An ontology of core ecological entities
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.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO:0000112
uberon
example_of_usage
true
example_of_usage
example of usage
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
has curation status
definition
definition
textual definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
true
curator_notes
curator note
curator note
curator notes
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
IAO:0000233
external
term_tracker_item
true
true
term_tracker_item
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
term tracker item
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
imported from
expand expression to
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand expression to
expand expression to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
has axiom label
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
term replaced by
term replaced by
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.
temporal interpretation
temporal interpretation
https://github.com/oborel/obo-relations/wiki/ROAndTime
tooth SubClassOf 'never in taxon' value 'Aves'
S never_in_taxon T iff: S SubClassOf in_taxon only not T
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
?X DisjointWith RO_0002162 some ?Y
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
RO:0002161
uberon
never_in_taxon
true
true
never_in_taxon
never in taxon
never_in_taxon
S never_in_taxon T iff: S SubClassOf in_taxon only not T
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
https://orcid.org/0000-0002-6601-2165
RO:0002174
uberon
dubious_for_taxon
true
true
dubious_for_taxon
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
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
dubious for taxon
dubious_for_taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
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
https://orcid.org/0000-0002-6601-2165
RO:0002175
applicable for taxon
uberon
present_in_taxon
true
true
present_in_taxon
present in taxon
present_in_taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
defined by inverse
logical macro assertion on an annotation property
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
is asymmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
is symmetric relational form of process class
https://github.com/oborel/obo-relations/wiki/InteractionRelations
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
Chris Mungall
is direct form of
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
RO:0002604
quality
is_opposite_of
true
true
is_opposite_of
is opposite of
is_opposite_of
cjm
2018-03-14T00:03:16Z
is positive form of
cjm
2018-03-14T00:03:24Z
is negative form of
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
cjm
2018-10-21T19:46:34Z
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
is homeomorphic for
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.
UBPROP:0000001
uberon
external_definition
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
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.
A textual description of an axiom loss in this ontology compared to an external ontology.
UBPROP:0000002
uberon
axiom_lost_from_external_ontology
true
axiom_lost_from_external_ontology
This annotation property may be replaced with an annotation property from an external ontology such as IAO
axiom_lost_from_external_ontology
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
true
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
Notes on the homology status of this class.
UBPROP:0000006
uberon
implements_design_pattern
true
implements_design_pattern
implements_design_pattern
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'.
UBPROP:0000007
uberon
has_relational_adjective
true
has_relational_adjective
has_relational_adjective
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
true
taxon_notes
taxon_notes
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000009
uberon
function_notes
true
function_notes
function_notes
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000010
uberon
structure_notes
true
structure_notes
structure_notes
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000011
uberon
development_notes
true
development_notes
development_notes
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
true
external_ontology_notes
external_ontology_notes
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.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000013
uberon
terminology_notes
true
terminology_notes
terminology_notes
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
UBPROP:0000100
uberon
is_count_of
true
is_count_of
is count of
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)
UBPROP:0000101
uberon
preceding_element_is
true
preceding_element_is
preceding element is
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)
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
gill arch N = PA N-2. the term branchial_arch is ambiguous.
UBPROP:0000103
uberon
pharyngeal_arch_number
true
pharyngeal_arch_number
pharyngeal arch number
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
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
UBPROP:0000202
uberon
fma_set_term
true
fma_set_term
fma_set_term
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
FMA
IUPAC NAME
Preliminary entries
Manually annotated by ChEBI Team
EnvO-Lite-GSC
Term not to be used for direct annotation
Term not to be used for direct manual annotation
AGR slim
Aspergillus GO slim
Candida GO slim
ChEMBL protein targets summary
Drosophila GO slim
FlyBase Drosophila GO ribbon slim
Generic GO slim
Metagenomics GO slim
Mouse GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
Yeast GO slim
Systematic synonym
Abnormal/normal slim
Attribute slim
cell_quality
Disposition slim
Pathology slim
Relational slim: types of quality that require an additional entity in order to exist
Scalar slim
Value slim
Term for angiosperms
Term used for Arabidopsis
plant cells
Term used for citrus
German synonym (exact)
Term used for gymnosperms
Japanese synonym (exact)
Term used for maize
Terms used for banana
Plural
Term used for grasses
Term used for potato
Term used for rice
Spanish synonym (exact)
Term used for tomato
Plant Functional Traits
reference plant structure term
eco subset
abbreviation
A historic synonym, no longer encouraged
dubious or contested synonym
indicates that a synonym is used in an inconsistent or confusing way, typically between species
latin term
expert consultation and attribution required
plural term
taxonomic disambiguation
CUMBO
developmental_classification
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
EFO slim
derived from the union of EHDAA2 and EMAPA - still to be checked
functional_classification
Subset consisting of classes creating for grouping purposes
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
Phenotype slim
A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA
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
uberon
dc-contributor
true
dc-contributor
contributor
uberon
dc-creator
true
dc-creator
creator
uberon
dc-source
true
dc-source
derived from resource
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
shorthand
label
label
uberon
depicted_by
true
depicted_by
depicted by
uberon
foaf-page
true
foaf-page
page
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
plant_ontology
quality
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
chebi_ontology
external
plant_ontology
quality
uberon
has_part
false
has_part
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
has part
has part
has_part
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
PATOC:CJM
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
BFO:0000056
uberon
participates_in
participates_in
participates in
preceded by
The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
Laurel_Cooper
2013-07-09T14:29:15Z
BFO:0000062
is preceded by
takes place after
plant_ontology
uberon
preceded_by
preceded_by
Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
preceded by
preceded_by
The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.
POC:Laurel_Cooper
is preceded by
SIO:000249
takes place after
Allen:precedes
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.
Laurel_Cooper
2015-06-04T17:18:40Z
BFO:0000063
plant_ontology
uberon
precedes
precedes
precedes
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
BFO:0000066
external
occurs_in
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
occurs in
occurs in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
BFO:0000067
uberon
contains_process
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
contains process
contains process
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
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 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).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
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.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior_to
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 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).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
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.
BSPO:0000107
uberon
deep_to
deep_to
deep_to
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.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:PATO_mtg_2009
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:PATO_mtg_2009
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in_posterior_side_of
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:PATO_mtg_2009
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in_anterior_side_of
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:PATO_mtg_2009
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
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
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
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
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x
Definition modified from 'surrounded by'.
partially_surrounded_by
obsolete determined by
true
obsolete determined by part of
true
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
uberon
bearer_of
bearer_of
bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
plant_ontology
participates_in
participates_in
participates in
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
plant_ontology
has_participant
has_participant
has participant
has_participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
RO:0000086
uberon
has_quality
has_quality
has quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
chebi_ontology
has_role
false
false
has_role
has role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
RO:0001015
uberon
location_of
location_of
location of
location_of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
RO:0001019
uberon
contains
contains
contains
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
rwalls
2012-05-23T09:52:02Z
RO:0001025
plant_ontology
uberon
located_in
located_in
located in
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
RO:0002000
uberon
boundary_of
boundary_of
2D boundary of
boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
David Osumi-Sutherland
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
David Osumi-Sutherland
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
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.
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
bounding layer of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
dos
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
dos
2017-07-19T17:30:36Z
has ligand
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
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].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
A overlaps B if they share some part in common.
x overlaps y if and only if there exists some z such that x has part z and z part of y
BFO_0000051 some (BFO_0000050 some ?Y)
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
uberon
overlaps
overlaps
overlaps
overlaps
true
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous_with
FMA:85972
lactation SubClassOf 'only in taxon' some 'Mammalia'
S only_in_taxon T iff: S SubClassOf in_taxon only T
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
plant_ontology
uberon
only_in_taxon
only_in_taxon
only in taxon
only_in_taxon
S only_in_taxon T iff: S SubClassOf in_taxon only T
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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.
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
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)
RO:0002176
uberon
connects
connects
connects
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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.
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attaches_to_part_of
true
true
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
supplies
arterial supply of
FMA:86003
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
uberon
has_component
has_component
has component
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
plant_ontology
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops_from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
develops_into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
RO:0002207
uberon
directly_develops_from
directly_develops_from
TODO - add child relations from DOS
directly develops from
directly_develops_from
inverse of directly develops from
developmental precursor of
directly develops into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
regulates (processual)
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO_0000053 some (RO_0000054 only ?Y)
RO:0002215
uberon
capable_of
capable_of
capable of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
RO:0002216
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
Obsoleted as the inverse property was obsoleted.
actively participates in
obsolete actively participates in
true
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Chris Mungall
has agent
obsolete has active participant
true
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded by
surrounded_by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
plant_ontology
uberon
adjacent_to
adjacent_to
adjacent to
adjacent_to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
inverse of surrounded_by
Chris Mungall
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
inverse of surrounded_by
Chris Mungall
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
RO:0002224
uberon
starts_with
starts_with
starts with
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
Chris Mungall
RO:0002225
uberon
develops_from_part_of
develops_from_part_of
develops from part of
develops_from_part_of
x develops_in y if x is located in y whilst x is developing
Chris Mungall
EHDAA2
Jonathan Bard, EHDAA2
RO:0002226
uberon
develops_in
develops_in
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
develops_in
Relation between occurrents, shares an end boundary with.
inverse of ends with
Chris Mungall
RO:0002229
finishes
uberon
ends
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
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.
Chris Mungall
finished by
RO:0002230
uberon
ends_with
ends_with
ends with
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
Chris Mungall
starts with process that occurs in
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
Chris Mungall
ends with process that occurs in
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
developmentally_contributes_to
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.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
developmentally_induced_by
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.
GO:0001759
Inverse of developmentally induced by
Chris Mungall
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
X developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p.
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
Laurel_Cooper
2013-06-27T13:16:56Z
RO:0002258
plant_ontology
uberon
developmentally_preceded_by
developmentally_preceded_by
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
developmentally preceded by
developmentally_preceded_by
X developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p.
RO:0002258
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
Chris Mungall
replaces
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally_replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
Chris Mungall
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
Chris Mungall
results_in_developmental_progression_of
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
Chris Mungall
GOC:mtg_berkeley_2013
results_in_formation_of
results in formation of
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'
where
'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
Pier Buttigieg
adapted for living in
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
has habitat
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
true
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say
if and only if
exists c', p'
c part_of c' and c' capable_of p
and
c capable_of p' and p' part_of p
then
c contributes_to p
However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
Chris Mungall
http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
part of structure that is capable of
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
RO:0002350
uberon
member_of
member_of
member of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
uberon
output_of
output_of
output of
output of
Chris Mungall
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
Chris Mungall
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_to
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary of
tributary_of
http://en.wikipedia.org/wiki/Tributary
drains into
dbpowl:drainsTo
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
Chris Mungall
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
branching_part_of
FMA:85994
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
Chris Mungall
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
RO:0002388
uberon
has_potential_to_directly_develop_into
has_potential_to_directly_develop_into
has potential to directly develop into
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Chris Mungall
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
Chris Mungall
interacts with on organism level
biotically interacts with
http://eol.org/schema/terms/interactsWith
An interaction relationship in which the partners are related via a feeding relationship.
Chris Mungall
trophically interacts with
A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
Baleen whale preys on krill
An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
Chris Mungall
Jorrit Poelen
Katja Shulz
is subject of predation interaction with
preys upon
preys on
http://eol.org/schema/terms/preysUpon
http://www.inaturalist.org/observations/2942824
A biotic interaction in which the two organisms live together in more or less intimate association.
