: http://www.hopkinsmedicine.org/healthlibrary/conditions/nervous_system_disorders/overview_of_nervous_system_disorders_85,P00799/
Not sure if it is same as respiratory system disorder or abnormal respiration. --Oliver He
According to the Vaccine Adverse Event Reporting System (VAERS), 'respiratory disorder' is an adverse event that was mentioned in 556 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543).
a respiratory system AE which has an outcome of abnormal respiration, an anomaly in the movement of gases into and out of the lung
MedDRA: 10002974 is for "apnoea"; MedDRA: 10002972 is for "apnea".
According to the Vaccine Adverse Event Reporting System (VAERS), 'apnea' is an adverse event that was mentioned in 1,618 VAERS reports (1.3%) during1991-2001 (Reference: PMID: 12825543).
WEB: http://medical-dictionary.thefreedictionary.com/apnea
an abnormal respiration AE which has an outcome of apnea, temporary cessation of breathing; sometimes episodic
an ear disorder AE which has an outcome of deafness, which is an inability to hear
an adverse event that occurs in a gustatory system
an eye disorder AE which has an outcome of abnormal vision, which is an inability or decreased ability to see
WEB: http://www.healthline.com/symptom/seizures
a behavior and neurological AE that shows a sudden surge of electrical activity in the brain.
WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/
an adverse event that has an outcome of an abnormal behavior and neurological phenotype.
any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls
a behavior and neurological AE that has an outcome of altered ability to coordinate voluntary movement or repetitive, compulsive movements
a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus
Hypersensitivity AE is a immune system AE that is a set of undesirable reactions produced by the normal immune system, including allergies and autoimmunity. These reactions may be damaging, uncomfortable, or occasionally fatal.
WEB: http://en.wikipedia.org/wiki/Hypersensitivity
WEB: https://en.wikipedia.org/wiki/Hypoventilation
According to the Vaccine Adverse Event Reporting System (VAERS), 'hypoventilation' is an adverse event that was mentioned in 321 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
an abnormal respiration AE which has an outcome of hypoventilation, i.e., reduced alveolar ventilation relative to metabolic carbon dioxide production; results in alveolar carbon dioxide pressure increasing above normal
an adverse event which occurs in a hematopoietic system, which is any structural or developmental anomaly of the blood cells or the organs associated with the development and formation of blood cells
an eye disorder AE which has an outcome of mydriasis, which is dilation of one or both pupils regardless of light conditions
WEB: http://en.wikipedia.org/wiki/Tachycardia
an arrhythmia AE that has an outcome of greater than average resting heart beats per minute, usually measured by the number of times the heart ventricles contract per unit of time, usually per minute
a muscle spasm AE that has an outcome of opisthotonus
opisthotonus is a form of tetanic spasm in which the head, neck and spine are bent backward and the body is bowed forward
a digestive system AE which has an outcome of dysphagia, which is a behavior and neurological AE that has an outcome of difficulty in swallowing food or liquid
an abnormal digestion AE which has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity
a digestive system AE that has an outcome of abnormal defecation, an anomaly in the production and excretion of feces
WEB: http://www.nlm.nih.gov/medlineplus/urinaryincontinence.html
a urinary system AE that has an outcome of the symptom of urinary incontinence, which is the inability to control the urinary excretory functions.
an hearing disorder AE that shows a persistent sensation of buzzing, ringing, clicking, or other noises in the ear
According to the Vaccine Adverse Event Reporting System (VAERS), 'mouth ulceration' was mentioned in 246 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
a digestive system AE which has an outcome of mouth mucosal ulceration, which is lesions through the mucous membrane of the mouth, usually associated with loss of tissue
WEB: http://medical-dictionary.thefreedictionary.com/diarrhea
an abnormal defecation AE that has an outcome of diarrhea, which is abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel
WEB: http://kidney.niddk.nih.gov/kudiseases/pubs/hematuria/
a urinary system AE that results in the presence of blood in the urine
UMLS CUI: C0018965 (hematuria AND haematuria); UMLS CUI: C0947999 (blood urine presence)
Hematuria AE can be caused by menstruation, vigorous exercise, sexual activity, viral illness, trauma, or infection, such as a urinary tract infection (UTI), along with more serious disorders such as cancer, disease, and clotting.
an adverse event that has an outcome of urinary system AE is a functional anomaly of any of the organs involved in the production or excretion of urine
a homeostasis AE whic has an outcome of abnomal body temperature, which is a deviation in the level of heat natural to a living being
an abnormal vision AE which has an outcome of double vision, which is two images perceived when only a single object is present
investigation result abnormal AE
This term is used to replace 'lab test abnormal AE'. The reason for this is that some test, like X-ray test, is not considered by many physicians as a lab test. Therefore, we have used this new term to cover a broader scope. All terms asserted under this term represent the investigation results without defined conclusion of disease.
an adverse event that is indicated by an abnormal result of an investigation that uses some laboratory equipment, device, or medical technology.
a hemorrhage AE that has an outcome of ecchymosis
an ecchymosis is a spot caused by loss of blood from a vessel; it implies a larger size than a petechiae, and has a more diffuse border than purpura; an ecchymosis can be caused by a bruise (which implies trauma), but can also be caused by bleeding diathesis
WEB: http://en.wikipedia.org/wiki/Erythema
Erythema AE is a skin adverse event that showns redness of the skin caused by hyperemia of the capillaries in the lower layers of the skin.
reproductive system AE is an AE that occurs in the reproductive system.
WEB: http://www.nhlbi.nih.gov/health/health-topics/topics/arr/
a cardiac disorder AE which has an outcome of abnormal heart rhythm
a digestive system AE which has an outcome of stomach discomfort
WEB: http://en.wikipedia.org/wiki/Ulcer_%28dermatology%29
a skin AE that shows a result of skin ulcer, i.e., a sore on the skin or a mucous membrane, accompanied by the disintegration of tissue. Ulcers can result in complete loss of the epidermis and often portions of the dermis and even subcutaneous fat.
a urinary system investigation result abnormal AE that has an outcome of a urine analysis abnormality
a cardiovascular disorder AE which has an outcome of vasodilatation, which refers to the widening of blood vessels resulting from relaxation of smooth muscle cells within the vessel walls, particularly in the large arteries, smaller arterioles and large veins.
WEB: http://en.wikipedia.org/wiki/Vasodilation
a liver related investigation result abnormal AE that has an outcome of an abnormal amount of bilirubin in the blood
WEB: http://medical-dictionary.thefreedictionary.com/bilirubin
a blood bilirubin level abnormal AE with an outcome of a increased amount of bilirubin, or a yellow breakdown product (broken down hemoglobin) of normal heme catabolism, in the blood
Bone marrow produces three types of blood cells; red blood cells, white blood cells and platelets. Bone marrow depression is characterized by an inability or reduced ability of the bone marrow to produce these cells. A low blood count can involve just one or all three types of blood cells.
WEB: http://www.drugs.com/condition/bone-marrow-depression-low-blood-counts.html
a bone marrow disorder AE that has an outcome of an abnormal condition in which the bone marrow is unable to produce normal amounts of red blood cells, white blood cells and platelets
WEB: http://en.diagnosispro.com/differential_diagnosis-for/bx-bone-marrow-biopsy-hypocellular/29777-154.html
a hematopoietic system AE that has an outcome of disease in the bone marrow, the spongy tissue inside of some bones that contain stem cells that can develop into red blood cells, white blood cells or platelets
WEB: http://www.nlm.nih.gov/medlineplus/bonemarrowdiseases.html
a cardiovascular disorder AE that results in the inability of the heart to provide sufficient pump action to distribute blood flow to meet the needs of the body
WEB: http://medical-dictionary.thefreedictionary.com/cardiac+failure
a hypotension AE that has an outcome of the inability of the heart to supply enough blood to the organs of the body because of heart damage
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001237/
WEB: https://en.wikipedia.org/wiki/Cardiomyopathy
a cardiovascular disorder AE that has an outcome of deterioration of the function of the myocardium, usually leads to heart failure
WEB: http://medical-dictionary.thefreedictionary.com/cardiomyopathy
a brain disorder AE with the outcome of hemorrhage or blood in the brain
a behavior and neurological AE that results in a loss of coordination
WEB: http://dermnetnz.org/vascular/vasculitis.html
an inflammation AE that has an outcome of inflamed blood vessels in the skin
a psychiatric disorder AE that results in a decline in level of cognitive function
WEB: http://medical-dictionary.thefreedictionary.com/delirium
a behavior and neurological AE that results in a loss of attention
a skin AE that has an outcome of a range of adverse drugs reactions of the skin, most commonly rashes resembling measles
WEB: http://medical-dictionary.thefreedictionary.com/drug+eruption
WEB: http://medical-dictionary.thefreedictionary.com/dysuria
Dysuria AE is an urinary system AE that results in painful urination
a cardiac function test abnormal AE that has an outcome of abnormal electrical activity in the heart
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003868.htm
a digestive system AE with an outcome of inflammation in the intestine, especially the small intestine
WEB: http://medical-dictionary.thefreedictionary.com/enteritis
an eye edema AE that has an outcome of swelling in either or both the lower and upper eyelids, due to fluid buildup or inflammation in the delicate tissues surrounding the eye.