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/19278549
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
symbiotically interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
Chris Mungall
http://www.ncbi.nlm.nih.gov/pubmed/19278549
This relation groups a pair of inverse relations, parasite of and parasitized by
interacts with via parasite-host interaction
Pediculus humanus capitis parasite of human
Chris Mungall
parasitizes
direct parasite of
parasite of
http://eol.org/schema/terms/parasitizes
Chris Mungall
has parasite
parasitised by
directly parasitized by
parasitized by
http://eol.org/schema/terms/hasParasite
Porifiera attaches to substrate
A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
Chris Mungall
semibiotically interacts with
participates in a abiotic-biotic interaction with
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
activity directly regulates activity of
directly regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
inhibits
molecularly decreases activity of
activity directly negatively regulates activity of
directly negatively regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
activates
directly activates
molecularly increases activity of
activity directly positively regulates activity of
directly positively regulates activity of
Chris Mungall
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
host of
Chris Mungall
has host
http://eol.org/schema/terms/hasHost
Chris Mungall
Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
acquires nutrients from
inverse of preys on
Chris Mungall
has predator
is target of predation interaction with
preyed upon by
http://eol.org/schema/terms/HasPredator
http://polytraits.lifewatchgreece.eu/terms/PRED
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
Chris Mungall
is symbiosis
Chris Mungall
is commensalism
Chris Mungall
is mutualism
Chris Mungall
is parasitism
Chris Mungall
provides nutrients for
Chris Mungall
is subject of eating interaction with
eats
Chris Mungall
eaten by
is target of eating interaction with
is eaten by
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
Chris Mungall
RO:0002473
uberon
RO:0002473
composed_primarily_of
composed_primarily_of
composed primarily of
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
relation between structure and stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
Chris Mungall
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence_starts_during
existence_starts_during
existence starts during
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.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
Chris Mungall
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
Chris Mungall
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence overlaps
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Chris Mungall
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
existence_ends_during
existence_ends_during
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during
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.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
Chris Mungall
RO:0002493
uberon
existence_ends_with
existence_ends_with
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
Chris Mungall
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
Chris Mungall
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
immediately transforms from
SIO:000658
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
Chris Mungall
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
causal relation between material entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
determined by
inverse of determined by
Chris Mungall
determines (material entity to system)
determines
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Chris Mungall
determined by part of
true
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
Chris Mungall
has supporting framework
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
Chris Mungall
results in ending of
x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
Chris Mungall
http://eol.org/schema/terms/hyperparasitoidOf
https://en.wikipedia.org/wiki/Hyperparasite
epiparasite of
hyperparasitoid of
hyperparasite of
inverse of hyperparasite of
Chris Mungall
has epiparasite
has hyperparasite
hyperparasitoidized by
hyperparasitized by
Chris Mungall
causally influenced by (entity-centric)
causally influenced by (material entity to material entity)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences (material entity to material entity)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
inverse of branching part of
Chris Mungall
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
Chris Mungall
GOC:cjm
RO:0002571
uberon
lumen_of
lumen_of
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
has modifier
Chris Mungall
participates in a biotic-biotic interaction with
inverse of has skeleton
Chris Mungall
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
obsolete related via dependence to
true
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
lives inside of
endoparasite of
has endoparasite
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
RO:0003000
uberon
produces
produces
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
RO:0003001
uberon
produced_by
produced_by
produced by
produced_by
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
cjm
2017-12-26T19:45:49Z
realized in response to stimulus
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
muffin 'has substance added' some 'baking soda'
"has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
Damion Dooley
has substance added
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
triggered by process
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
triggered by process
RO:cjm
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
p has anatomical participant c iff p has participant c, and c is an anatomical entity
cjm
2018-09-26T01:08:58Z
has anatomical participant
chebi_ontology
has_functional_parent
false
false
has functional parent
chebi_ontology
is_conjugate_acid_of
true
false
is conjugate acid of
chebi_ontology
is_conjugate_base_of
true
false
is conjugate base of
chebi_ontology
is_substituent_group_from
false
false
is substituent group from
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
decreased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
decreased_in_magnitude_relative_to
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
different_in_magnitude_relative_to
different_in_magnitude_relative_to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
uberon
anteriorly_connected_to
anteriorly connected to
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
uberon
existence_starts_and_ends_during
existence starts and ends during
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s
add to RO
uberon
indirectly_supplies
indirectly_supplies
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
posteriorly_connected_to
posteriorly connected to
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
uberon
transitively_connected_to
transitively_connected to
A carnivorous process during which a living entity acquires food and energy by consuming dead or decaying animal matter.
https://orcid.org/0000-0002-2908-3327
scavenging
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
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])
(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]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(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]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
fiat-object-part
FiatObjectPart
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
site
Site
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
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)
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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
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])
object
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])
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
cf-boundary
ContinuantFiatBoundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
history
History
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
anatomical entity
connected anatomical structure
material anatomical entity
immaterial anatomical entity
cell part (CARO)
cell part
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
Melissa Haendel
9/18/11
organism or virus or viroid
multicellular anatomical structure
An individual member of a clade.
organism
mah
7.16.2011
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
organism
biological entity
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.
-1
0.000548579903
0.0
KEGG:C05359
PMID:21614077
Wikipedia:Electron
electron
chebi_ontology
Elektron
beta
beta(-)
beta-particle
e
e(-)
e-
negatron
CHEBI:10545
electron
PMID:21614077
Europe PMC
PMID:21614077
Europe PMC
electron
ChEBI
electron
IUPAC
electron
KEGG_COMPOUND
Elektron
ChEBI
beta
IUPAC
beta(-)
ChEBI
beta-particle
IUPAC
e
IUPAC
e(-)
UniProt
e-
KEGG_COMPOUND
negatron
IUPAC
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
chebi_ontology
Mycoplasma genitalium metabolites
CHEBI:131604
Mycoplasma genitalium metabolite
Mycoplasma genitalium metabolites
ChEBI
A carboxylic acid anion resultig from the deprotonation of the carboxy group of a dicarboxylic acid monoester.
chebi_ontology
CHEBI:131605
dicarboxylic acid monoester(1-)
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
chebi_ontology
dicarboxylic acids and derivatives
CHEBI:131927
dicarboxylic acids and O-substituted derivatives
dicarboxylic acids and derivatives
ChEBI
Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.
Wikipedia:Volatile_organic_compound
chebi_ontology
VOC
VOCs
volatile organic compounds
CHEBI:134179
volatile organic compound
VOC
ChEBI
VOCs
ChEBI
volatile organic compounds
ChEBI
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Wikipedia:Mineral_acid
chebi_ontology
inorganic acids
mineral acid
mineral acids
CHEBI:138103
inorganic acid
inorganic acids
ChEBI
mineral acid
ChEBI
mineral acids
ChEBI
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
Wikipedia:https://en.wikipedia.org/wiki/Gas
chebi_ontology
gas molecular entities
gaseous molecular entities
gaseous molecular entity
CHEBI:138675
gas molecular entity
gas molecular entities
ChEBI
gaseous molecular entities
ChEBI
gaseous molecular entity
ChEBI
A cyclic tetrapyrrole anion that is the carbanion obtained by removal of the acidic proton from position 21 of any chlorophyll. Major species at pH 7.3
-1
C49H57MgN4O5R4
806.308
805.41794
C1=2N3C(C=C4[N+]5=C(C=C6N7C8=C(C9=[N+](C(=C1)[C@H]([C@@H]9CCC(OC/C=C(/CCC[C@@H](CCC[C@@H](CCCC(C)C)C)C)\C)=O)C)[Mg-2]735)[C-](C(C8=C6C)=O)C(=O)OC)C(=C4*)*)=C(C2*)*
Wikipedia:Chlorophyll
chebi_ontology
a chlorophyll
CHEBI:139291
chlorophyll(1-)
Wikipedia:Chlorophyll
SUBMITTER
a chlorophyll
UniProt
A cyclic tetrapyrrole anion obtained by removal of the acidic proton from position 21 as well as deprotonation of the carboxy group of any chlorophyllide. Major species at pH 7.3
-2
C29H18MgN4O5R4
526.783
526.11276
C1=2N3C(C=C4[N+]5=C(C=C6N7C8=C(C9=[N+](C(=C1)[C@H]([C@@H]9CCC([O-])=O)C)[Mg-2]735)[C-](C(C8=C6C)=O)C(=O)OC)C(=C4*)*)=C(C2*)*
chebi_ontology
a chlorophyllide
CHEBI:139292
chlorophyllide(2-)
a chlorophyllide
UniProt
Any agent that induces nausea and vomiting.
chebi_ontology
emetics
CHEBI:149552
emetic
emetics
ChEBI
A molecular entity that can transfer an electron to another molecular entity.
electron donor
chebi_ontology
Elektronendonator
donneur d'electron
CHEBI:15022
electron donor
electron donor
IUPAC
Elektronendonator
ChEBI
donneur d'electron
IUPAC
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
CHEBI:13699
CHEBI:2377
KEGG:C00028
KEGG:C16722
Acceptor
chebi_ontology
A
Akzeptor
Hydrogen-acceptor
Oxidized donor
accepteur
CHEBI:15339
acceptor
Acceptor
KEGG_COMPOUND
A
KEGG_COMPOUND
Akzeptor
ChEBI
Hydrogen-acceptor
KEGG_COMPOUND
Oxidized donor
KEGG_COMPOUND
accepteur
ChEBI
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
0
H2O
InChI=1S/H2O/h1H2
XLYOFNOQVPJJNP-UHFFFAOYSA-N
18.01530
18.01056
[H]O[H]
CHEBI:10743
CHEBI:13352
CHEBI:27313
CHEBI:42043
CHEBI:42857
CHEBI:43228
CHEBI:44292
CHEBI:44701
CHEBI:44819
CHEBI:5585
Beilstein:3587155
CAS:7732-18-5
Gmelin:117
HMDB:HMDB0002111
KEGG:C00001
KEGG:D00001
MetaCyc:WATER
MolBase:1
PDBeChem:HOH
Reaxys:3587155
Wikipedia:Water
WATER
Water
oxidane
water
chebi_ontology
BOUND WATER
H2O
HOH
Wasser
[OH2]
acqua
agua
aqua
dihydridooxygen
dihydrogen oxide
eau
hydrogen hydroxide
CHEBI:15377
water
Beilstein:3587155
Beilstein
Beilstein:3587155
Beilstein
CAS:7732-18-5
ChemIDplus
CAS:7732-18-5
KEGG COMPOUND
CAS:7732-18-5
NIST Chemistry WebBook
CAS:7732-18-5
ChemIDplus
CAS:7732-18-5
KEGG COMPOUND
CAS:7732-18-5
NIST Chemistry WebBook
Gmelin:117
Gmelin
Gmelin:117
Gmelin
Reaxys:3587155
Reaxys
Reaxys:3587155
Reaxys
WATER
PDBeChem
Water
KEGG_COMPOUND
oxidane
IUPAC
water
IUPAC
BOUND WATER
PDBeChem
H2O
KEGG_COMPOUND
H2O
UniProt
HOH
ChEBI
Wasser
ChEBI
[OH2]
IUPAC
acqua
ChEBI
agua
ChEBI
aqua
ChEBI
dihydridooxygen
IUPAC
dihydrogen oxide
IUPAC
eau
ChEBI
hydrogen hydroxide
ChEBI
0
O2
InChI=1S/O2/c1-2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
31.99880
31.98983
O=O
CHEBI:10745
CHEBI:13416
CHEBI:23833
CHEBI:25366
CHEBI:30491
CHEBI:44742
CHEBI:7860
CAS:7782-44-7
Gmelin:485
HMDB:HMDB0001377
KEGG:C00007
KEGG:D00003
MetaCyc:OXYGEN-MOLECULE
MolBase:750
PDBeChem:OXY
PMID:10906528
PMID:16977326
PMID:18210929
PMID:18638417
PMID:19840863
PMID:7710549
PMID:9463773
Wikipedia:Oxygen
dioxygen
chebi_ontology
Disauerstoff
E 948
E-948
E948
O2
OXYGEN MOLECULE
Oxygen
[OO]
dioxygene
molecular oxygen
CHEBI:15379
dioxygen
CAS:7782-44-7
ChemIDplus
CAS:7782-44-7
KEGG COMPOUND
CAS:7782-44-7
NIST Chemistry WebBook
Gmelin:485
Gmelin
PMID:10906528
Europe PMC
PMID:16977326
Europe PMC
PMID:18210929
Europe PMC
PMID:18638417
Europe PMC
PMID:19840863
Europe PMC
PMID:7710549
Europe PMC
PMID:9463773
Europe PMC
dioxygen
IUPAC
Disauerstoff
ChEBI
E 948
ChEBI
E-948
ChEBI
E948
ChEBI
O2
IUPAC
O2
KEGG_COMPOUND
O2
UniProt
OXYGEN MOLECULE
PDBeChem
Oxygen
KEGG_COMPOUND
[OO]
MolBase
dioxygene
ChEBI
molecular oxygen
ChEBI
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.
0
CH3OR
31.034
31.01839
*C(O)([H])[H]
CHEBI:13676
CHEBI:14887
CHEBI:26262
CHEBI:57489
CHEBI:8406
KEGG:C00226
Primary alcohol
chebi_ontology
1-Alcohol
a primary alcohol
primary alcohols
CHEBI:15734
primary alcohol
Primary alcohol
KEGG_COMPOUND
1-Alcohol
KEGG_COMPOUND
a primary alcohol
UniProt
primary alcohols
ChEBI
A monoatomic monoanion resulting from the addition of an electron to any halogen atom.
-1
X
0.0
0.0
[*-]
CHEBI:14384
CHEBI:5605
KEGG:C00462
halide ions
chebi_ontology
HX
Halide
a halide anion
halide anions
halide(1-)
halides
halogen anion
CHEBI:16042
halide anion
halide ions
IUPAC
HX
KEGG_COMPOUND
Halide
KEGG_COMPOUND
a halide anion
UniProt
halide anions
ChEBI
halide(1-)
ChEBI
halides
ChEBI
halogen anion
ChEBI
A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. It is a colourless, odourless, non-toxic but flammable gas (b.p. -161degreeC).