WEB: http://www.localhealth.com/article/eyelid-swelling
a behavior and neurological AE that has an outcome of patient falling
a bone disorder AE that has an outcome of complete or incomplete break in a bone resulting from the application of excessive force
WEB: http://medical-dictionary.thefreedictionary.com/Fractures
a gastric disorder AE that has an outcome of inflammation in the lining of the stomach
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002135/
a digestive system AE that has an outcome of the passage of bloody stools
WEB: http://medical-dictionary.thefreedictionary.com/hematochezia
a hematopoietic system AE that has an outcome of hemolytic anemia, acute kidney failure and a low platelet count
WEB: http://www.ncbi.nlm.nih.gov/pubmed/23307876
a liver/biliary system AE that has an outcome of the inability of the liver to perform its normal synthetic and metabolic function
WEB: http://medical-dictionary.thefreedictionary.com/liver+failure
a liver/biliary system AE that has an outcome of swelling of the liver
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003275.htm
WEB: http://medical-dictionary.thefreedictionary.com/hyperhidrosis
a skin AE that results in excess perspiration
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000575.htm
Immune system disorder AE that results in an increase in white blood cell count as a result of stress or infection
WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154209/
a hematopoietic system AE that has an outcome of a lower than normal number of leukocytes, or nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue
WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695750/
a psychiatric disorder AE that results in a disorder in the patient's desire for sexual interaction
WEB: http://www.nlm.nih.gov/medlineplus/liverdiseases.html
Liver/biliary system AE that results in the disease of the liver
Abnormal defecation AE that results in black feces associated with gastrointestinal hemorrhage
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003130.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001204/
an inflammation AE that has an outcome of inflammation of the heart muscle
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001520/
a kidney disorder AE that has an outcome of a group of symptoms that include protein in the urine, low blood protein levels, high cholesterol levels, high triglyceride levels and swelling
WEB: http://en.wikipedia.org/wiki/Neurotoxicity
a nervous system AE that alters the normal activity of the nervous system due to exposure to neurotoxins (which can be natural or artificial toxic substances), and causes damage to nervous tissue
toxic neuropathy AE
Digestive System AE that results in oral lesions
WEB: http://medical-dictionary.thefreedictionary.com/pancytopenia
Hematopoietic System AE that results in a reduction in the amount of red and white blood cells and platelets in blood
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001305/
a digestive system AE that has an outcome of infection in the large intestine with an overgrowth of Clostridium difficile bacteria
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003644.htm
a red blood cell count abnormal AE that has an outcome of a decrease in red blood cells
As shown on the renal.org website (http://www.renal.org/guidelines/modules/acute-kidney-injury), Acute kidney injury (AKI) has now replaced the term acute renal failure.
Acute kidney failure occurs when kidneys become unable to filter waste products from blood.
WEB: http://www.mayoclinic.org/diseases-conditions/kidney-failure/basics/definition/con-20024029
WEB: http://medical-dictionary.thefreedictionary.com/acute+renal+failure
a kidney disorder AE that results in the rapid loss or decline of kidney function
a respiratory system AE that has an outcome of a condition where lungs cannot remove all the carbon dioxide the body produces, makes body fluid too acidic
WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001154/
a skin AE that has an outcome of darkening in an area of skin or nails caused by increased melanin
WEB: http://medical-dictionary.thefreedictionary.com/hyperpigmentation
a behavior and neurological AE that results in irregular sleep patterns
WEB: http://medical-dictionary.thefreedictionary.com/sleep+disorder
A gastrointestinal hemorrhage AE that has an outcome of the bleeding in the stomach
a psychiatric disorder AE that results in attempted suicide
an abnormal repiration AE that shows an outcome of tachypnoea (i.e., abnormally rapid breathing or respiration)
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000586.htm
a hematopoietic system AE that has an outcome of decrease in platelets in the blood
WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/gastrointestinal+bleeding Secondary Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1237869/
a gastrointestinal hemorrhage AE that has an outcome of bleeding in the upper gastrointestinal tract
Urinary system AE that results in an inability to urinate
WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/urinary+retention Secondary Source: http://www.medtronic.com/patients/urinary-retention/index.htm
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003147.htm
a urine abnormality AE that has an outcome of decreased urine output, less than 500 milliliters of urine in 24 hours
an abnormal vision AE that results in unclear vision
WEB: Primary Source: http://www.nlm.nih.gov/medlineplus/ency/article/003029.htm Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23111613
A systematic adverse event that has an outcome of failure in mulitple organs
brain AE
cardiovascular investigation result abnormal AE
an investigation result abnormal AE that involves an abnormal result of an investigation involving the cardiovascular system
blood sodium increased
A physical quality that has an increased level of sodium in the blood
urinary system investigation result abnormal AE
renal and urinary tract investigation and urinalysis result abnormal AE
an investigation result abnormal AE that involves the renal and urinary tract and urinalyses
renal system investigation result abnormal AE
endocrine investigation result abnormal AE
an investigation result abnormal AE that involves an abnormal result of an endocrine investigation
hematology investigation result abnormal AE
an investigation result abnormal AE that is characterized by an abnormal result of a hematology investigation
red blood cell profile abnormal AE
a hematology investigation result abnormal AE that results in an abnormal red blood cell profile
white blood cell profile abnormal AE
a hematology investigation result abnormal AE that is characterized by an abnormal white blood cell profile
leukocyte cell number abnormal AE
a white blood cell profile abnormal AE that is characterized by an abnormal leukocyte cell number
liver related investigation result abnormal AE
an investigation result abnormal AE that is characterized by an abnormal liver related investigation result
red blood cell count abnormal AE
a red blood cell profile abnormal AE that is characterized by an abnormal red blood cell count
severity of adverse event
a process quality that represents the level of severity of an adverse event.
WEB: http://en.wikipedia.org/wiki/Mental_disorder
a behavior and neurological AE that has an outcome of a mental illness or psychiatiric disorder. The mental illness is a mental or behavioral pattern or anomaly that causes either suffering or an impaired ability to function in ordinary life (disability), and which is not developmentally or socially normative.
mental disorder AE
AE severity G1
a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated.
Note the AE severity Grade 1 equals to CTCAE G1 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event
AE severity G2
a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances).
Note the AE severity Grade 2 equals to CTCAE G2 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event
AE severity G3
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event
Note the AE severity Grade 3 equals to CTCAE G3 AE severity.
a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet).
AE severity G4
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event
a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral).
Note the AE severity Grade 4 equals to CTCAE G4 AE severity.
AE severity G5
Note the AE severity Grade 5 equals to CTCAE G5 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event
gastric disorder AE
a gastrointestinal disorder AE that shows a problem with the stomach, ranging from indigestion and heartburn to peptic ulcers and GERD.
WEB: http://www.nlm.nih.gov/medlineplus/stomachdisorders.html
numbness AE
a sensory capability AE that has an outcome of numbness, a loss of sensation of feeling in a part of the body.
WEB: http://www.mayoclinic.org/symptoms/numbness/basics/definition/sym-20050938
WEB: http://en.wikipedia.org/wiki/Hemolytic_anemia
Hemolytic anemia AE is an anemia AE associated with hemolysis, the abnormal breakdown of red blood cells (RBCs), either in the blood vessels (intravascular hemolysis) or elsewhere in the human body (extravascular). Such an AE can be relatively harmless or life-threatening.
Heartburn AE is a gastric disorder AE that also known as pyrosis, cardialgia, or acid indigestion. It's a burning sensation in the chest, just behind the breastbone or in the epigastrium, the upper central abdomen. The pain often rises in the chest and may radiate to the neck, throat, or angle of the jaw.
WEB: http://en.wikipedia.org/wiki/Heartburn
WEB: http://medical-dictionary.thefreedictionary.com/mastauxe
Mastauxea AE is a reproductive system AE that shows enlargement of the breast.