0
CH4
InChI=1S/CH4/h1H4
VNWKTOKETHGBQD-UHFFFAOYSA-N
16.04246
16.03130
[H]C([H])([H])[H]
CHEBI:14585
CHEBI:25220
CHEBI:6811
Beilstein:1718732
CAS:74-82-8
Gmelin:59
HMDB:HMDB0002714
KEGG:C01438
MetaCyc:CH4
PMID:17791569
PMID:23104415
PMID:23353606
PMID:23376302
PMID:23397538
PMID:23718889
PMID:23739479
PMID:23742231
PMID:23756351
PMID:24132456
PMID:24161402
PMID:24259373
Patent:FR994032
Patent:US2583090
Reaxys:1718732
UM-BBD_compID:c0095
Wikipedia:Methane
Methane
methane
tetrahydridocarbon
chebi_ontology
CH4
Methan
marsh gas
metano
methyl hydride
CHEBI:16183
methane
Beilstein:1718732
ChemIDplus
CAS:74-82-8
ChemIDplus
CAS:74-82-8
KEGG COMPOUND
CAS:74-82-8
NIST Chemistry WebBook
Gmelin:59
Gmelin
PMID:17791569
Europe PMC
PMID:23104415
Europe PMC
PMID:23353606
Europe PMC
PMID:23376302
Europe PMC
PMID:23397538
Europe PMC
PMID:23718889
Europe PMC
PMID:23739479
Europe PMC
PMID:23742231
Europe PMC
PMID:23756351
Europe PMC
PMID:24132456
Europe PMC
PMID:24161402
Europe PMC
PMID:24259373
Europe PMC
Reaxys:1718732
Reaxys
UM-BBD_compID:c0095
UM-BBD
Methane
KEGG_COMPOUND
methane
ChEBI
methane
IUPAC
methane
UniProt
tetrahydridocarbon
IUPAC
CH4
IUPAC
Methan
ChEBI
marsh gas
NIST_Chemistry_WebBook
metano
ChEBI
methyl hydride
ChemIDplus
-1
HO
InChI=1S/H2O/h1H2/p-1
XLYOFNOQVPJJNP-UHFFFAOYSA-M
17.00734
17.00329
[O-][H]
CHEBI:13365
CHEBI:13419
CHEBI:44641
CHEBI:5594
CAS:14280-30-9
Gmelin:24714
KEGG:C01328
PDBeChem:OH
hydridooxygenate(1-)
hydroxide
oxidanide
chebi_ontology
HO-
HYDROXIDE ION
Hydroxide ion
OH(-)
OH-
CHEBI:16234
hydroxide
CAS:14280-30-9
ChemIDplus
CAS:14280-30-9
NIST Chemistry WebBook
CAS:14280-30-9
ChemIDplus
CAS:14280-30-9
NIST Chemistry WebBook
Gmelin:24714
Gmelin
Gmelin:24714
Gmelin
hydridooxygenate(1-)
IUPAC
hydroxide
IUPAC
oxidanide
IUPAC
HO-
KEGG_COMPOUND
HYDROXIDE ION
PDBeChem
Hydroxide ion
KEGG_COMPOUND
OH(-)
IUPAC
OH-
KEGG_COMPOUND
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
0
CO2
InChI=1S/CO2/c2-1-3
CURLTUGMZLYLDI-UHFFFAOYSA-N
44.010
43.98983
O=C=O
CHEBI:13282
CHEBI:13283
CHEBI:13284
CHEBI:13285
CHEBI:23011
CHEBI:3283
CHEBI:48829
Beilstein:1900390
CAS:124-38-9
Drug_Central:4256
Gmelin:989
HMDB:HMDB0001967
KEGG:C00011
KEGG:D00004
MetaCyc:CARBON-DIOXIDE
MolBase:752
PDBeChem:CO2
PMID:10826146
PMID:11094503
PMID:11584085
PMID:11802652
PMID:14639145
PMID:15050588
PMID:16591971
PMID:16656478
PMID:16659660
PMID:17190796
PMID:17448243
PMID:17878298
PMID:17884085
PMID:19043767
PMID:19259576
PMID:19854893
PMID:23384758
PMID:23828359
PMID:24258718
PMID:8482095
PMID:8818713
PMID:8869828
PMID:9611769
PMID:9730350
PPDB:119
Reaxys:1900390
UM-BBD_compID:c0131
Wikipedia:Carbon_dioxide
CARBON DIOXIDE
Carbon dioxide
carbon dioxide
dioxidocarbon
methanedione
chebi_ontology
CO2
E 290
E-290
E290
R-744
[CO2]
carbonic anhydride
CHEBI:16526
carbon dioxide
Beilstein:1900390
Beilstein
CAS:124-38-9
ChemIDplus
CAS:124-38-9
KEGG COMPOUND
CAS:124-38-9
NIST Chemistry WebBook
Drug_Central:4256
DrugCentral
Gmelin:989
Gmelin
PMID:10826146
Europe PMC
PMID:11094503
Europe PMC
PMID:11584085
Europe PMC
PMID:11802652
Europe PMC
PMID:14639145
Europe PMC
PMID:15050588
Europe PMC
PMID:16591971
Europe PMC
PMID:16656478
Europe PMC
PMID:16659660
Europe PMC
PMID:17190796
Europe PMC
PMID:17448243
Europe PMC
PMID:17878298
Europe PMC
PMID:17884085
Europe PMC
PMID:19043767
Europe PMC
PMID:19259576
Europe PMC
PMID:19854893
Europe PMC
PMID:23384758
Europe PMC
PMID:23828359
Europe PMC
PMID:24258718
Europe PMC
PMID:8482095
Europe PMC
PMID:8818713
Europe PMC
PMID:8869828
Europe PMC
PMID:9611769
Europe PMC
PMID:9730350
Europe PMC
Reaxys:1900390
Reaxys
UM-BBD_compID:c0131
UM-BBD
CARBON DIOXIDE
PDBeChem
Carbon dioxide
KEGG_COMPOUND
carbon dioxide
IUPAC
dioxidocarbon
IUPAC
methanedione
IUPAC
CO2
KEGG_COMPOUND
CO2
UniProt
E 290
ChEBI
E-290
ChEBI
E290
ChEBI
R-744
ChEBI
[CO2]
MolBase
carbonic anhydride
UM-BBD
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.
CHEBI:15131
CHEBI:23008
CHEBI:9318
Wikipedia:Carbohydrate
carbohydrate
carbohydrates
chebi_ontology
Kohlenhydrat
Kohlenhydrate
carbohidrato
carbohidratos
glucide
glucides
glucido
glucidos
hydrates de carbone
saccharide
saccharides
saccharidum
CHEBI:16646
carbohydrate
carbohydrate
IUPAC
carbohydrates
IUPAC
Kohlenhydrat
ChEBI
Kohlenhydrate
ChEBI
carbohidrato
IUPAC
carbohidratos
IUPAC
glucide
ChEBI
glucides
ChEBI
glucido
ChEBI
glucidos
ChEBI
hydrates de carbone
ChEBI
saccharide
IUPAC
saccharides
IUPAC
saccharidum
ChEBI
0
C35H34MgN4O5
InChI=1S/C35H36N4O5.Mg/c1-8-19-15(3)22-12-24-17(5)21(10-11-28(40)41)32(38-24)30-31(35(43)44-7)34(42)29-18(6)25(39-33(29)30)14-27-20(9-2)16(4)23(37-27)13-26(19)36-22;/h8,12-14,17,21,31H,1,9-11H2,2-7H3,(H3,36,37,38,39,40,41,42);/q;+2/p-2/t17-,21-,31+;/m0./s1
ANWUQYTXRXCEMZ-NYABAGMLSA-L
614.97300
614.23796
CCC1=C(C)C2=Cc3c(C=C)c(C)c4C=C5[C@@H](C)[C@H](CCC(O)=O)C6=[N+]5[Mg--]5(n34)n3c(=CC1=[N+]25)c(C)c1C(=O)[C@H](C(=O)OC)C6=c31
CHEBI:13976
CHEBI:13977
CHEBI:23159
CHEBI:3633
Beilstein:5801116
CAS:14897-06-4
KEGG:C02139
KNApSAcK:C00007316
Chlorophyllide a
chebi_ontology
Chlorophyllid a
CHEBI:16900
chlorophyllide a
Beilstein:5801116
Beilstein
CAS:14897-06-4
ChemIDplus
CAS:14897-06-4
KEGG COMPOUND
Chlorophyllide a
KEGG_COMPOUND
Chlorophyllid a
ChEBI
A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.
0
CO
InChI=1S/CO/c1-2
UGFAIRIUMAVXCW-UHFFFAOYSA-N
28.01010
27.99491
[C-]#[O+]
CHEBI:13281
CHEBI:23013
CHEBI:3282
CHEBI:41526
Beilstein:1900508
Beilstein:3535285
Beilstein:3587264
CAS:630-08-0
Gmelin:421
HMDB:HMDB0001361
KEGG:C00237
KEGG:D09706
MetaCyc:CARBON-MONOXIDE
MolBase:753
PDBeChem:CMO
PMID:10085152
PMID:10679539
PMID:11572959
PMID:14527438
PMID:14563665
PMID:15127883
PMID:15598489
PMID:16371440
PMID:16520836
PMID:17041734
PMID:18094356
PMID:19909254
PMID:23762709
PMID:7022476
PMID:8240252
PMID:8620577
UM-BBD_compID:c0369
Wikipedia:Carbon_monoxide
CARBON MONOXIDE
Carbon monoxide
carbon monooxide
carbon monoxide
carbon(II) oxide
chebi_ontology
C#O
CO
[CO]
CHEBI:17245
carbon monoxide
Beilstein:1900508
Beilstein
Beilstein:3535285
Beilstein
Beilstein:3587264
Beilstein
CAS:630-08-0
ChemIDplus
CAS:630-08-0
KEGG COMPOUND
CAS:630-08-0
NIST Chemistry WebBook
Gmelin:421
Gmelin
PMID:10085152
Europe PMC
PMID:10679539
Europe PMC
PMID:11572959
Europe PMC
PMID:14527438
Europe PMC
PMID:14563665
Europe PMC
PMID:15127883
Europe PMC
PMID:15598489
Europe PMC
PMID:16371440
Europe PMC
PMID:16520836
Europe PMC
PMID:17041734
Europe PMC
PMID:18094356
Europe PMC
PMID:19909254
Europe PMC
PMID:23762709
Europe PMC
PMID:7022476
Europe PMC
PMID:8240252
Europe PMC
PMID:8620577
Europe PMC
UM-BBD_compID:c0369
UM-BBD
CARBON MONOXIDE
PDBeChem
Carbon monoxide
KEGG_COMPOUND
carbon monooxide
IUPAC
carbon monoxide
IUPAC
carbon(II) oxide
IUPAC
C#O
ChEBI
CO
KEGG_COMPOUND
CO
UniProt
[CO]
MolBase
A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3.
-1
NO3
InChI=1S/NO3/c2-1(3)4/q-1
NHNBFGGVMKEFGY-UHFFFAOYSA-N
62.00490
61.98837
[O-][N+]([O-])=O
CHEBI:14654
CHEBI:44487
CHEBI:71263
Beilstein:3587575
CAS:14797-55-8
Gmelin:1574
MetaCyc:NITRATE
PDBeChem:NO3
Wikipedia:Nitrate
nitrate
trioxidonitrate(1-)
trioxonitrate(1-)
trioxonitrate(V)
chebi_ontology
NITRATE ION
NO3
NO3(-)
[NO3](-)
nitrate(1-)
CHEBI:17632
nitrate
Beilstein:3587575
Beilstein
CAS:14797-55-8
ChemIDplus
CAS:14797-55-8
NIST Chemistry WebBook
Gmelin:1574
Gmelin
MetaCyc:NITRATE
SUBMITTER
nitrate
IUPAC
nitrate
UniProt
trioxidonitrate(1-)
IUPAC
trioxonitrate(1-)
IUPAC
trioxonitrate(V)
IUPAC
NITRATE ION
PDBeChem
NO3
ChEBI
NO3(-)
IUPAC
[NO3](-)
IUPAC
nitrate(1-)
ChemIDplus
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
0
CH4O
InChI=1S/CH4O/c1-2/h2H,1H3
OKKJLVBELUTLKV-UHFFFAOYSA-N
32.04186
32.02621
CO
CHEBI:14588
CHEBI:25227
CHEBI:44080
CHEBI:44553
CHEBI:6816
Beilstein:1098229
CAS:67-56-1
Gmelin:449
HMDB:HMDB0001875
KEGG:C00132
KEGG:D02309
MetaCyc:METOH
PDBeChem:MOH
PMID:11141607
PMID:11430978
PMID:11489599
PMID:11680737
PMID:11684179
PMID:14012711
PMID:14678513
PMID:14760634
PMID:15172721
PMID:15906011
PMID:16705261
PMID:17451998
PMID:17733096
PMID:19064074
PMID:19850112
PMID:20314698
Reaxys:1098229
UM-BBD_compID:c0132
Wikipedia:Methanol
METHANOL
Methanol
methanol
chebi_ontology
CH3OH
MeOH
Methyl alcohol
Methylalkohol
carbinol
spirit of wood
wood alcohol
wood naphtha
wood spirit
CHEBI:17790
methanol
Beilstein:1098229
Beilstein
Beilstein:1098229
Beilstein
CAS:67-56-1
ChemIDplus
CAS:67-56-1
KEGG COMPOUND
CAS:67-56-1
NIST Chemistry WebBook
CAS:67-56-1
ChemIDplus
CAS:67-56-1
KEGG COMPOUND
CAS:67-56-1
NIST Chemistry WebBook
Gmelin:449
Gmelin
Gmelin:449
Gmelin
PMID:11141607
Europe PMC
PMID:11141607
Europe PMC
PMID:11430978
Europe PMC
PMID:11430978
Europe PMC
PMID:11489599
Europe PMC
PMID:11489599
Europe PMC
PMID:11680737
Europe PMC
PMID:11680737
Europe PMC
PMID:11684179
Europe PMC
PMID:11684179
Europe PMC
PMID:14012711
Europe PMC
PMID:14012711
Europe PMC
PMID:14678513
Europe PMC
PMID:14678513
Europe PMC
PMID:14760634
Europe PMC
PMID:14760634
Europe PMC
PMID:15172721
Europe PMC
PMID:15172721
Europe PMC
PMID:15906011
Europe PMC
PMID:15906011
Europe PMC
PMID:16705261
Europe PMC
PMID:16705261
Europe PMC
PMID:17451998
Europe PMC
PMID:17451998
Europe PMC
PMID:17733096
Europe PMC
PMID:17733096
Europe PMC
PMID:19064074
Europe PMC
PMID:19064074
Europe PMC
PMID:19850112
Europe PMC
PMID:19850112
Europe PMC
PMID:20314698
Europe PMC
PMID:20314698
Europe PMC
Reaxys:1098229
Reaxys
Reaxys:1098229
Reaxys
UM-BBD_compID:c0132
UM-BBD
UM-BBD_compID:c0132
UM-BBD
METHANOL
PDBeChem
Methanol
KEGG_COMPOUND
methanol
IUPAC
methanol
UniProt
CH3OH
ChEBI
MeOH
ChEBI
Methyl alcohol
KEGG_COMPOUND
Methylalkohol
NIST_Chemistry_WebBook
carbinol
ChemIDplus
spirit of wood
HMDB
wood alcohol
ChemIDplus
wood naphtha
ChemIDplus
wood spirit
NIST_Chemistry_WebBook
A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms.