WEB: http://en.wikipedia.org/wiki/Hypoactive_sexual_desire_disorder
Hypoactive sexual desire disorder AE is a libido disorder AE that is considered a sexual dysfunction and is characterized as a lack or absence of sexual fantasies and desire for sexual activity, as judged by a clinician.
WEB: http://www.merriam-webster.com/medical/chromatosis
Chromatos AE is a skin AE shows that deposit of pigment in a normally unpigmented area or excessive pigmentation in a normally pigmented site.
Allergic rhinitis AE is a rhinitis AE that is an allergic inflammation of the nasal airways. It occurs when an allergen, such as pollen, dust, or animal dander (particles of shed skin and hair) is inhaled by an individual with a sensitized immune system.
WEB: http://en.wikipedia.org/wiki/Allergic_rhinitis
Loose stools AE is a abnormal stool AE that is usually a form of diarrhea and many conditions causing loose stool will be listed under diarrhea. It may also be related to watery stool (also within the spectrum of diarrhea).
WEB: http://www.rightdiagnosis.com/sym/loose_stool.htm
WEB: http://en.wikipedia.org/wiki/Burping
Eructation AE is a digestive system AE that is the release of gas from the digestive tract (mainly esophagus and stomach) through the mouth. It is usually accompanied with a typical sound and, at times, an odor.
Glossolalia AE is a speech disorder AE that is the fluid vocalizing of speech-like syllables that lack any readily comprehended meaning.
WEB: http://en.wikipedia.org/wiki/Glossolalia
Stomachache AE is a pain AE that the pain in or near your stomach. It is a common symptom associated with transient disorders or serious disease.
Conduction block AE is a conduction system disorder AE that shows failure of impulse transmission at some point along a nerve fiber, although conduction along the segments proximal and distal to it are unaffected.
WEB: http://www.medilexicon.com/medicaldictionary.php?t=10757
WEB: http://en.wikipedia.org/wiki/Photodermatitis
Photodermatitis AE is a dermatitis AE that referred to as sun poisoning or photoallergy, is a form of allergic contact dermatitis in which the allergen must be activated by light to sensitize the allergic response, and to cause a rash or other systemic effects on subsequent exposure.
Interstitial nephritis AE is an inflammation AE that is a form of nephritis affecting the interstitium of the kidneys surrounding the tubules. This disease can be either acute, meaning it occurs suddenly, or chronic, meaning it is ongoing and eventually ends in kidney failure.
WEB: http://en.wikipedia.org/wiki/Interstitial_nephritis
Dysphoria AE is a behavior and neurological AE that is a profound state of unease or dissatisfaction. In a psychiatric context, dysphoria may accompany depression, anxiety, or agitation. Common reactions to dysphoria include emotional distress or indifference.
WEB: http://en.wikipedia.org/wiki/Dysphoria
WEB: http://en.wikipedia.org/wiki/Herpes_simplex
a herpes viral infection AE tha is caused by both Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2).
Unconsciousness AE is a sensory capability AE that is a state which occurs when the ability to maintain a awareness of self and environment is lost, it involves a complete or near-complete lack of responsiveness to people and other environmental stimuli.
WEB: http://en.wikipedia.org/wiki/Unconsciousness
Miosis AE is an eye AE that is a term with various definitions, which generally include constriction of the pupil.
WEB: http://en.wikipedia.org/wiki/Miosis
WEB: http://en.wikipedia.org/wiki/Albuminuria
Albuminuria AE is a urine abnormality AE that is a pathological condition wherein albumin is present in the urine. It is a type of proteinuria.
Contact dermatitis AE is a dermatitis AE that is a type of skin inflammation.It results from exposure to allergens (allergic contact dermatitis) or irritants (irritant contact dermatitis). Phototoxic dermatitis occurs when the allergen or irritant is activated by sunlight.
WEB: http://en.wikipedia.org/wiki/Contact_dermatitis
peripheral coldness AE
a sensory capability AE that has an outcome of peripheral coldness, or coldness of extremeties
WEB: http://www.patient.co.uk/leaflets/peripheral_coldness.htm
hyperesthesia AE
a sensory capability AE that has an outcome of hyperaesthesia, meaning unusual or pathological sensitivity of the skin or of a particular sense
WEB: http://www.merriam-webster.com/dictionary/hyperesthesia
idiopathic thrombocytopenic purpura AE
a thrombocytopenic purpura AE with no known cause (idiopathic). Idiopathic thrombocytopenic purpura is a bleeding disorder in which the immune system destroys platelets, which are necesssary for normal blood clotting. Persons with this disorder have too few platelets in the blood.
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000535.htm
fecal incontinence AE
WEB: http://digestive.niddk.nih.gov/ddiseases/pubs/fecalincontinence/#what
an abnormal defecation AE that has an outcome of fecal incontinence, the accidental passing of solid or liquid stool or mucus from the rectum
fear AE
WEB: http://www.merriam-webster.com/dictionary/fear
a behavior and neurological AE that has an outcome of fear, which is to be afraid and/or worried
WEB: http://www.medicinenet.com/script/main/art.asp?articlekey=10092
WEB: http://smschile.cl/documentos/cursos2010/MedicalClinicsNorthAmerica/Acute%20Symptoms%20of%20Drug%20Hypersensitivity%20%28Urticaria,%20Angioedema,%20Anaphylaxis,%20Anaphylactic%20Shock%29.pdf
a circulatory AE that is a serious allergic reaction associated with systemic vasodilation that causes low blood pressure which is by definition 30% lower than the person's baseline or below standard values.
WEB: http://en.wikipedia.org/wiki/Anaphylaxis
WEB: http://www.rightdiagnosis.com/sym/epigastric_discomfort.htm
Epigastric discomfort is a discomfort AE that shows discomfort in the upper central region of the abdomen.
Acute intravascular hemolysis AE is a cardiovascular AE that has an outcome of disruption of red blood cells occurs while they are within blood vessels.
Skin redness AE is an erythema AE that is abnormal redness of the skin, often signaling a pathological condition, such as inflammation, infection, or sunburn.
WEB: http://www.healthline.com/health/skin-redness
Hearing disorder AE is an ear disorder that shows impairment of the sense of hearing.
Increased defecation frequency AE is a abnormal stool AE that shows defecation number increased.
Pain over the liver AE is a pain AE that shows pain over the liver.
Numbness of tongue AE is a numbness AE that shows abnormal feeling or loss of sensation in the tongue.
Numbness of the limbs AE is a numbness AE that shows reduced or loss of sensation on the skin of the arm and leg.
a sleep disorder AE in which there is an inability to fall asleep or to stay asleep as long as desired.
WEB: https://en.wikipedia.org/wiki/Insomnia
Insomnia is a symptom of a sleeping disorder characterized by persistent difficulty falling asleep or staying asleep despite the opportunity. Insomnia is a symptom, not a stand-alone diagnosis or a disease.
Bleeding and coagulation disorders AE is a hematopoietic system AE that shows bleeding and coagulation disorders.
an allergy AE that shows swelling and irritation of the skin, caused by an allergy to a substance in the environment.
Acousma AE is a sensory capability AE that shows a hallucinatory impression of strange sounds.
significantly decreased blood pressure AE
Obviously decreased blood pressure AE is a hypotension AE that shows obviously sustained low blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states.
Proarrhythmic effect AE is an arrhythmia AE that is a new or more frequent occurrence of pre-existing arrhythmias, paradoxically precipitated by antiarrhythmic therapy, which means it is a side effect associated with the administration of some existing antiarrhythmic drugs, as well as drugs for other indications. In other words, it is a tendency of antiarrhythmic drugs to facilitate emergence of new arrhythmias.
WEB: http://en.wikipedia.org/wiki/Proarrhythmia
low bone density AE
a bone disorder AE that has an outcome of low bone densityl, but not low enough to be considered osteoporosis
A palsy AE that has a symmetric limitation of the movements of both eyes in the same direction.
WEB: http://one.aao.org/bcscsnippetdetail.aspx?id=f5a77965-de2a-4fb0-82fb-5f4089671ad6
Menstrual disorder AE is an abnormal condition in a woman's menstrual cycle.
WEB: http://en.wikipedia.org/wiki/Menstrual_disorder
a psychiatric disorder AE that is a category of mental health disorders that primarily affect learning, memory, perception, and problem solving, and include amnesia, dementia, and delirium.
WEB: http://en.wikipedia.org/wiki/Cognitive_disorder
Menstruation irregular AE is a endocrine system AE that is an abnormal variation in length of menstrual cycles in a female.
WEB: http://en.wikipedia.org/wiki/Irregular_menstruation
WEB: http://en.wikipedia.org/wiki/Tonic%E2%80%93clonic_seizure
Generalised tonic-clonic seizure AE is a seizure AE that is a type of generalized seizure that affects the entire brain. Tonic–clonic seizures are the seizure type most commonly associated with epilepsy and seizures in general, though it is a misconception that they are the only type.
cryptorchidism AE
cryptorchidism AE is a male reproductive system AE which results in the absence of one or both testes from the scrotum.
WEB: http://en.wikipedia.org/wiki/Cryptorchidism
delusion AE
WEB: http://www.merriam-webster.com/dictionary/delusion
a psychiatric disorder AE that results in a persistent false psychotic belief regarding the self or objects outside the self that is maintained despite indisputable evidence to the contrary.
epileptic seizure AE
a seizure AE that shows a brief episode of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain.
WEB: http://en.wikipedia.org/wiki/Epileptic_seizure
cardiac function test abnormal AE
a cardiovascular investigation result abnormal AE that results in an abnormal result on a test used to evaluate heart function
WEB: http://www.drsinatra.com/heart-function-tests-to-assess-heart-disease-risk/
WEB: https://en.wikipedia.org/wiki/Cardiology_diagnostic_tests_and_procedures
injury or procedural complication AE
an adverse event that shows a result of injury or procedural complication.
a male reproductive system AE that has involvement of the testis.
a behavior and neurological AE that has an exaggerated feeling of well-being which is disproportionate to events and stimuli.
a male reproductive system AE that has a decrease in the number of spermatozoa in the semen.
medical procedure
a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
behavior abnormal quality
a behavioral quality where the behavior in an organism is abnormal.
WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior)
herpes viral infection AE
a viral infection AE that is caused by a herpes virus. Note that there are 8 herpesvirus types.
WEB: https://en.wikipedia.org/wiki/Herpesviridae
coordination and balance disorder AE
a cross product of coordination abnormal AE and balance disorder AE
aversion to greasy food AE
an anorexia AE that has loss of appetite of greasy food.
WEB: http://www.anxietycare.org.uk/docs/eating.asp
dysstasia AE
a coordination and balance disorder AE that has difficulty in standing
WEB: http://medical-dictionary.thefreedictionary.com/dysstasia
dystasia AE
gastrorrhexis AE
WEB: http://medical-dictionary.thefreedictionary.com/gastrorrhexis
a gastric disorder AE that shows an rupture in the stomach
stomach rupture
rupture AE
WEB: https://en.wikipedia.org/wiki/Rupture
YH. QL
an injury AE that refers to break or burst suddenly (esp. of a pipe, a vessel, or a bodily part such as an organ or membrane)
acute gastric mucosal lesion AE
WEB: http://medmantic.com/wiki/Acute_Gastric_Mucosal_Lesion
a gastric disorder AE that shows the body under stress, causing acute erosion, bleeding and ulcers, stomach or duodenal mucosa damage collectively. The main clinical manifestations include upper gastrointestinal bleeding and a small perforation.
bowel sounds increased AE
a bowel sounds abnormal AE that shows an increased amount of bowel sounds.
WEB: https://www.nlm.nih.gov/medlineplus/ency/article/003137.htm
bowel sounds abnormal AE
a gastrointestinal disorder AE that shows an abnormal amount of bowel sounds.
hyperacusia AE
WEB: https://en.wikipedia.org/wiki/Hyperacusis
a hearing disorder AE with an abnormally disproportionate increase in the sensation of loudness in response to auditory stimuli of normal volume
lumbago AE
a back pain AE that occurs at the low back
WEB: https://en.wikipedia.org/wiki/Low_back_pain
kidney area percussion pain AE
a pain AE that shows the pain in the kidney area identified by a percussion procedure.
URL http://howshealth.com/kidney-pain-location-causes-symptoms-treatment/#percussion
physical examination
a medical procedure by which a medical professional investigates the body of a patient for signs of disease.
WEB: http://www.webmd.com/a-to-z-guides/annual-physical-examinations
WEB: https://en.wikipedia.org/wiki/Physical_examination
percussion procedure
a physical test by which a surface is tapped to determine the underlying structure, and is used in clinical examinations to assess the condition of the thorax or abdomen.
WEB: https://en.wikipedia.org/wiki/Percussion_(medicine)
cylindruria AE
a urine analysis result abnomal AE that shows cylindrical structures produced by the kidney and present in the urine.
WEB: http://medical-dictionary.thefreedictionary.com/cylindruria
visual disturbance AE
an eye disorder AE that causes visual disturbance and interfere with normal sight.
WEB: http://www.healthline.com/symptom/visual-disturbance
eye edema AE
an edema AE that has an outcome of swelling in the eye.
feces pale AE
an abnormal stool AE that shows pale or clay-colored stool.
WEB: http://www.healthline.com/symptom/pale-stools
hypomenorrhea AE
WEB: https://en.wikipedia.org/wiki/Hypomenorrhea
a menstrual disorder AE that shows an extremely light menstrual blood flow
necrospermia AE
WEB: https://en.wikipedia.org/wiki/Necrospermia
a male reproductive system AE in which spermatozoa in seminal fluid are dead or motionless
subfertility AE
WEB: https://en.wikipedia.org/wiki/Infertility
a reproductive system AE that results in diminished ability to produce live offspring
infertility AE
WEB: http://www.mayoclinic.org/diseases-conditions/infertility/basics/definition/con-20034770
a reproductive system AE that results in an inability to conceive for at least one year after trying and having unprotected sex.
low estrogen level AE
WEB: http://www.md-health.com/Low-Estrogen.html
an endocrine investigation result abnormal AE that is characterized by a lower than normal level of estrogen, the primary sex hormone in women
WEB: https://en.wikipedia.org/wiki/Hypoestrogenism
dysfunctional uterine bleeding AE
WEB: http://emedicine.medscape.com/article/257007-overview
a hemorrhage AE that occurs at the uterus, but it is not related to menstruation. The irregular and unpredictable bleeding usually comes from a dysfunctional endometrium.
testicular atrophy AE
WEB: https://en.wikipedia.org/wiki/Testicular_atrophy
a testicular disorder AE that has a loss of testicular volume
pure red cell aplasia AE
WEB: http://emedicine.medscape.com/article/205695-overview
an aplastic anemia AE that results in the suppression of erythropoiesis with little or no abnormality of leukocyte or platelet production.
allergic cutaneous vasculitis AE
WEB: https://www.nlm.nih.gov/medlineplus/ency/article/000874.htm
a cutaneous vasculitis AE that results in inflammation of small blood vessels, characterized clinically by palpable purpura, which is a slightly elevated purpuric rash over one or more areas of the kin.
melanoplakia AE
a skin hyperpigmentation AE that shows the occurrence of pigmented patches on the tongue and buccal mucousmembranes.
WEB: http://www.medilexicon.com/medicaldictionary.php?t=53725
erythema nodosum AE
an erythema AE that showns an erythematous eruption characterized by inflammatory nodules that are usually tender, multiple, and bilateral. Such a symptom is commonly associated with drug reactions or infection.
WEB: https://en.wikipedia.org/wiki/Erythema_nodosum
tonic spasm AE
WEB: http://medical-dictionary.thefreedictionary.com/tonic+spasm
a muscle spasm AE that occurs when the contraction of a spasm is sustained or continuing. Such a spasm is generally severe because is is often caused by diseases that affect the central nervous system or brain, such as tetanus, rabies, and cerebral palsy.
premature ovarian failure AE
a female reproductive system AE that occurs at the ovaries where ovaries do not produce estrogen despite high levels of circulating gonadotropins in women under 40.
WEB: https://www.nlm.nih.gov/medlineplus/prematureovarianfailure.html
WEB: http://www.mayoclinic.org/diseases-conditions/premature-ovarian-failure/basics/definition/con-20028351
skin erosion AE
a skin adverse event that has an outcome of a discontinuity of the skin exhibiting incomplete loss of the epidermis, a lesion that is moist, circumscribed, and usually depressed.
arrest of hematopoiesis AE
WEB: https://en.wikipedia.org/wiki/Haematopoiesis
a hematopoietic system AE that has an outcome of an arrest of the formation of blood cellular components.
acute arrest of hematopoiesis AE
an arrest of hematopoiesis AE that occurs quickly
palsy AE
A paralysis AE accompanied by involuntary tremors.