0
ClH
HCl
InChI=1S/ClH/h1H
VEXZGXHMUGYJMC-UHFFFAOYSA-N
36.46064
35.97668
Cl[H]
CHEBI:13364
CHEBI:24635
CHEBI:5590
CAS:7647-01-0
Drug_Central:4568
Gmelin:322
HMDB:HMDB0002306
KEGG:C01327
KEGG:D02057
MetaCyc:HCL
PMID:15823700
PMID:17492841
PMID:22804993
Reaxys:1098214
Wikipedia:HCl
Wikipedia:Hydrochloric_acid
Hydrogen chloride
chlorane
chloridohydrogen
hydrogen chloride
chebi_ontology
Chlorwasserstoff
HCl
Hydrochloride
Hydrogenchlorid
Wasserstoffchlorid
[HCl]
chlorure d'hydrogene
cloruro de hidrogeno
hydrochloric acid
CHEBI:17883
hydrogen chloride
CAS:7647-01-0
ChemIDplus
CAS:7647-01-0
KEGG COMPOUND
CAS:7647-01-0
NIST Chemistry WebBook
Drug_Central:4568
DrugCentral
Gmelin:322
Gmelin
PMID:15823700
Europe PMC
PMID:17492841
Europe PMC
PMID:22804993
Europe PMC
Reaxys:1098214
Reaxys
Hydrogen chloride
KEGG_COMPOUND
chlorane
IUPAC
chloridohydrogen
IUPAC
hydrogen chloride
IUPAC
Chlorwasserstoff
ChEBI
HCl
KEGG_COMPOUND
Hydrochloride
KEGG_COMPOUND
Hydrogenchlorid
ChEBI
Wasserstoffchlorid
ChEBI
[HCl]
IUPAC
chlorure d'hydrogene
ChEBI
cloruro de hidrogeno
ChEBI
hydrochloric acid
ChemIDplus
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
CHEBI:14202
CHEBI:4697
KEGG:C01351
Donor
chebi_ontology
Donator
donneur
CHEBI:17891
donor
Donor
KEGG_COMPOUND
Donator
ChEBI
donneur
ChEBI
A halide anion formed when chlorine picks up an electron to form an an anion.
-1
Cl
InChI=1S/ClH/h1H/p-1
VEXZGXHMUGYJMC-UHFFFAOYSA-M
35.45270
34.96940
[Cl-]
CHEBI:13291
CHEBI:13970
CHEBI:3616
CHEBI:3731
CHEBI:48804
Beilstein:3587171
CAS:16887-00-6
Gmelin:14910
KEGG:C00115
KEGG:C00698
PDBeChem:CL
UM-BBD_compID:c0884
Chloride
chloride
chloride(1-)
chebi_ontology
CHLORIDE ION
Chloride ion
Chloride(1-)
Chlorine anion
Cl(-)
Cl-
CHEBI:17996
chloride
Beilstein:3587171
Beilstein
CAS:16887-00-6
ChemIDplus
CAS:16887-00-6
KEGG COMPOUND
CAS:16887-00-6
NIST Chemistry WebBook
Gmelin:14910
Gmelin
UM-BBD_compID:c0884
UM-BBD
Chloride
KEGG_COMPOUND
chloride
IUPAC
chloride
UniProt
chloride(1-)
IUPAC
CHLORIDE ION
PDBeChem
Chloride ion
KEGG_COMPOUND
Chloride(1-)
ChemIDplus
Chlorine anion
NIST_Chemistry_WebBook
Cl(-)
IUPAC
Cl-
KEGG_COMPOUND
An elemental molecule consisting of two trivalently-bonded nitrogen atoms.
0
N2
InChI=1S/N2/c1-2
IJGRMHOSHXDMSA-UHFFFAOYSA-N
28.01348
28.00615
N#N
CHEBI:13388
CHEBI:14660
CHEBI:25365
CHEBI:43128
CHEBI:7593
CAS:7727-37-9
Drug_Central:4251
Gmelin:150
HMDB:HMDB0001371
KEGG:C00697
KEGG:D00083
MetaCyc:NITROGEN-MOLECULE
PDBeChem:HDZ
PMID:18334638
PMID:22237545
Reaxys:15940095
Wikipedia:Nitrogen
dinitrogen
chebi_ontology
N#N
N2
Nitrogen
molecular nitrogen
CHEBI:17997
dinitrogen
CAS:7727-37-9
ChemIDplus
CAS:7727-37-9
KEGG COMPOUND
CAS:7727-37-9
NIST Chemistry WebBook
Drug_Central:4251
DrugCentral
Gmelin:150
Gmelin
PMID:18334638
Europe PMC
PMID:22237545
Europe PMC
Reaxys:15940095
Reaxys
dinitrogen
IUPAC
N#N
ChEBI
N2
IUPAC
N2
KEGG_COMPOUND
N2
UniProt
Nitrogen
KEGG_COMPOUND
molecular nitrogen
ChEBI
0
HX
1.008
1.00783
[F,Cl,Br,I]
CHEBI:13368
CHEBI:37140
CHEBI:5599
hydrogen halide
hydrogen halides
chebi_ontology
HX
hydrogen halides
CHEBI:18140
hydrogen halide
hydrogen halide
IUPAC
hydrogen halides
IUPAC
HX
UniProt
hydrogen halides
ChEBI
0
C55H72MgN4O5
InChI=1S/C55H73N4O5.Mg/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42;/h13,26,28-33,37,41,51H,1,14-25,27H2,2-12H3,(H-,56,57,58,59,61);/q-1;+2/p-1/b34-26+;/t32-,33-,37+,41+,51-;/m1./s1
ATNHDLDRLWWWCB-AENOIHSZSA-M
893.48900
892.53531
CCC1=C(C)C2=Cc3c(C=C)c(C)c4C=C5[C@@H](C)[C@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C6=[N+]5[Mg--]5(n34)n3c(=CC1=[N+]25)c(C)c1C(=O)[C@H](C(=O)OC)C6=c31
CHEBI:13974
CHEBI:23157
CHEBI:3631
CHEBI:48807
Beilstein:1208847
Beilstein:4651978
CAS:479-61-8
COMe:MOL000003
DrugBank:DB02133
Gmelin:475109
KEGG:C05306
KNApSAcK:C00001528
PDBeChem:CLA
CHLOROPHYLL A
Chlorophyll a
[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl (2(2)R,17S,18S)-7-ethyl-2(1),2(2),17,18-tetrahydro-2(2)-(methoxycarbonyl)-3,8,13,17-tetramethyl-2(1)-oxo-12-ethenylcyclopenta[at]porphyrin-18-propanoato(2-)]magnesium
chebi_ontology
(SP-4-2)-((2E,7R,11R)-3,7,11,15-tetramethyl-2-hexadecenyl (3S,4S,21R)-9-ethenyl-14-ethyl-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoato(2-)-kappaN(23),kappaN(24),kappaN(25),kappaN(26))-magnesium
Chlorophyll
CHEBI:18230
chlorophyll a
Beilstein:1208847
Beilstein
Beilstein:4651978
Beilstein
CAS:479-61-8
ChemIDplus
CAS:479-61-8
KEGG COMPOUND
Gmelin:475109
Gmelin
CHLOROPHYLL A
PDBeChem
Chlorophyll a
KEGG_COMPOUND
[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl (2(2)R,17S,18S)-7-ethyl-2(1),2(2),17,18-tetrahydro-2(2)-(methoxycarbonyl)-3,8,13,17-tetramethyl-2(1)-oxo-12-ethenylcyclopenta[at]porphyrin-18-propanoato(2-)]magnesium
IUPAC
(SP-4-2)-((2E,7R,11R)-3,7,11,15-tetramethyl-2-hexadecenyl (3S,4S,21R)-9-ethenyl-14-ethyl-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoato(2-)-kappaN(23),kappaN(24),kappaN(25),kappaN(26))-magnesium
ChemIDplus
Chlorophyll
ChemIDplus
An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
0
CH3R
15.035
15.02348
C[*]
CHEBI:13435
CHEBI:22317
CHEBI:2576
KEGG:C01371
Alkane
alkane
alkanes
chebi_ontology
Alkan
RH
alcane
alcanes
alcano
alcanos
an alkane
CHEBI:18310
alkane
Alkane
KEGG_COMPOUND
alkane
IUPAC
alkanes
IUPAC
Alkan
ChEBI
RH
KEGG_COMPOUND
alcane
IUPAC
alcanes
IUPAC
alcano
IUPAC
alcanos
IUPAC
an alkane
UniProt
alkaline earth metals
chebi_ontology
Erdalkalimetall
Erdalkalimetalle
alkaline earth metal
alkaline-earth metal
alkaline-earth metals
metal alcalino-terreux
metal alcalinoterreo
metales alcalinoterreos
metaux alcalino-terreux
CHEBI:22313
alkaline earth metal atom
alkaline earth metals
IUPAC
Erdalkalimetall
ChEBI
Erdalkalimetalle
ChEBI
alkaline earth metal
ChEBI
alkaline-earth metal
ChEBI
alkaline-earth metals
ChEBI
metal alcalino-terreux
ChEBI
metal alcalinoterreo
ChEBI
metales alcalinoterreos
ChEBI
metaux alcalino-terreux
ChEBI
alkali metals
chebi_ontology
Alkalimetall
Alkalimetalle
alkali metal
metal alcalin
metal alcalino
metales alcalinos
metaux alcalins
CHEBI:22314
alkali metal atom
alkali metals
IUPAC
Alkalimetall
ChEBI
Alkalimetalle
ChEBI
alkali metal
ChEBI
metal alcalin
ChEBI
metal alcalino
ChEBI
metales alcalinos
ChEBI
metaux alcalins
ChEBI
A monoatomic or polyatomic species having one or more elementary charges of the electron.
Anion
anion
chebi_ontology
Anionen
aniones
anions
CHEBI:22563
anion
Anion
ChEBI
anion
ChEBI
anion
IUPAC
Anionen
ChEBI
aniones
ChEBI
anions
IUPAC
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).
KEGG:C00701
Base
base
chebi_ontology
Base1
Base2
Basen
Nucleobase
bases
CHEBI:22695
base
Base
ChEBI
base
ChEBI
base
IUPAC
Base1
KEGG_COMPOUND
Base2
KEGG_COMPOUND
Basen
ChEBI
Nucleobase
KEGG_COMPOUND
bases
ChEBI
chebi_ontology
carbon oxides
oxides of carbon
CHEBI:23014
carbon oxide
carbon oxides
ChEBI
oxides of carbon
ChEBI
0
CO
28.01010
27.99491
O=C(*)*
carbonyl
carbonyl group
chebi_ontology
>C=O
CHEBI:23019
carbonyl group
carbonyl
IUPAC
carbonyl group
ChEBI
carbonyl group
UniProt
>C=O
IUPAC
chebi_ontology
chloride salts
chlorides
CHEBI:23114
chloride salt
chloride salts
ChEBI
chlorides
ChEBI
0
Cl
InChI=1S/Cl
ZAMOUSCENKQFHK-UHFFFAOYSA-N
35.45270
34.96885
[Cl]
WebElements:Cl
chlorine
chebi_ontology
17Cl
Chlor
Cl
chlore
chlorine
chlorum
cloro
CHEBI:23116
chlorine atom
chlorine
IUPAC
17Cl
IUPAC
Chlor
ChEBI
Cl
IUPAC
chlore
ChEBI
chlorine
ChEBI
chlorum
ChEBI
cloro
ChEBI
A halogen molecular entity containing one or more atoms of chlorine.
chebi_ontology
CHEBI:23117
chlorine molecular entity
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).
Wikipedia:Cofactor_(biochemistry)
cofactor
cofactors
chebi_ontology
CHEBI:23357
cofactor
cofactor
IUPAC
cofactors
IUPAC
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
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.
chebi_ontology
drugs
medicine
CHEBI:23888
drug
drugs
ChEBI
medicine
ChEBI
chebi_ontology
monoatomic anions
CHEBI:23905
monoatomic anion
monoatomic anions
ChEBI
chebi_ontology
monoatomic cations
CHEBI:23906
monoatomic cation
monoatomic cations
ChEBI
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.
enzyme inhibitor
chebi_ontology
enzyme inhibitors
inhibidor enzimatico
inhibidores enzimaticos
inhibiteur enzymatique
inhibiteurs enzymatiques
CHEBI:23924
enzyme inhibitor
enzyme inhibitor
IUPAC
enzyme inhibitors
ChEBI
inhibidor enzimatico
ChEBI
inhibidores enzimaticos
ChEBI
inhibiteur enzymatique
ChEBI
inhibiteurs enzymatiques
ChEBI
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
A role played by the molecular entity or part thereof within a biological context.
chebi_ontology
biological function
CHEBI:24432
biological role
biological function
ChEBI
A defined linked collection of atoms or a single atom within a molecular entity.
group
chebi_ontology
Gruppe
Rest
groupe
grupo
grupos
CHEBI:24433
group
group
IUPAC
Gruppe
ChEBI
Rest
ChEBI
groupe
IUPAC
grupo
IUPAC
grupos
IUPAC
halogen molecular entity
chebi_ontology
halogen compounds
halogen molecular entities
CHEBI:24471
halogen molecular entity
halogen molecular entity
ChEBI
halogen compounds
ChEBI
halogen molecular entities
ChEBI
halogen
halogens
chebi_ontology
Halogene
group 17 elements
group VII elements
halogene
halogenes
halogeno
halogenos
CHEBI:24473
halogen
halogen
IUPAC
halogens
IUPAC
Halogene
ChEBI
group 17 elements
ChEBI
group VII elements
ChEBI
halogene
ChEBI
halogenes
ChEBI
halogeno
ChEBI
halogenos
ChEBI
A cyclic compound having as ring members atoms of carbon and at least of one other element.
chebi_ontology
organic heterocycle
organic heterocyclic compounds
CHEBI:24532
organic heterocyclic compound
organic heterocycle
ChEBI
organic heterocyclic compounds
ChEBI
A compound consisting of carbon and hydrogen only.
hydrocarbon
hydrocarbons
chebi_ontology
Kohlenwasserstoff
Kohlenwasserstoffe
hidrocarburo
hidrocarburos
hydrocarbure
CHEBI:24632
hydrocarbon
hydrocarbon
IUPAC
hydrocarbons
IUPAC
Kohlenwasserstoff
ChEBI
Kohlenwasserstoffe
ChEBI
hidrocarburo
IUPAC
hidrocarburos
IUPAC
hydrocarbure
IUPAC
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
chebi_ontology
CHEBI:24651
hydroxides
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).
oxoacid
oxoacids
chebi_ontology
oxacids
oxiacids
oxo acid
oxy-acids
oxyacids
CHEBI:24833
oxoacid
oxoacid
IUPAC
oxoacids
IUPAC
oxacids
ChEBI
oxiacids
ChEBI
oxo acid
ChEBI
oxy-acids
ChEBI
oxyacids
ChEBI
chebi_ontology
inorganic anions
CHEBI:24834
inorganic anion
inorganic anions
ChEBI
A molecular entity that contains no carbon.
chebi_ontology
anorganische Verbindungen
inorganic compounds
inorganic entity
inorganic molecular entities
inorganics
CHEBI:24835
inorganic molecular entity
inorganic entity
ChEBI
inorganic molecular entities
ChEBI
inorganics
ChEBI
anorganische Verbindungen
ChEBI
inorganic compounds
ChEBI
chebi_ontology
anorganisches Salz
inorganic salts
CHEBI:24839
inorganic salt
anorganisches Salz
ChEBI
inorganic salts
ChEBI
A salt is an assembly of cations and anions.
salt
chebi_ontology
Salz
Salze
ionic compound
ionic compounds
sal
sales
salts
sel
sels
CHEBI:24866
salt
salt
IUPAC
Salz
ChEBI
Salze
ChEBI
ionic compound
ChEBI
ionic compounds
ChEBI
sal
ChEBI
sales
ChEBI
salts
ChEBI
sel
ChEBI
sels
ChEBI
chebi_ontology
monoatomic ions
CHEBI:24867
monoatomic ion
monoatomic ions
ChEBI
A molecular entity having a net electric charge.
Ion
ion
chebi_ontology
Ionen
iones
ions
CHEBI:24870
ion
Ion
ChEBI
ion
ChEBI
ion
IUPAC
Ionen
ChEBI
iones
ChEBI
ions
ChEBI
0
Mg
InChI=1S/Mg
FYYHWMGAXLPEAU-UHFFFAOYSA-N
24.30500
23.98504
[Mg]
CAS:7439-95-4
DrugBank:DB01378
Gmelin:16207
KEGG:C00305
WebElements:Mg
magnesium
chebi_ontology
12Mg
Magnesium
Mg
magnesio
magnesium
CHEBI:25107
magnesium atom
CAS:7439-95-4
ChemIDplus
Gmelin:16207
Gmelin
magnesium
IUPAC
12Mg
IUPAC
Magnesium
ChEBI
Mg
IUPAC
magnesio
ChEBI
magnesium
ChEBI
magnesium molecular entity
chebi_ontology
magnesium compounds
magnesium molecular entities
CHEBI:25108
magnesium molecular entity
magnesium molecular entity
ChEBI
magnesium compounds
ChEBI
magnesium molecular entities
ChEBI
chebi_ontology
magnesium porphyrins
CHEBI:25111
magnesium porphyrin
magnesium porphyrins
ChEBI
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
CHEBI:26619
CHEBI:35220
metabolite
chebi_ontology
metabolites
primary metabolites
secondary metabolites
CHEBI:25212
metabolite
metabolite
IUPAC
metabolites
ChEBI
primary metabolites
ChEBI
secondary metabolites
ChEBI
chebi_ontology
a metal cation
metal cations
CHEBI:25213
metal cation
a metal cation
UniProt
metal cations
ChEBI
chebi_ontology
metalloporphyrins
metaloporphyrins
CHEBI:25216
metalloporphyrin
metalloporphyrins
ChEBI
metaloporphyrins
ChEBI
Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol.
0
C2H3O2R
59.044
59.01330
COC([*])=O
chebi_ontology
carboxylic acid methyl ester
carboxylic acid methyl esters
CHEBI:25248
methyl ester
carboxylic acid methyl ester
ChEBI
carboxylic acid methyl esters
ChEBI
chebi_ontology
mitochondrial electron transport chain inhibitors
mitochondrial electron-transport chain inhibitor
mitochondrial respiratory chain inhibitors
CHEBI:25355
mitochondrial respiratory-chain inhibitor
mitochondrial electron transport chain inhibitors
ChEBI
mitochondrial electron-transport chain inhibitor
ChEBI
mitochondrial respiratory chain inhibitors
ChEBI
A molecule all atoms of which have the same atomic number.
chebi_ontology
homoatomic molecule
homoatomic molecules
CHEBI:25362
elemental molecule
homoatomic molecule
ChEBI
homoatomic molecules
ChEBI
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
molecule
chebi_ontology
Molekuel
molecula
molecules
neutral molecular compounds
CHEBI:25367
molecule
molecule
IUPAC
Molekuel
ChEBI
molecula
IUPAC
molecules
IUPAC
neutral molecular compounds
IUPAC
An oxoacid containing a single carboxy group.
chebi_ontology
monocarboxylic acids
CHEBI:25384
monocarboxylic acid
monocarboxylic acids
ChEBI
+1
0.00000
[*+]
chebi_ontology
monoatomic monocations
monovalent inorganic cations
CHEBI:25414
monoatomic monocation
monoatomic monocations
ChEBI
monovalent inorganic cations
ChEBI
An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.
Wikipedia:Neurotransmitter
chebi_ontology
neurotransmitters
CHEBI:25512
neurotransmitter
neurotransmitters
ChEBI
0
N
14.007
14.00307
WebElements:N
nitrogen
chebi_ontology
7N
N
Stickstoff
azote
nitrogen
nitrogeno
CHEBI:25555
nitrogen atom
nitrogen
IUPAC
7N
IUPAC
N
IUPAC
Stickstoff
ChEBI
azote
IUPAC
nitrogen
ChEBI
nitrogeno
ChEBI
nonmetal
chebi_ontology
Nichtmetall
Nichtmetalle
no metal
no metales
non-metal
non-metaux
nonmetal
nonmetals
CHEBI:25585
nonmetal atom
nonmetal
IUPAC
Nichtmetall
ChEBI
Nichtmetalle
ChEBI
no metal
ChEBI
no metales
ChEBI
non-metal
ChEBI
non-metaux
ChEBI
nonmetal
ChEBI
nonmetals
ChEBI
Any organic ion with a net negative charge.
chebi_ontology
organic anions
CHEBI:25696
organic anion
organic anions
ChEBI
Any organic ion with a net positive charge.
chebi_ontology
organic cations
CHEBI:25697
organic cation
organic cations
ChEBI
chebi_ontology
organic ions
CHEBI:25699
organic ion
organic ions
ChEBI
An oxide in which the oxygen atom is bonded to a carbon atom.
chebi_ontology
organic oxides
CHEBI:25701
organic oxide
organic oxides
ChEBI
An alcohol derived from an aliphatic compound.
0
HOR
17.007
17.00274
O*
KEGG:C02525
Aliphatic alcohol
chebi_ontology
aliphatic alcohols
an aliphatic alcohol
CHEBI:2571
aliphatic alcohol
Aliphatic alcohol
KEGG_COMPOUND
aliphatic alcohols
ChEBI
an aliphatic alcohol
UniProt
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
chebi_ontology
oxides
CHEBI:25741
oxide
oxide
ChEBI
oxides
ChEBI
0
O
InChI=1S/O
QVGXLLKOCUKJST-UHFFFAOYSA-N
15.99940
15.99491
[O]
KEGG:C00007
WebElements:O
oxygen
chebi_ontology
8O
O
Sauerstoff
oxigeno
oxygen
oxygene
CHEBI:25805
oxygen atom
oxygen
IUPAC
8O
IUPAC
O
IUPAC
Sauerstoff
ChEBI
oxigeno
ChEBI
oxygen
ChEBI
oxygene
ChEBI
oxygen molecular entity
chebi_ontology
oxygen molecular entities
CHEBI:25806
oxygen molecular entity
oxygen molecular entity
ChEBI
oxygen molecular entities
ChEBI
Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
Wikipedia:Porphyrin
porphyrins
chebi_ontology
CHEBI:26214
porphyrins
porphyrins
IUPAC
0
Na
InChI=1S/Na
KEAYESYHFKHZAL-UHFFFAOYSA-N
22.98977
22.98977
[Na]
CAS:7440-23-5
Gmelin:16221
KEGG:C01330
WebElements:Na
sodium
chebi_ontology
11Na
Na
Natrium
natrium
sodio
sodium
CHEBI:26708
sodium atom
CAS:7440-23-5
ChemIDplus
Gmelin:16221
Gmelin
sodium
IUPAC
11Na
IUPAC
Na
IUPAC
Natrium
ChemIDplus
natrium
IUPAC
sodio
ChemIDplus
sodium
ChEBI
An inorganic chloride salt having sodium(1+) as the counterion.