WEB: https://en.oxforddictionaries.com/definition/palsy
WEB: https://en.wikipedia.org/wiki/Palsy
optic hyperesthesia AE
WEB: http://medical-dictionary.thefreedictionary.com/optic+hyperesthesia
A hyperaesthesia AE that occurs at the optic area, reflected by an abnormal sensitivity to light.
asphyxia AE
An abnormal respiration AE that shows a severely deficient supply of oxygen to the body that arises from abnormal breathing.
WEB: https://en.wikipedia.org/wiki/Asphyxia
myotonia AE
WEB: https://en.wikipedia.org/wiki/Myotonia
An muscle AE showing delayed relaxation (prolonged contraction) of the skeletal muscles after voluntary contraction or electrical stimulation
neck myotonia AE
An myotonia AE that occurs in the neck.
planned process
'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.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Injecting mice with a vaccine in order to test its efficacy
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.
A processual entity that realizes a plan which is the concretization of a plan specification.
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)
scattered molecular aggregate
the sodium and chloride ions in a glass of salt water
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
PERSON: Alan Ruttenberg
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.
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.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
plant
virus
A bodily process that is clinically abnormal.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
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.
multiply inhering quality of a physical entity
A quality that inheres in an entire organism or part of an organism.
A portion of plant tissue (PO:0009007) outside the vascular cambium (PO:0005598) or the xylem (PO:0005352); in older trees may be divided into dead outer bark and living inner bark, which consists of secondary phloem (PO:0005043).
A portion of epidermis (PO:0005679) that is part of a root (PO:0009005).
The root epidermis is different from the shoot epidermis in its origin, function and structure.
epidermis de la ra&#237z (Spanish, exact)
A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).
A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
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.
sistema de epiblasto (epiblastema) (Spanish, exact)
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
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.
porci&#243n de un tejido vegetal (Spanish, exact)
A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).
A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
'Part' includes both proper parts and the whole plant. CARO:0000003 anatomical structure is defined as: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
An anatomical structure that is or was part of a plant, or was derived from a part of a plant.
A shoot axis (PO:0025029) that is the primary axis of a plant.
A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic.
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
eje del epiblasto (epiblastema) (Spanish, exact)
A phyllome (PO:0006001) that is not associated with a reproductive structure.
A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.
An anatomical entity that is or was part of a plant.
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 anatomical entity is defined as: 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.
entidad anat&#243mica vegetal (Spanish, exact)
A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
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).
estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
traditional Chinese medicine decoction pieces
中药饮片
Decoction Pieces
With crude medicine as raw materials, according to Chinese medicine theory, after processing, it can be directly used in traditional Chinese medicine clinical or pharmaceutical production and use of prescription drugs.
中华人民共和国国家质量监督检验检疫总局中国国家标准化管理委员会.GB/T 31774-2015 中华人民共和国国家标准，中药编码规则及编码[S].2015.
以中药材为原材料，按中医药理论，经过加工炮制后，可直接用于中医临床或制剂生产使用的处方药品。
TCM dispelling pathogenic wind and dampeness drug
祛风湿药
Dispelling Pathogenic Wind and Dampeness Drugs
温里药
Warming Interior Drug
TCM promoting blood circulation and removing blood stasis drug
活血化瘀药
Promoting Blood Circulation and Removing Blood Stasis Drugs
补虚药
Supplementing and Boosting Drugs
TCM wind-damp dispelling and cold-dispersing drug
祛风湿散寒药
Wind-damp Dispelling and Cold-dispersing Drugs
TCM winddamp-dispelling and heat-clearing drug
祛风湿清热药
Winddamp-dispelling and Heat-clearing Drugs
TCM winddamp-dispelling and tendon-bone-strengthening drug
祛风湿强筋骨药
Winddamp-dispelling and Tendon-bone-strengthening Drugs
TCM blood-activating and trauma-curing drug
活血疗伤药
Blood-activating and Trauma-curing Drugs
补血药
Blood-supplementing Drugs
Channel Tropism
药物作用部位
药物对于机体某部分的选择性作用。
钟赣生主编.中药学[M].北京：中国中医药出版社，2012.
TCD nature
四气（中药）
寒热温凉四种不同的药性。
TCD flavour
中药五味
药物所具有的酸、苦、甘、辛、咸不同的药味。
Toxicity of Chinese Medicine
毒性
侯士良主编.中药八百种详解[M].郑州：河南科学技术出版社.2009.
药物对机体的损害性。
Liver Meridian
肝经
Cold (TCD)
寒（中药）
Hot (TCD)
热（中药）
Gallbladder Meridian
胆经
Sour (TCD)
酸（中药）
Warm (TCM)
温（中药）
Cool (TCD)
凉（中药）
Mild(TCM)
平（中药）
bitter (TCD)
苦（中药）
Sweet (TCD)
甘（中药）
Pungent (TCD)
辛（中药）
Salty (TCD)
咸（中药）
Strong Toxicity
大毒
Slightly Toxicity
有毒
Spleen Meridian
脾经
Stomach Meridian
胃经
Heart Meridian
心经
Kidney Meridian
肾经
Bladder Meridian
膀胱经
Black-tail Snake TCD
郑艳青王艳敏.乌梢蛇的化学成分及分析方法研究进展.中国药业,2006,15(21):59-60
Zaocys
乌梢蛇
Cynanchi Paniculati Radix et Rhizoma
徐长卿
Paniculate Swallowwort Root
Chinese Clematis Root
罗奎元,强宇靖,高慧琴.威灵仙化学成分及药理作用研究进展.甘肃中医学院学报,2015,32(5):60-63
Clematidis Radix et Rhizoma
威灵仙
陈宇.独活化学成分研究进展,辽宁中医药大学学报,2014,16(5):255-256
Doubleteeth Pubescent Angelica Root
Angelicae Pubescentis Radix
独活
Oriental Variegated Coralbean Bark
Erythrinae Cortex
海桐皮
徐瑞兰,师彦平.中药臭梧桐的化学成分研究.南昌工程学院学报,2015,34(4):15-19
Harlequin Glorybower Leaf
Clerodendri Trichotomi Ramulus et Folium
臭梧桐
Siegesbeckia Herb
Siegesbeckiae Herba
豨莶草
邢冬杰,项东宇,张彩坤.桑枝活性成分提取及药理作用研究进展.中国现代中药,2014,16(11):957-960
Mulberry Twig
Mori Ramulus
桑枝
Largeleaf Gentian Root
Gentianae Macrophyllae Radix
穆祯强，于洋，高昊，等.龙胆属秦艽组植物的化学成分和药理作用研究进展[J]．中国中药杂志，2009，34(16)：2012-2017; 郑姜彬.麻花秦艽的化学成分研究[D]．陕西：西北大学，2010：6-29
秦艽
谢丽莎,龚志强,李娉.千年健研究进展.上海中医药杂志,2011,45(11):90-92
Obscured Homalomena Rhizome
Homalomenae Rhizoma
千年健
Chinese Taxillus Herb
Talxilli Herba
朱晓薇.桑寄生科植物的化学成分与抗肿瘤作用.国外医药·植物药分册,2001,16(4):142-145
桑寄生
郑婧,张贵君,韦敏.五加皮药材基原、化学成分及药理作用研究进展.辽宁中医药大学学报,2015,17(8):104-107
Acanthopanax Root Bark
Acanthopanacis Cortex
五加皮
Prepared Common Monkshood Branched Root TCD
朱林平.附子毒性研究概况[J]Jiangxi journal of traditional Chinese medicine,2004,35(6):53-55
唐春雪,宋苹.附子临床应用安全性文献系统评价[J]新中医,2008,40(4):95-101
吴克红，唐力英.附子的化学和生物活性研究进展,中国实验方剂学杂志,2004,20(2):212-220
骆梅娟,周至安.附子的毒性及临床应用浅析[J]Journal of Guangzhou University of Traditional Chinese Medicine,2009,26(5):512-514
Prepared Common Monkshood Branched Root
Aconiti Lateralis Radix Praeparaka
附子
Nux Vomica
Strychni Semen
解宝仙,唐文照,王晓静.马钱子的化学成分和药理作用研究进展.药学研究,2014,33(4):603-606
马钱子
Debark Peony Root
胡永顺，张宝霞.白芍总苷对寻常型银屑病的治疗作用观察[J].中医药临床杂志,2013,25(2):148-150
翟乾勋.白芍总苷致男性乳腺增生一例[J].山西医药杂志，2005，34（8）
唐宗忠，陈燕等.白芍总苷胶囊致疱疹一例[J].中药新药与临床药理，
CHEN Ji-hong， LAO Zhi-ying，et al.Effects of two different doses of total glucosides of paeony with rheumatoid arthritis in 150 patients[J]Chin J New Drugs Clin Rem.2011,30(10):771-774
白芍总苷治疗强直性脊柱炎的疗效及其机制探讨[J].中药药理与临床，2009,25(3):68-70
Paeoniae Radix Alba
白芍
slightly bitter(TCD)
微苦（中药）
Slightly Warm(TCD)
微温（中药）
Extremely Hot(TCD)
大热
Yin chengxia. Literature analysis of 55 cases of adverse drug reaction by G lucoside tripterygium total[J]. Chinese Journal of Pharmacovigilance,2013,10(8):478-482
Gao yuping ,Chen defu. Clinical study on effect of Tripterygium wilfordii hook.f.on uterin leiomyoma[J] Chin J Obstet Gynecol,2000,35(7):430-432
Liu xumei,Liu zhihong, et al.Study progress on clinical application and side effects of Tripterygium wilfordii[J] Journal of pharmaceutical practice,2015,33(2):110-113
唐永,张霞.雷公藤在皮肤科应用中的不良反应 (附 163 例临床分析 )[J]临床皮肤科杂志,1998,27(6):377
柯坤字.雷公藤多苷片引起肝损害一例报告[J]实用临床医学杂志社,2009,10(7):40-42
Tripterygii Radix et Rhizoma
张世应.雷公藤的毒性研究[J]Hubei Journal of TCM,2015,37(3):71-73
邱颖文 ,吴松武.雷公藤多苷的不良反应［Ｊ］西北药学杂志,2004,19(5):220-222
徐国荣.雷公藤的临床应用与毒性反应及中毒解救[J]黑龙江中医药,2004,(3):50-51
马哲,梁茂新.中药雷公藤化学成分及药理作用研究进展,亚太传统医药,2011,7(3):157-160
邹爱英,刘秀书.雷公藤多苷片的不良反应及防治对策[J].天津药学,2008,20(1):25-26
文纪纯.雷公藤中毒致严重骨髓抑制6 例[J].海峡药学,1995,7(11):152 .