0
ClNa
InChI=1S/ClH.Na/h1H;/q;+1/p-1
FAPWRFPIFSIZLT-UHFFFAOYSA-M
58.44247
57.95862
[Na+].[Cl-]
Beilstein:3534976
CAS:7647-14-5
Gmelin:13673
KEGG:C13563
KEGG:D02056
MetaCyc:NACL
PPDB:595
Reaxys:3534976
Wikipedia:Sodium_Chloride
sodium chloride
chebi_ontology
Kochsalz
NaCl
Natriumchlorid
chlorure de sodium
cloruro sodico
common salt
halite
natrii chloridum
rock salt
salt
table salt
CHEBI:26710
sodium chloride
Beilstein:3534976
Beilstein
CAS:7647-14-5
ChemIDplus
CAS:7647-14-5
KEGG COMPOUND
CAS:7647-14-5
NIST Chemistry WebBook
Gmelin:13673
Gmelin
Reaxys:3534976
Reaxys
sodium chloride
ChEBI
sodium chloride
IUPAC
Kochsalz
ChEBI
NaCl
IUPAC
Natriumchlorid
NIST_Chemistry_WebBook
chlorure de sodium
ChEBI
cloruro sodico
ChEBI
common salt
ChemIDplus
halite
NIST_Chemistry_WebBook
natrii chloridum
ChEBI
rock salt
ChemIDplus
salt
ChemIDplus
table salt
ChemIDplus
chebi_ontology
sodium compounds
sodium molecular entities
CHEBI:26712
sodium molecular entity
sodium compounds
ChEBI
sodium molecular entities
ChEBI
Any alkali metal salt having sodium(1+) as the cation.
chebi_ontology
Natriumsalz
Natriumsalze
sodium salts
CHEBI:26714
sodium salt
Natriumsalz
ChEBI
Natriumsalze
ChEBI
sodium salts
ChEBI
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.
tetrapyrrole
tetrapyrroles
chebi_ontology
CHEBI:26932
tetrapyrrole
tetrapyrrole
IUPAC
tetrapyrroles
IUPAC
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
Wikipedia:Micronutrient
chebi_ontology
micronutrients
trace elements
CHEBI:27027
micronutrient
micronutrients
ChEBI
trace elements
ChEBI
0
C
InChI=1S/C
OKTJSMMVPCPJKN-UHFFFAOYSA-N
12.01070
12.00000
[C]
CHEBI:23009
CHEBI:3399
CAS:7440-44-0
KEGG:C06265
WebElements:C
carbon
chebi_ontology
6C
C
Carbon
Kohlenstoff
carbon
carbone
carbonium
carbono
CHEBI:27594
carbon atom
CAS:7440-44-0
ChemIDplus
CAS:7440-44-0
KEGG COMPOUND
CAS:7440-44-0
ChemIDplus
CAS:7440-44-0
KEGG COMPOUND
carbon
IUPAC
6C
IUPAC
C
IUPAC
C
KEGG_COMPOUND
Carbon
KEGG_COMPOUND
Kohlenstoff
ChEBI
carbon
ChEBI
carbone
ChEBI
carbonium
ChEBI
carbono
ChEBI
A family of magnesium porphyrins, defined by the presence of a fifth ring beyond the four pyrrole-like rings. The rings can have various side chains which usually include a long phytol chain.
0
C49H58MgN4O5R4
807.316
806.42576
C1=2N3C(C=C4[N+]5=C(C=C6N7C8=C(C9=[N+](C(=C1)[C@H]([C@@H]9CCC(OC/C=C(/CCC[C@@H](CCC[C@@H](CCCC(C)C)C)C)\C)=O)C)[Mg-2]735)[C@H](C(C8=C6C)=O)C(=O)OC)C(=C4*)*)=C(C2*)*
CHEBI:13973
CHEBI:23161
CHEBI:3630
CHEBI:3635
CAS:1406-65-1
COMe:MOL000012
KEGG:C01793
PMID:29286160
Chlorophyll
chlorophyll
chlorophylls
chebi_ontology
CHEBI:28966
chlorophyll
CAS:1406-65-1
ChemIDplus
CAS:1406-65-1
KEGG COMPOUND
PMID:29286160
Europe PMC
Chlorophyll
KEGG_COMPOUND
chlorophyll
JCBN
chlorophylls
IUPAC
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
-1
CO2R
44.00950
43.98983
[O-]C([*])=O
CHEBI:13626
CHEBI:13945
CHEBI:23026
CHEBI:58657
chebi_ontology
a carboxylate
carboxylic acid anions
carboxylic anions
CHEBI:29067
carboxylic acid anion
a carboxylate
UniProt
carboxylic acid anions
ChEBI
carboxylic anions
ChEBI
A monoatomic monocation obtained from sodium.
+1
Na
InChI=1S/Na/q+1
FKNQFGJONOIPTF-UHFFFAOYSA-N
22.98977
22.98922
[Na+]
CHEBI:26717
CHEBI:49766
CHEBI:9175
CAS:17341-25-2
Gmelin:15196
KEGG:C01330
PDBeChem:NA
sodium cation
sodium(1+)
sodium(1+) ion
sodium(I) cation
chebi_ontology
Na(+)
Na+
SODIUM ION
CHEBI:29101
sodium(1+)
CAS:17341-25-2
ChemIDplus
CAS:17341-25-2
NIST Chemistry WebBook
Gmelin:15196
Gmelin
sodium cation
IUPAC
sodium(1+)
IUPAC
sodium(1+) ion
IUPAC
sodium(I) cation
IUPAC
Na(+)
IUPAC
Na(+)
UniProt
Na+
KEGG_COMPOUND
SODIUM ION
PDBeChem
-2
CH2
InChI=1S/CH2/h1H2/q-2
PZPOWPOFQLSNJO-UHFFFAOYSA-N
14.02658
14.01675
[H][C--][H]
Beilstein:5915711
Gmelin:322698
dihydridocarbonate(2-)
methanediide
chebi_ontology
CH2(2-)
[CH2](2-)
CHEBI:29360
methanediide
Beilstein:5915711
Beilstein
Gmelin:322698
Gmelin
dihydridocarbonate(2-)
IUPAC
methanediide
IUPAC
CH2(2-)
IUPAC
[CH2](2-)
ChEBI
+1
H3O
InChI=1S/H2O/h1H2/p+1
XLYOFNOQVPJJNP-UHFFFAOYSA-O
19.02322
19.01784
[H][O+]([H])[H]
CAS:13968-08-6
Gmelin:141
MolBase:1646
aquahydrogen(1+)
oxidanium
oxonium
trihydridooxygen(1+)
chebi_ontology
H3O(+)
Hydronium cation
Hydronium ion
[OH3](+)
CHEBI:29412
oxonium
CAS:13968-08-6
ChemIDplus
CAS:13968-08-6
NIST Chemistry WebBook
CAS:13968-08-6
ChemIDplus
CAS:13968-08-6
NIST Chemistry WebBook
Gmelin:141
Gmelin
Gmelin:141
Gmelin
aquahydrogen(1+)
IUPAC
oxidanium
IUPAC
oxonium
IUPAC
trihydridooxygen(1+)
IUPAC
H3O(+)
IUPAC
Hydronium cation
NIST_Chemistry_WebBook
Hydronium ion
ChemIDplus
[OH3](+)
MolBase
-1
CH3
InChI=1S/CH3/h1H3/q-1
LGRLWUINFJPLSH-UHFFFAOYSA-N
15.03452
15.02402
[H][C-]([H])[H]
Beilstein:1813938
CAS:15194-58-8
Gmelin:259263
methanide
trihydridocarbonate(1-)
chebi_ontology
CH3(-)
[CH3](-)
lambda(2)-methanuide
methyl anion
CHEBI:29438
methanide
Beilstein:1813938
Beilstein
CAS:15194-58-8
NIST Chemistry WebBook
Gmelin:259263
Gmelin
methanide
IUPAC
trihydridocarbonate(1-)
IUPAC
CH3(-)
IUPAC
[CH3](-)
ChEBI
lambda(2)-methanuide
IUPAC
methyl anion
IUPAC
+1
HO2
InChI=1S/O2/c1-2/p+1
MYMOFIZGZYHOMD-UHFFFAOYSA-O
33.00674
32.99711
[H][O+]=O
Gmelin:508
dioxidenium
hydridodioxygen(1+)
chebi_ontology
HO2(+)
HOO(+)
[HO2](+)
CHEBI:29793
hydridodioxygen(1+)
Gmelin:508
Gmelin
dioxidenium
IUPAC
hydridodioxygen(1+)
IUPAC
HO2(+)
IUPAC
HOO(+)
ChEBI
[HO2](+)
ChEBI
+2
H2N2
InChI=1S/H2N2/c1-2/h1-2H/q+2
DIDSLFHMVHAEHA-UHFFFAOYSA-N
30.02936
30.02070
[H][N+]#[N+][H]
diazynediium
chebi_ontology
HNNH(2+)
[HNNH](2+)
CHEBI:30099
diazynediium
diazynediium
IUPAC
HNNH(2+)
IUPAC
[HNNH](2+)
ChEBI
+1
HN2
InChI=1S/N2/c1-2/p+1
IJGRMHOSHXDMSA-UHFFFAOYSA-O
29.02142
29.01342
[H][N+]#N
CAS:12357-66-3
diazynium
chebi_ontology
HN2+
N#NH(+)
CHEBI:30102
diazynium
CAS:12357-66-3
NIST Chemistry WebBook
diazynium
IUPAC
HN2+
NIST_Chemistry_WebBook
N#NH(+)
IUPAC
0
He
InChI=1S/He
SWQJXJOGLNCZEY-UHFFFAOYSA-N
4.00260
4.00260
[He]
CAS:7440-59-7
Drug_Central:4262
Gmelin:16294
WebElements:He
helium
chebi_ontology
2He
He
Helium
helio
helium
CHEBI:30217
helium atom
CAS:7440-59-7
NIST Chemistry WebBook
Drug_Central:4262
DrugCentral
Gmelin:16294
Gmelin
helium
IUPAC
2He
IUPAC
He
IUPAC
Helium
ChEBI
helio
ChEBI
helium
ChEBI
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
0
HOR
17.007
17.00274
O[*]
CHEBI:13804
CHEBI:22288
CHEBI:2553
KEGG:C00069
Alcohol
alcohols
chebi_ontology
an alcohol
CHEBI:30879
alcohol
Alcohol
KEGG_COMPOUND
alcohols
IUPAC
an alcohol
UniProt
Intended use of the molecular entity or part thereof by humans.
chebi_ontology
CHEBI:33232
application
A particle not known to have substructure.
elementary particle
chebi_ontology
elementary particles
CHEBI:33233
fundamental particle
elementary particle
IUPAC
elementary particles
ChEBI
A monoatomic entity is a molecular entity consisting of a single atom.
chebi_ontology
atomic entity
monoatomic entities
CHEBI:33238
monoatomic entity
atomic entity
ChEBI
monoatomic entities
ChEBI
An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
coordination entities
coordination entity
chebi_ontology
coordination compounds
CHEBI:33240
coordination entity
coordination entities
IUPAC
coordination entity
IUPAC
coordination compounds
ChEBI
chebi_ontology
inorganic hydrides
CHEBI:33242
inorganic hydride
inorganic hydrides
ChEBI
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.
chebi_ontology
organic fundamental parents
organic parent hydrides
CHEBI:33245
organic fundamental parent
organic fundamental parents
ChEBI
organic parent hydrides
ChEBI
Any substituent group which does not contain carbon.
chebi_ontology
inorganic groups
CHEBI:33246
inorganic group
inorganic groups
ChEBI
Any substituent group or skeleton containing carbon.
chebi_ontology
organic groups
CHEBI:33247
organic group
organic groups
ChEBI
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
organyl group
organyl groups
chebi_ontology
groupe organyle
grupo organilo
grupos organilo
CHEBI:33249
organyl group
organyl group
IUPAC
organyl groups
IUPAC
groupe organyle
IUPAC
grupo organilo
IUPAC
grupos organilo
IUPAC
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
CHEBI:22671
CHEBI:23907
atom
chebi_ontology
atome
atomo
atoms
atomus
element
elements
CHEBI:33250
atom
atom
IUPAC
atome
IUPAC
atomo
IUPAC
atoms
ChEBI
atomus
ChEBI
element
ChEBI
elements
ChEBI
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
nucleus
chebi_ontology
Atomkern
Kern
noyau
noyau atomique
nuclei
nucleo
nucleo atomico
nucleus atomi
CHEBI:33252
atomic nucleus
nucleus
IUPAC
Atomkern
ChEBI
Kern
ChEBI
noyau
IUPAC
noyau atomique
ChEBI
nuclei
ChEBI
nucleo
IUPAC
nucleo atomico
ChEBI
nucleus atomi
ChEBI
Heavy nuclear particle: proton or neutron.
nucleon
chebi_ontology
Nukleon
Nukleonen
nucleons
CHEBI:33253
nucleon
nucleon
IUPAC
nucleon
IUPAC
Nukleon
ChEBI
Nukleonen
ChEBI
nucleons
ChEBI
A molecular entity all atoms of which have the same atomic number.
chebi_ontology
homoatomic entity
homoatomic molecular entities
homoatomic molecular entity
CHEBI:33259
elemental molecular entity
homoatomic entity
ChEBI
homoatomic molecular entities
ChEBI
homoatomic molecular entity
ChEBI
chebi_ontology
CHEBI:33262
elemental oxygen
0
O2
31.999
31.98983
chebi_ontology
CHEBI:33263
diatomic oxygen
0
N2
28.013
28.00615
chebi_ontology
CHEBI:33266
diatomic nitrogen
chebi_ontology
CHEBI:33267
elemental nitrogen
An anion consisting of more than one atom.
chebi_ontology
polyatomic anions
CHEBI:33273
polyatomic anion
polyatomic anions
ChEBI
chebi_ontology
chemical messenger
CHEBI:33280
molecular messenger
chemical messenger
ChEBI
A nutrient is a food component that an organism uses to survive and grow.
chebi_ontology
nutrients
CHEBI:33284
nutrient
nutrients
ChEBI
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
chebi_ontology
heteroorganic entities
organoelement compounds
CHEBI:33285
heteroorganic entity
heteroorganic entities
ChEBI
organoelement compounds
ChEBI
An agrochemical is a substance that is used in agriculture or horticulture.