刘雪梅,刘志宏等.雷公藤临床应用及不良反应的研究进展[J] Jorunal of pharmaceutical practic,2015,33(2):110-113
贾春伶.雷公藤不良反应的文献调查与分析[J].北京中医,2006,25(1):45-48
Common Threewingnut Root
范兴忠, 陈勇, 李新东.雷公藤在免疫性疾病治疗中副作用的观察[ J] .中国中西医结合肾病杂志, 2001 , 2(2):83-85
谢宝官,钟文.雷公藤多甙片副作用的临床观察[J].Guang x i M edical Journal,2002,24(4):576-579
张立放,杨淑清.雷公藤的不良反应[J].Journal of Mathematical Medicine,2003,16(5):442-443
张青.雷公藤治疗肾炎引起类白血病反应1 例报告[J].青海医药杂志,1997,10:60
万同己.雷公藤的不良反应[J]Practical Clinical Medicine,2005,6(6):149-150
Yu dihua,He dong-chu. Research progress on the toxicity of Tripterygium wilfordii and attenuated synergistic approaches[J].Medical recapitulate,2015,21(3):502-504
刘为萍,刘素香.雷公藤研究新进展[J]Chinese Traditional and Herbal Drugs,2010,41(7):1215-1218
高丽,白赟.雷公藤毒性反应研究进展[J].Chinese Journal of Information on TCM,2012,19(4):107-110
许杰州,黄少弼.雷公藤多贰的副作用12例报告[J]汕头大学医学院学报,1996(2):36-37
潘贵光,高文平.雷公藤多苷片致过敏反应１例[J].药物不良反应与相互作用,2003,21(1):52
雷公藤
舒尚义. 口服昆明山海棠引起经闭42 例临床观察[J].昆明医学院学报,1980,(3):38-42.
王金平,李红星等.火把花根的化学成分和临床应用及不良反应综述[J]重庆中草药研究,2011,(63):41-44
Tripterygii Hypoglauci Radix
Zhong, J., Xian, D., Xu, Y. & Liu, J. Efficacy of Tripterygium hypoglaucum Hutch in adults with chronic urticaria. Journal of alternative and complementary medicine 17, 459-464 (2011)
昆明山海棠
李顺英,张超等.昆明山海棠的临床应用[J]中国民族民间医药杂志,2006,(83):325-330
徐棠本. 服昆明山海棠片出现过敏反应1 例[ J] . 中国中药杂志,1996, 21( 12): 755.
谢晨琼，周 萍昆明山海棠化学成分及药理作用和临床应用研究进展
Faeces Bombycis
蚕沙
Silk-worm Droppings
Fourstamen Stephania Root
Stephaniae Tetrandrae Radix
为防己科多年生木质藤本植物粉防己或马兜铃科多年生缠绕草本植物广防己的根，具有祛风湿、止痛、利水的功效，临床用于治疗风湿痹痛、水肿、腹水、脚气浮肿。
张晓红.粉防己与广防己的鉴别及临床应用研究.中医当代医药,2015,22(24):111-113
粉防己
宋敬丽, 袁林.海风藤化学成分和药理作用的研究进展.湖北中医学院学报,2007,9(3):70-72
Kadsura Pepper Stem
Piperis Kadsurae Caulis
海风藤
李超英,张大方,刘力.虎骨的本草学与现代研究,长春中医学院学报,1994,10(5):81-82
Tiger Bone
Os Panthera Tigris
为猫科动物虎的骨胳，具有追风定痛、健骨镇惊的功效，临床用于治疗历节风痛、四肢拘挛、腰脚不随、惊悸癫痫、痔瘘脱肛等。
虎骨
Chinese Starjasmine Stem TCD
Trachlospermi Caulis et Folium
西部三省,韩英梅.络石藤化成分及其抗癌活性.国外医药植物药分册,2002,17(2):57-58
谭兴起,郭良君,陈海生.络石藤中黄酮类化学成分研究,中药材,2010,33(1):58-60
络石藤
Slightly Cold（TCD）
微寒（中药）
何义富,魏伟,金娟,常艳,张玲玲,唐丽琴,陈尹.木瓜苷和儿茶素抗类风湿关节炎作用研究进展.[A];中医药理论与应用研究——安徽中医药继承与创新博士科技论坛论文集.[C];2008年
Common Floweringqince Fruit
Chaenomelis Fructus
木瓜
林萍,易宏伟,张斐.金丝桃苷药理作用研究进展[J]中国现代中药.2012(14).23-26
Lignum Pini Nodi
松节
高 阳,孙凡森,苏娅萍.华山松松节的化学成分及黄嘌呤氧化酶抑制活性研究.西北药学杂志,2013,28(6):559-562
Chinese Pine Nodular Branch
Aristolochiae Mollissimae Herba
寻骨风
Wooly Datchmanspipe Herb
Sunruihua,Linzongguang.Observation of the Therapeutic Effect of“True Wind_Pain Eliminator”in Treating 38 Cases of Rheumatoid Arthritis[J]. Shanghai jorunal of traditional Chinese medicine,1999,33(2): 21-23
余建强, 黄宇明.正清风痛宁治疗风湿病 695 例临床总结[J].Hunan journal of traditional Chinese medicine,1998,10(2):18-20
Hu Yonghong, Lai Xianyang. Therapeutic effects and side effects of Zhengqingfengtongning in the Treatment of Osteoarthritis[J].Zhongguo Kang fu, 2001,16(2):85-88
青风藤
顾越英,陈顺乐等. 正清风痛宁治疗类风湿性关节炎临床疗效及安全性的观察[A]. 中国中西医结合学会.第四届全国中西医结合风湿类疾病学术会议论文汇编[C] 2000:11-19
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Wu Juan, Li Yan-hong. The Side Effects and Prevention of Drug Treatment byZhengqingfengtongning[J].Chinese Journal of Medicinal Guide,2012,14(2):250-252
Cheng zongq i,Miao liyan. Literatrue analysisi of ADR of Zhengqingfengtongning[J].Anti-infection pharmacy,2007,4(4):184-186
李宏.服正清风痛宁片引起月经紊乱 2 例[J].China Journal of Chinese Materia Medica, 2002,27(4)：314-315
Ge hongxing, Li qing, et al. 正清风痛宁的不良反应与合理用药建议[J] Chinese Traditional Patent Medicine.2010,32(2):287-289
Ovientvine Stem
陈忠德.正清风痛宁和复方双氯芬酸钠治疗类风湿性关节炎 60例[J].医药导报,1999,18(5):309
刘丙欣 ,吴士云.正清风痛宁肠清片致自身免疫性溶血性贫血[J]齐鲁药事，2010，29（12）：750-751
Sinomenii Caulis
曹吉慧,赵桂森,冯延江.青风藤的化学成分与药理作用,国外医药· 植物药分册,2008,23(2):62-66
Xiao wenxing, Shi ruhai, et al. Acute hematopoietic disorder caused by Zhengqingfengtongning[J]. Adverse Drug Reactions Journal,2006,8(1):62
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)
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]
the clusters of hormone-producing cells that are scattered throughout the pancreas
(...) 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]
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)
lateral part of the basal amygdalar nucleus
nucleus amygdalae basalis, pars lateralis
nucleus amygdaloideus basalis, pars lateralis magnocellularis
pars peripherica; systema nervosum periphericum
(...) 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]
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
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
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.
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]
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 part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
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]
create a separate class for distributed pancreas, eg cyclostomes?
endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
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]
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].
A cavitated compound organ that transduces light waves into neural signals.[TAO]
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
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
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]
camera-type eye plus associated structures
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)
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].
Major subdivision of an organism that protrudes from the body[DOS, CARO].
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
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]
The head is the anterior-most division of the body [GO].
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
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.
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
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
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.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [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]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
A tubular structure that transports secreted or excreted substances.
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
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
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 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
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A stage that is part of the embryo stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
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.
(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
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)
A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]
The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
stage succeeding embryo, including mature structure
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]
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
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]
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.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
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.
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.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
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.
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
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
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]
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]
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
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
hindgut endoderm and proctodeal ectoderm.
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.
In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females
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]
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).
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
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
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 complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
A fluid that is composed of blood plasma and erythrocytes.
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[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]
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
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
The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
The upper ventral region of an animal's torso.
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.
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.
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
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
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.
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
Anatomical system that consists of the muscles of the body.[VSAO]
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
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
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
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]
The organs and associated structures associated with bearing offspring in a female animal.
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.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
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]
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
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]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium that consists of a single layer of epithelial cells.[CARO]
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
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.
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]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
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.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
The middle germ layer of the embryo, between the endoderm and ectoderm.
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 alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
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.
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.
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
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
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 an ectodermal terminal part of the digestive tract.
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
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.
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]
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
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
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
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]
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]
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)" http://dx.doi.org/10.1101/gad.1485706
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
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]
(...) 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]
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 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].
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)
requires review for applicability to invertebrate structures, e.g. synganglion
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
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
The lens is avascular and nourished by diffusion from the aqueous and vitreous
This class excludes compound eye corneal lenses.
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
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
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]
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.
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,
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)
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster that consists of two or more adjacent skeletal structures, 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]
Anatomical system that has as its parts the organs concerned with reproduction.
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]
consider splitting genitalia from reproductive system
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
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]
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
(...) 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]
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
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
the gonad of a female organism which contains germ cells
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
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
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
tubular parts of female reproductive system
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.
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]
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]
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
(...) 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]
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]
The outer epithelial layer of the skin that is superficial to the dermis.
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).
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
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]
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
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
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
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
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..
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
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]
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
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]
Connective tissue in which fat is stored.[TAO]
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.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
in FMA this is dense irregular connective tissue
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
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.
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]
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].
(...) 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]
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).
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.
A portion of tissue which is a fasiculated group of axons.[TAO]
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.
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]
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
The sensory system for the sense of taste.
The sensory system for the sense of taste[NIFSTD:nlx_anat_090803].
The sensory system used for the sense of taste.[AAO]
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
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]
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
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 FMA this represents an embryonic region.
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 caudalmost subdivision of a digestive tract.
in FMA this class has no children. In MA it has a single child hindgut epithelium
the caudal portion of the primitive digestive tube of the embryo
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
(...) 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]
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
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].
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][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
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
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
Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
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].
This class was created automatically from a combination of ontologies
Portion of the liver which develops on the fish's left side.[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].
Muscle tissue that consists primarily of skeletal muscle fibers.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
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]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
(...) 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]
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
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.
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
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].
textus muscularis levis; textus muscularis nonstriatus
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ 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
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]
the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct
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
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]
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]
We follow Kardong in defining stomach regions by glands
the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum
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].
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]
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]
the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct
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]
Artery that supplies blood to the liver.[TAO]
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 mucosal layer that lines the stomach.
(...) 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 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].
A mucosa that is part of a small intestine [Automatically generated definition].
A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP].
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)
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
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.
A saccular organ in which urine accumulates before discharge from the body. [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]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
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 enzymes[GO].
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)
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
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
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
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]
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 pectoral 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
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
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]
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 tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule
The anus and surrounding regions. Encompasses both internal and external regions, where present
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.
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
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
System that provides physical support to the organism.[AAO]
FMA:24216 present in FMA1, but gone in subsequent versions
Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax 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; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].
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)
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.
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]
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
A tube extending from the mouth to the anus.
FMA also has a term 'gastrointestinal tract', but this includes the liver.
The alimentary or digestive tract, and associated organs.[TAO]
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
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
Subdivision of urinary system which consists of the urinary bladder and the urethra.
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].
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]
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]
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]
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
TODO - check with MA - vein vs venous blood vessel
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
A primate's nail consists of the unguis alone; the subunguis has disappeared
The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane
FMA divides this into skin, fascia, conjunctiva
In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
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 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 adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
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
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]
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Disease notes: implicated in rheumatoid arthritis.
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].
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709].
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]
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
MP treats posterior uvea and optic choroid as distinct
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
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].
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
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)
In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]
Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]
The most anterior region the brain including both the telencephalon and diencephalon.
The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain neural tube (TAO:0007041)[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]
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]
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
part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]
In mammals the cortex covers almost the whole of the cerebral hemispheres.
In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.
In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum.
In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.
Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000].
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]
The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]
The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure.
dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.
relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]
Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965].
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
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].
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]
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]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). 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
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]
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. 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].
The liquid component of blood, in which erythrocytes are suspended.
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
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.
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[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, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
A vessel through which blood circulates in the body.
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]
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
annelids have blood vessels, but this class is not applicable to annelids.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the smallest blood vessels connecting arterioles with venules.
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
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Excretion in semisolid state processed by the intestine.[FMA]
Portion of semisolid bodily waste discharged through the anus[MW,modified]
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]
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]
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].
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
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]
However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]
The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]
almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
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]
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]
Consider adding a layer-of-skin grouping class for all skin layers
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].
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]
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.
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].
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
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.
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
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]
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 post-cranial 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].
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
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]
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
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.
MA uses the term skin to refer to what is called here: zone of skin
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
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 cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
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]
Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]
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]
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 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].
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).
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.
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
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.
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
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].
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]
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]
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)
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]
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
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.
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]
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
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]
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.
Vasculature that is part of a head [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]
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]
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]
In many species, the diaphragm separates thoracic and abdominal cavities
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
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)
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
TODO - add superclass to unify with VNC?
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).
'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 (ISBN10:0471888893). 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).
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].
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].
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]
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
In mammals it forms the peritoneal, pleural, and pericardial cavities
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.
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].
check the FMA placement here; ncit placement of body cavity here probably not correct
(...) 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]
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]
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.
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]
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]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[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]
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
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.
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]
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]
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
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]
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].
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]
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].
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]
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.
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
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]
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
Embryonic ectoderm that gives rise to nervous tissue.
epithelium tubi neuralis; neuroectoderma
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
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].
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
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
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
the soft tissue that fills the cavities of bones
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.
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 consists of the blood and blood forming tissues.[AAO]
Anatomical system that is involved in the production of hematopoietic cells.
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
(...) 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]
A duct that carries bile from the liver to the intestine.
Any of the ducts that form the biliary tree, carrying bile from the liver to the small 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
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]
(...) 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]
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.
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]
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]
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]
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]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
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]
The part of the digestive system that contains the liver and the biliary system
A bone that is part of a limb [Automatically generated definition].
NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle
the formal definition is very inclusive, and includes sesamoids
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]
Naming conventions for pod terms under discussion within phenoscape group
The proximal free limb segment. Includes as parts the stylopod skeleton.
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.
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]
see https://github.com/obophenotype/uberon/issues/27
Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition
an organ that functions as a secretory or excretory organ
An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Embryonic surface structure that develops into a paired fin.[ZFA]
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]
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]
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
Fin that is one of a pair located ventrally on the organism.
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
digit (phalangeal portion) plus soft tissue
this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion
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
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.
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. Do not merge.
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.
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.
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
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
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.