Wikipedia:Agrochemical
chebi_ontology
agrichemical
agrichemicals
agricultural chemicals
agrochemicals
CHEBI:33286
agrochemical
agrichemical
ChEBI
agrichemicals
ChEBI
agricultural chemicals
ChEBI
agrochemicals
ChEBI
A fertilizer is any substance that is added to soil or water to assist the growth of plants.
chebi_ontology
fertiliser
fertilizers
CHEBI:33287
fertilizer
fertiliser
ChEBI
fertilizers
ChEBI
Any material that can be ingested by an organism.
chebi_ontology
food material
food materials
food role
foods
foodstuff
foodstuffs
CHEBI:33290
food
food material
ChEBI
food materials
ChEBI
food role
ChEBI
foods
ChEBI
foodstuff
ChEBI
foodstuffs
ChEBI
An energy-rich substance that can be transformed with release of usable energy.
chebi_ontology
CHEBI:33292
fuel
A molecular entity containing one or more atoms of an alkali metal.
chebi_ontology
alkali metal molecular entities
CHEBI:33296
alkali metal molecular entity
alkali metal molecular entities
ChEBI
An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal.
alkaline earth molecular entity
chebi_ontology
alkaline earth compounds
alkaline earth molecular entities
alkaline-earth compounds
CHEBI:33299
alkaline earth molecular entity
alkaline earth molecular entity
ChEBI
alkaline earth compounds
ChEBI
alkaline earth molecular entities
ChEBI
alkaline-earth compounds
ChEBI
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
pnictogens
chebi_ontology
group 15 elements
group V elements
nitrogenoideos
nitrogenoides
pnictogene
pnictogenes
CHEBI:33300
pnictogen
pnictogens
IUPAC
group 15 elements
ChEBI
group V elements
ChEBI
nitrogenoideos
ChEBI
nitrogenoides
ChEBI
pnictogene
ChEBI
pnictogenes
ChEBI
A p-block molecular entity containing any pnictogen.
pnictogen molecular entity
chebi_ontology
pnictogen molecular entities
CHEBI:33302
pnictogen molecular entity
pnictogen molecular entity
ChEBI
pnictogen molecular entities
ChEBI
Any p-block element belonging to the group 16 family of the periodic table.
PMID:17084588
chalcogen
chalcogens
chebi_ontology
Chalkogen
Chalkogene
anfigeno
anfigenos
calcogeno
calcogenos
chalcogene
chalcogenes
group 16 elements
group VI elements
CHEBI:33303
chalcogen
PMID:17084588
Europe PMC
PMID:17084588
Europe PMC
chalcogen
IUPAC
chalcogens
IUPAC
Chalkogen
ChEBI
Chalkogene
ChEBI
anfigeno
ChEBI
anfigenos
ChEBI
calcogeno
ChEBI
calcogenos
ChEBI
chalcogene
ChEBI
chalcogenes
ChEBI
group 16 elements
ChEBI
group VI elements
ChEBI
Any p-block molecular entity containing a chalcogen.
chalcogen molecular entity
chebi_ontology
chalcogen compounds
chalcogen molecular entities
CHEBI:33304
chalcogen molecular entity
chalcogen molecular entity
ChEBI
chalcogen compounds
ChEBI
chalcogen molecular entities
ChEBI
group 14 elements
chebi_ontology
carbon group element
carbon group elements
carbonoides
cristallogene
cristallogenes
group IV elements
CHEBI:33306
carbon group element atom
group 14 elements
IUPAC
carbon group element
ChEBI
carbon group elements
ChEBI
carbonoides
ChEBI
cristallogene
ChEBI
cristallogenes
ChEBI
group IV elements
ChEBI
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
0
CO2R2
44.010
43.98983
[*]C(=O)O[*]
CHEBI:13204
CHEBI:23028
CHEBI:3408
KEGG:C02391
Wikipedia:Ester
Carboxylic ester
carboxylic esters
chebi_ontology
a carboxylic ester
carboxylic acid esters
CHEBI:33308
carboxylic ester
Carboxylic ester
KEGG_COMPOUND
carboxylic esters
IUPAC
a carboxylic ester
UniProt
carboxylic acid esters
ChEBI
noble gas
noble gases
chebi_ontology
Edelgas
Edelgase
gas noble
gases nobles
gaz noble
gaz nobles
group 18 elements
group VIII elements
inert gases
noble gas
rare gases
CHEBI:33309
noble gas atom
noble gas
IUPAC
noble gases
IUPAC
Edelgas
ChEBI
Edelgase
ChEBI
gas noble
ChEBI
gases nobles
ChEBI
gaz noble
ChEBI
gaz nobles
ChEBI
group 18 elements
IUPAC
group VIII elements
ChEBI
inert gases
ChEBI
noble gas
ChEBI
rare gases
ChEBI
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group elements
chebi_ontology
Hauptgruppenelement
Hauptgruppenelemente
main group element
CHEBI:33318
main group element atom
main group elements
IUPAC
Hauptgruppenelement
ChEBI
Hauptgruppenelemente
ChEBI
main group element
ChEBI
A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
hydracid
chebi_ontology
hydracids
CHEBI:33405
hydracid
hydracid
IUPAC
hydracids
ChEBI
chebi_ontology
pnictogen oxoacids
CHEBI:33408
pnictogen oxoacid
pnictogen oxoacids
ChEBI
-1
0.00000
[*-]
chebi_ontology
monoatomic monoanions
CHEBI:33429
monoatomic monoanion
monoatomic monoanions
ChEBI
chebi_ontology
CHEBI:33431
elemental chlorine
0
Cl
35.453
34.96885
chebi_ontology
atomic chlorine
CHEBI:33432
monoatomic chlorine
atomic chlorine
ChEBI
chebi_ontology
monoatomic halogens
CHEBI:33433
monoatomic halogen
monoatomic halogens
ChEBI
elemental halogen
chebi_ontology
elemental halogens
CHEBI:33434
elemental halogen
elemental halogen
ChEBI
elemental halogens
ChEBI
chebi_ontology
nitrogen oxoacids
oxoacids of nitrogen
CHEBI:33455
nitrogen oxoacid
nitrogen oxoacids
ChEBI
oxoacids of nitrogen
ChEBI
nitrogen oxoanion
chebi_ontology
nitrogen oxoanions
oxoanions of nitrogen
CHEBI:33458
nitrogen oxoanion
nitrogen oxoanion
ChEBI
nitrogen oxoanions
ChEBI
oxoanions of nitrogen
ChEBI
pnictogen oxoanion
chebi_ontology
pnictogen oxoanions
CHEBI:33459
pnictogen oxoanion
pnictogen oxoanion
ChEBI
pnictogen oxoanions
ChEBI
elemental pnictogen
chebi_ontology
elemental pnictogens
CHEBI:33465
elemental pnictogen
elemental pnictogen
ChEBI
elemental pnictogens
ChEBI
chebi_ontology
alkali metal cations
CHEBI:33504
alkali metal cation
alkali metal cations
ChEBI
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
CHEBI:25217
CHEBI:6788
KEGG:C00050
PMID:21784043
Wikipedia:Metal
chebi_ontology
elemental metal
elemental metals
metal element
metal elements
metals
CHEBI:33521
metal atom
PMID:21784043
Europe PMC
elemental metal
ChEBI
elemental metals
ChEBI
metal element
ChEBI
metal elements
ChEBI
metals
ChEBI
chebi_ontology
s-block element
s-block elements
CHEBI:33559
s-block element atom
s-block element
ChEBI
s-block elements
ChEBI
Any main group element atom belonging to the p-block of the periodic table.
chebi_ontology
p-block element
p-block elements
CHEBI:33560
p-block element atom
p-block element
ChEBI
p-block elements
ChEBI
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.
0
CHO2R
45.01740
44.99765
OC([*])=O
CHEBI:13428
CHEBI:13627
CHEBI:23027
PMID:17147560
PMID:18433345
Wikipedia:Carboxylic_acid
carboxylic acid
carboxylic acids
chebi_ontology
Carbonsaeure
Carbonsaeuren
Karbonsaeure
RC(=O)OH
acide carboxylique
acides carboxyliques
acido carboxilico
acidos carboxilicos
CHEBI:33575
carboxylic acid
PMID:17147560
Europe PMC
PMID:17147560
Europe PMC
PMID:18433345
Europe PMC
PMID:18433345
Europe PMC
carboxylic acid
IUPAC
carboxylic acids
IUPAC
Carbonsaeure
ChEBI
Carbonsaeuren
ChEBI
Karbonsaeure
ChEBI
RC(=O)OH
IUPAC
acide carboxylique
IUPAC
acides carboxyliques
IUPAC
acido carboxilico
IUPAC
acidos carboxilicos
IUPAC
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.
chebi_ontology
main group compounds
main group molecular entities
CHEBI:33579
main group molecular entity
main group compounds
ChEBI
main group molecular entities
ChEBI
carbon group molecular entity
chebi_ontology
carbon group molecular entities
CHEBI:33582
carbon group molecular entity
carbon group molecular entity
ChEBI
carbon group molecular entities
ChEBI
A main group molecular entity containing one or more atoms of any noble gas.
noble gas molecular entity
chebi_ontology
noble gas compounds
noble gas molecular entities
CHEBI:33583
noble gas molecular entity
noble gas molecular entity
ChEBI
noble gas compounds
ChEBI
noble gas molecular entities
ChEBI
Any molecule that consists of a series of atoms joined together to form a ring.
Wikipedia:Cyclic_compound
chebi_ontology
cyclic compounds
CHEBI:33595
cyclic compound
cyclic compounds
ChEBI
chebi_ontology
hydrogen compounds
hydrogen molecular entities
CHEBI:33608
hydrogen molecular entity
hydrogen compounds
ChEBI
hydrogen molecular entities
ChEBI
Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds.
aliphatic compounds
chebi_ontology
CHEBI:33653
aliphatic compound
aliphatic compounds
IUPAC
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.
aromatic compounds
aromatic molecular entity
chebi_ontology
aromatics
aromatische Verbindungen
CHEBI:33655
aromatic compound
aromatic compounds
IUPAC
aromatic molecular entity
IUPAC
aromatics
ChEBI
aromatische Verbindungen
ChEBI
chebi_ontology
organic aromatic compounds
CHEBI:33659
organic aromatic compound
organic aromatic compounds
ChEBI
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
s-block molecular entity
chebi_ontology
s-block compounds
s-block molecular entities
CHEBI:33674
s-block molecular entity
s-block molecular entity
ChEBI
s-block compounds
ChEBI
s-block molecular entities
ChEBI
A main group molecular entity that contains one or more atoms of a p-block element.
chebi_ontology
p-block compounds
p-block molecular entities
p-block molecular entitiy
CHEBI:33675
p-block molecular entity
p-block compounds
ChEBI
p-block molecular entities
ChEBI
p-block molecular entitiy
ChEBI
helium molecular entity
chebi_ontology
helium compounds
helium molecular entities
CHEBI:33679
helium molecular entity
helium molecular entity
ChEBI
helium compounds
ChEBI
helium molecular entities
ChEBI
Hydrides are chemical compounds of hydrogen with other chemical elements.
chebi_ontology
CHEBI:33692
hydrides
oxygen hydride
chebi_ontology
hydrides of oxygen
oxygen hydrides
CHEBI:33693
oxygen hydride
oxygen hydride
ChEBI
hydrides of oxygen
ChEBI
oxygen hydrides
ChEBI
A macromolecule formed by a living organism.
biopolymer
chebi_ontology
Biopolymere
biomacromolecules
biopolymers
CHEBI:33694
biomacromolecule
biopolymer
IUPAC
Biopolymere
ChEBI
biomacromolecules
ChEBI
biopolymers
ChEBI
An organic compound having at least one hydroxy group attached to a carbon atom.
CHEBI:64710
hydroxy compounds
chebi_ontology
organic alcohol
organic hydroxy compounds
CHEBI:33822
organic hydroxy compound
hydroxy compounds
IUPAC
organic alcohol
ChEBI
organic hydroxy compounds
ChEBI
Any organic molecule that consists of atoms connected in the form of a ring.
chebi_ontology
organic cyclic compounds
CHEBI:33832
organic cyclic compound
organic cyclic compounds
ChEBI
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).
heteroarenes
chebi_ontology
hetarenes
CHEBI:33833
heteroarene
heteroarenes
IUPAC
hetarenes
IUPAC
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.