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 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]
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
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]
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]
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, http://www.ncbi.nlm.nih.gov/pubmed/15647339, XAO:0000063, ZFA:0000150]
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].
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
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]
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]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
(...)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]
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
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').
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]
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.
(...) 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]
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. (...) 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]
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
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)
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
Consider adding subclasses for male and female specific variants
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
TODO - mesonephric portion of the nephric duct
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]
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]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
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)
TODO - add grouping class for the anterior end of the neural tube at all stages
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]
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
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].
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 transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
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]
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
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]
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.
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]
should probably be merged with heart rudiment.
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
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].
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]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[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.
Gonochoristic organism that can produce female gametes.
Gonochoristic organism that can produce male 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
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]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
GO uses genitalia for the singular organ
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]
one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three
A gland that is part of a foregut [Automatically generated definition].
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
A layer of epithelial cells on the surface of the mucosa.
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
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
A gland that is part of a digestive tract [Automatically generated definition].
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A long bone that is part of a limb [Automatically generated definition].
Any joint that is part of a (free) limb.
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
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
Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]
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
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
A limb joint that is part of an autopod [Automatically generated definition].
joint of limb of distal free limb segment
An anatomical space that surrounded_by a neural tube.
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a telencephalon.
Cranial neural crest that is part of the telencephalon.[TAO]
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]
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
(...) 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]
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
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
(...) 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]
The part of the retina that contains neurons and photoreceptor cells[GO].
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
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
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].
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]
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
pancreatic bud that gives rise to the accessory pancreatic duct.
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
pancreatic bud that gives rise to the major pancreatic duct.
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 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'.
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]
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
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)
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]
The layer of undifferentiated, proliferating cells that line the neural tube lumen
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 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 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
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
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]
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]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
(...) 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 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].
(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]
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
The first recognizable structure derived from the heart field
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.
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
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]
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].
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
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
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 external genitalia are the outer sex organs, such as the penis or vulva in mammals
A portions of the gut that is derived from endoderm.
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]
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]
The bilaminar epithelium formed from the myotome and dermatome.
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]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
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]
In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.
A phalanx located between proximal and distal phalanges.
Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin
consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
in some groups such as whales, there are multiple intermediate phalanges
Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]
VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
primitive streak - blastopore - germ ring
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Early outgrowth of presumptive limb.[AAO]
developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
The embryonic structure that gives rise to the corneal ectoderm
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]
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
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.
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
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].
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]
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]
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
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
EHDAA2 considers hip and shoulder joints part of limb skeleton.
Skeletal subdivision that is part of the limb.[VSAO]
The collection of all skeletal elements in an individual limb.
Sum of all sensory systems in an organism.
A projection or outgrowth of tissue from a larger body or organ.
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
Anatomical system that has as its parts the heart and blood vessels.
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]
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
A vascular network consisting of blood vessels.
The part of the cardiovascular system consisting of all arteries.
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.
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]
the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein
An appendage that is part of a appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
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
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].
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
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]
Anatomical system that consists of all the joints of the body.
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
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
the cellular avascular layer of the kidney luminar surfaces
splanchnic layer of lateral plate mesoderm
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
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
A portion of the urogenital ridge which is the source of much of the urinary system[WP].
part_of or develops_from urogenital ridge?
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
The central region of trunk mesoderm. This tissue forms the notochord
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body 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.
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.
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
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].
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].
One of the two elevated edges of the neural groove[GO,MP].
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]
The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].
The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
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.
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous.
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
class added for consistency with GO - consider merging with kidney mesenchyme.
An epithelium that is part of a mesonephros [Automatically generated definition].
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
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.'
A duct that carries bile from the liver to the small intestine.[TAO]
A duct that carries bile from the liver to the small intestine[ZFA].
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
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.
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]
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.
Mesenchyme that is part of a developing trunk.
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 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 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.
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
alimentary part of 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]
The part of the digestive system that excludes the hepatobiliary system.
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
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.
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
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
Portion of tissue that gives rise to the lens.
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.
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Portion of tissue that gives rise to the immature gonad.
A mesoderm that has the potential to develop into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud.
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
limb/fin field of lateral plate mesoderm
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.
A ring of cells capable of forming a limb.
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
A 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.
Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
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].
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 closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
encompasses digits and prepollex. requires review
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]
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
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]
The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]
dorsal part of alar plate of metencephalon
the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
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]
An anatomical junctions that overlaps the foregut and midgut.
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A presumptive structure that has the potential to develop into a forebrain.
TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
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.
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.
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.
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 tube in the kidney that collect and transport urine.
in ZFA this is defined as part of mesonephros
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.
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 joint that connects one phalanx to another along a proximodistal axis.
Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint].
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)
Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]
The collection of all skeletal elements in an autopodium region.
An epithelium that is composed primarily of secretory cells.
consider splitting epithelium from epithelial tissue
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.
An anatomical space that surrounded_by a digestive tract.
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
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.
A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
stomach glandular region glandular mucous membrane
stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
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 two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
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
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]
mesenchyme derived from head neural crest
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
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].
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.
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]
A presumptive structure that has the potential to develop into a paraxial mesoderm.
A presumptive structure that has the potential to develop into a pronephric mesoderm.
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 is part of the pancreas and connected to the duodenum.
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
this class groups together accessory (dorsal) and main (ventral) pancreatic ducts
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.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[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.
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]
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
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.
An anatomical structure that connects two structures
region of the embryo into the area in which the kidney rudiment will develop.
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.
the FMA def is Transudate contained in a serous sac
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
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.
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]
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]
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
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.
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]
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
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)
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.
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 mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
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].
An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO].
Surface structure involved in locomotion.[TAO]
Surface structure involved in locomotion.[VSAO]
This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean
An organ part that is part of a stomach.
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]
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A nephric duct is a tube that drains a primitive kidney[GO].
An epithelium that is part of a foregut-midgut junction.
An endoderm that is part of a foregut-midgut junction.
A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).
Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults
midbrain hindbrain boundary neural plate
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx.
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
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
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region
Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
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)
An anatomical structure that has more than one cell as a part.
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
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 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.
The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw)
The core globe-shaped component of the camera-type eye.
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
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.
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
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
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 vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
An appendage segment that is part of a limb/fin.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
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]
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 pelvic appendage and the pelvic girdle.[VSAO]
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
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
Skeletal subdivision that is a segment of the limb skeleton.
note the distinction between this and skeleton of limb
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO]
The collection of all skeletal elements in a single paired fin.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
The subdivision of the skeleton of either the pectoral or pelvic girdle.
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).
subdivision of organism along appendicular axis
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
A skeletal element that is part of a limb and composed of cartilage tissue.
A skeletal element that is part of a limb and composed of pre-cartilage tissue.
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]
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 post-cranial axial skeleton plus associated joints.
Any synovial joint that is part of a (free) limb.
Subdivision of urinary system which consists of the kidney and the ureters.
A sphincter muscle that is part of the gastrointestinal system
central nervous system cell part cluster
A multi cell part structure that is part of a central nervous system.
Muscles within the eye (bulbus oculi).[AAO]
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
The collection of all skeletal elements in an individual limb or fin.
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]
Section of the forelimb skeleton located between the stylopodium and the autopodium.
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
subdivision of organism along main body axis
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
A cardiovascular system that is part of a conceptus.
Ectodermal placode that does not develop into a component of the nervous system.
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)
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
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.
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
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
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
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 aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
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 the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
Skeletal subdivision consisting of all the skeletal elements in a single fin.
The segment of the autopod that is distal to the metapodial region and consists of the digits.
class refers to an entire limb segment, not just the bones
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue
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.
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 secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week
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
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
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.
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].
The region of the organism associated with the visceral organs.
Anatomical projection that is part of the integumentl system.
A 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.
Embryonic structure that gives rise to the telencephalon.
paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP]
Mesenchyme that develops_from the neural crest[Automatically generated definition].
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 duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
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 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.
A phalanx bone or its cartilage or pre-cartilage precursor.
A limb bone or its cartilage or pre-cartilage precursor.
A endochondral element that is part of a autopod region.
A autopod endochondral element that is composed primarily of a cartilage tissue.
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 epithelium that is part of a camera-type eye.
An roughly circular indentation in a surface.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
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.
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
The part of the eye that consists of both the retina and the optic choroid
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
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.
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
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.
organ region with floating fiat boundary
The primordial mouth region of the developing head.
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
A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit ( phalanges plus metapodial) plus soft tissue
this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.
individual digit of digitopodial skeleton
A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.
this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Alan Ruttenberg
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.
axiom holds for all times