Wikipedia:Macromolecule
macromolecule
chebi_ontology
macromolecules
polymer
polymer molecule
polymers
CHEBI:33839
macromolecule
macromolecule
IUPAC
macromolecules
ChEBI
polymer
ChEBI
polymer molecule
IUPAC
polymers
ChEBI
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
reagent
chebi_ontology
reactif
reactivo
reagents
CHEBI:33893
reagent
reagent
IUPAC
reactif
IUPAC
reactivo
IUPAC
reagents
ChEBI
chebi_ontology
metal-tetrapyrrole
metal-tetrapyrrole complex
metallotetrapyrroles
CHEBI:33909
metallotetrapyrrole
metal-tetrapyrrole
ChEBI
metal-tetrapyrrole complex
ChEBI
metallotetrapyrroles
ChEBI
chebi_ontology
CHEBI:33937
macronutrient
chebi_ontology
halide salts
halides
CHEBI:33958
halide salt
halide salts
ChEBI
halides
ChEBI
magnesium coordination entity
chebi_ontology
magnesium coordination compounds
magnesium coordination entities
CHEBI:33976
magnesium coordination entity
magnesium coordination entity
ChEBI
magnesium coordination compounds
ChEBI
magnesium coordination entities
ChEBI
chebi_ontology
nitrogen hydrides
CHEBI:35106
nitrogen hydride
nitrogen hydrides
ChEBI
alkaline earth coordination entity
chebi_ontology
alkaline earth coordination compounds
alkaline earth coordination entities
CHEBI:35217
alkaline earth coordination entity
alkaline earth coordination entity
ChEBI
alkaline earth coordination compounds
ChEBI
alkaline earth coordination entities
ChEBI
A substance that diminishes the rate of a chemical reaction.
inhibitor
chebi_ontology
inhibidor
inhibiteur
inhibitors
CHEBI:35222
inhibitor
inhibitor
IUPAC
inhibidor
ChEBI
inhibiteur
ChEBI
inhibitors
ChEBI
A fuel such as coal, oil and natural gas which has formed over many years through the decomposition of deposited vegetation which was under extreme pressure of an overburden of earth.
fossil fuel
chebi_ontology
CHEBI:35230
fossil fuel
fossil fuel
IUPAC
Any heteroorganic entity containing at least one carbon-nitrogen bond.
organonitrogen compounds
chebi_ontology
organonitrogens
CHEBI:35352
organonitrogen compound
organonitrogen compounds
IUPAC
organonitrogens
ChEBI
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
CHEBI:33274
CHEBI:33436
oxoanion
chebi_ontology
oxoacid anions
oxoanions
CHEBI:35406
oxoanion
oxoanion
ChEBI
oxoacid anions
ChEBI
oxoanions
ChEBI
A substance that reduces or suppresses inflammation.
chebi_ontology
anti-inflammatory drugs
antiinflammatory agent
antiinflammatory drug
antiinflammatory drugs
CHEBI:35472
anti-inflammatory drug
anti-inflammatory drugs
ChEBI
antiinflammatory agent
ChEBI
antiinflammatory drug
ChEBI
antiinflammatory drugs
ChEBI
chebi_ontology
alkali metal salts
CHEBI:35479
alkali metal salt
alkali metal salts
ChEBI
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
chebi_ontology
cardiovascular agent
cardiovascular drugs
CHEBI:35554
cardiovascular drug
cardiovascular agent
ChEBI
cardiovascular drugs
ChEBI
chebi_ontology
carbon oxoacids
oxoacids of carbon
CHEBI:35605
carbon oxoacid
carbon oxoacids
ChEBI
oxoacids of carbon
ChEBI
A drug used to cause dilation of the blood vessels.
chebi_ontology
vasodilator
vasodilator agents
CHEBI:35620
vasodilator agent
vasodilator
ChEBI
vasodilator agents
ChEBI
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.
CHEBI:23960
CHEBI:4859
KEGG:C00287
Wikipedia:Ester
Ester
chebi_ontology
esters
CHEBI:35701
ester
Ester
KEGG_COMPOUND
esters
ChEBI
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
-1
CO2R
44.01000
43.98983
[O-]C([*])=O
CHEBI:13657
CHEBI:25382
CHEBI:3407
KEGG:C00060
chebi_ontology
Carboxylate
Monocarboxylate
a monocarboxylate
monocarboxylates
monocarboxylic acid anions
CHEBI:35757
monocarboxylic acid anion
Carboxylate
KEGG_COMPOUND
Monocarboxylate
KEGG_COMPOUND
a monocarboxylate
UniProt
monocarboxylates
ChEBI
monocarboxylic acid anions
ChEBI
pnictogen hydride
chebi_ontology
pnictogen hydrides
CHEBI:35881
pnictogen hydride
pnictogen hydride
ChEBI
pnictogen hydrides
ChEBI
chebi_ontology
inorganic chloride salt
inorganic chloride salts
inorganic chlorides
CHEBI:36093
inorganic chloride
inorganic chloride salt
ChEBI
inorganic chloride salts
ChEBI
inorganic chlorides
ChEBI
A monoester of a dicarboxylic acid.
chebi_ontology
dicarboxylic acid monoesters
CHEBI:36244
dicarboxylic acid monoester
dicarboxylic acid monoesters
ChEBI
macrocyclic tetrapyrroles
chebi_ontology
cyclic tetrapyrroles
macrocyclic tetrapyrrole
CHEBI:36309
cyclic tetrapyrrole
macrocyclic tetrapyrroles
IUPAC
cyclic tetrapyrroles
ChEBI
macrocyclic tetrapyrrole
ChEBI
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
chebi_ontology
leptons
CHEBI:36338
lepton
leptons
ChEBI
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
chebi_ontology
baryons
CHEBI:36339
baryon
baryons
ChEBI
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
fermion
chebi_ontology
fermions
CHEBI:36340
fermion
fermion
IUPAC
fermions
ChEBI
A particle smaller than an atom.
chebi_ontology
subatomic particles
CHEBI:36342
subatomic particle
subatomic particles
ChEBI
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
chebi_ontology
composite particles
CHEBI:36343
composite particle
composite particles
ChEBI
Hadron is a subatomic particle which experiences the strong force.
chebi_ontology
hadrons
CHEBI:36344
hadron
hadrons
ChEBI
A nucleus or any of its constituents in any of their energy states.
nuclear particle
chebi_ontology
CHEBI:36347
nuclear particle
nuclear particle
IUPAC
Any molecular entity consisting of more than one atom.
chebi_ontology
polyatomic entities
CHEBI:36357
polyatomic entity
polyatomic entities
ChEBI
An ion consisting of more than one atom.
chebi_ontology
polyatomic ions
CHEBI:36358
polyatomic ion
polyatomic ions
ChEBI
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.
chebi_ontology
main group coordination compounds
main-group coordination entities
CHEBI:36562
main-group coordination entity
main group coordination compounds
ChEBI
main-group coordination entities
ChEBI
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.
carbonyl compounds
chebi_ontology
CHEBI:36586
carbonyl compound
carbonyl compounds
IUPAC
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
oxo compounds
chebi_ontology
organic oxo compounds
CHEBI:36587
organic oxo compound
oxo compounds
IUPAC
organic oxo compounds
ChEBI
-1
chebi_ontology
monoanions
CHEBI:36830
monoanion
monoanions
ChEBI
chalcogen hydride
chebi_ontology
chalcogen hydrides
CHEBI:36902
chalcogen hydride
chalcogen hydride
ChEBI
chalcogen hydrides
ChEBI
argon molecular entity
chebi_ontology
argon compounds
argon molecular entities
CHEBI:36908
argon molecular entity
argon molecular entity
ChEBI
argon compounds
ChEBI
argon molecular entities
ChEBI
chebi_ontology
inorganic ions
CHEBI:36914
inorganic ion
inorganic ions
ChEBI
chebi_ontology
inorganic cations
CHEBI:36915
inorganic cation
inorganic cations
ChEBI
A monoatomic or polyatomic species having one or more elementary charges of the proton.
CHEBI:23058
CHEBI:3473
KEGG:C01373
Cation
cation
chebi_ontology
Kation
Kationen
cationes
cations
CHEBI:36916
cation
Cation
KEGG_COMPOUND
cation
ChEBI
cation
IUPAC
Kation
ChEBI
Kationen
ChEBI
cationes
ChEBI
cations
ChEBI
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
organochalcogen compound
chebi_ontology
organochalcogen compounds
CHEBI:36962
organochalcogen compound
organochalcogen compound
ChEBI
organochalcogen compounds
ChEBI
An organochalcogen compound containing at least one carbon-oxygen bond.
PMID:17586126
organooxygen compound
chebi_ontology
organooxygen compounds
CHEBI:36963
organooxygen compound
PMID:17586126
Europe PMC
PMID:17586126
Europe PMC
organooxygen compound
ChEBI
organooxygen compounds
ChEBI
chebi_ontology
organic hydrides
CHEBI:37175
organic hydride
organic hydrides
ChEBI
mononuclear parent hydrides
chebi_ontology
mononuclear hydride
mononuclear hydrides
CHEBI:37176
mononuclear parent hydride
mononuclear parent hydrides
IUPAC
mononuclear hydride
ChEBI
mononuclear hydrides
IUPAC
chebi_ontology
CHEBI:37246
elemental sodium
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).
CHEBI:13800
CHEBI:13801
CHEBI:22209
CHEBI:2426
KEGG:C00174
Acid
acid
chebi_ontology
Saeure
Saeuren
acide
acido
acids
CHEBI:37527
acid
Acid
KEGG_COMPOUND
acid
IUPAC
Saeure
ChEBI
Saeuren
ChEBI
acide
IUPAC
acido
ChEBI
acids
ChEBI
A molecular entity consisting of two or more chemical elements.
chebi_ontology
chemical compound
heteroatomic molecular entities
CHEBI:37577
heteroatomic molecular entity
chemical compound
ChEBI
heteroatomic molecular entities
ChEBI
Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements.
Wikipedia:Halide
chebi_ontology
halides
CHEBI:37578
halide
halides
ChEBI
A compound composed of two or more pyrrole units.
Beilstein:8538310
chebi_ontology
PPys
poly(pyrrole)s
polypyrroles
CHEBI:38077
polypyrrole
Beilstein:8538310
Beilstein
PPys
ChEBI
poly(pyrrole)s
ChEBI
polypyrroles
ChEBI
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
chebi_ontology
heterocyclic organonitrogen compounds
organonitrogen heterocyclic compounds
CHEBI:38101
organonitrogen heterocyclic compound
heterocyclic organonitrogen compounds
ChEBI
organonitrogen heterocyclic compounds
ChEBI
Chlorophylls lacking the terpenoid side chain such as phytyl or farnesyl.
CHEBI:13975
CHEBI:23160
CHEBI:3634
chebi_ontology
Chlorophyllid
chlorophyllides
CHEBI:38206
chlorophyllide
Chlorophyllid
ChEBI
chlorophyllides
ChEBI
chebi_ontology
CHEBI:38222
hydrocarbyl anion
chebi_ontology
magnesium tetrapyrroles
CHEBI:38251
magnesium tetrapyrrole
magnesium tetrapyrroles
ChEBI
chebi_ontology
CHEBI:38496
electron-transport chain inhibitor
chebi_ontology
CHEBI:38497
respiratory-chain inhibitor
An EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor that interferes with the action of cytochrome c oxidase (EC 1.9.3.1).
CHEBI:38501
CHEBI:62966
PMID:12969439
Wikipedia:Cytochrome_c_oxidase
chebi_ontology
CcO inhibitor
EC 1.9.3.1 (cytochrome c oxidase) inhibitors
EC 1.9.3.1 inhibitor
EC 1.9.3.1 inhibitors
NADH cytochrome c oxidase inhibitor
NADH cytochrome c oxidase inhibitors
Warburg's respiratory enzyme inhibitor
Warburg's respiratory enzyme inhibitors
complex IV (mitochondrial electron transport) inhibitor
complex IV (mitochondrial electron transport) inhibitors
cytochrome a3 inhibitor
cytochrome a3 inhibitors
cytochrome aa3 inhibitor
cytochrome aa3 inhibitors
cytochrome c oxidase (EC 1.9.3.1) inhibitor
cytochrome c oxidase (EC 1.9.3.1) inhibitors
cytochrome c oxidase inhibitor
cytochrome c oxidase inhibitors
cytochrome oxidase inhibitor
cytochrome oxidase inhibitors
cytochrome-c oxidase inhibitor
cytochrome-c oxidase inhibitors
ferrocytochrome c oxidase inhibitor
ferrocytochrome c oxidase inhibitors
ferrocytochrome-c:oxygen oxidoreductase inhibitor
ferrocytochrome-c:oxygen oxidoreductase inhibitors
indophenol oxidase inhibitor
indophenol oxidase inhibitors
indophenolase inhibitor
indophenolase inhibitors
mitochondrial complex IV inhibitor
mitochondrial complex IV inhibitors
mitochondrial cytochrome-c oxidase inhibitors
CHEBI:38500
EC 1.9.3.1 (cytochrome c oxidase) inhibitor
PMID:12969439
Europe PMC
CcO inhibitor
ChEBI
EC 1.9.3.1 (cytochrome c oxidase) inhibitors
ChEBI
EC 1.9.3.1 inhibitor
ChEBI
EC 1.9.3.1 inhibitors
ChEBI
NADH cytochrome c oxidase inhibitor
ChEBI
NADH cytochrome c oxidase inhibitors
ChEBI
Warburg's respiratory enzyme inhibitor
ChEBI
Warburg's respiratory enzyme inhibitors
ChEBI
complex IV (mitochondrial electron transport) inhibitor
ChEBI
complex IV (mitochondrial electron transport) inhibitors
ChEBI
cytochrome a3 inhibitor
ChEBI
cytochrome a3 inhibitors
ChEBI
cytochrome aa3 inhibitor
ChEBI
cytochrome aa3 inhibitors
ChEBI
cytochrome c oxidase (EC 1.9.3.1) inhibitor
ChEBI
cytochrome c oxidase (EC 1.9.3.1) inhibitors
ChEBI
cytochrome c oxidase inhibitor
ChEBI
cytochrome c oxidase inhibitors
ChEBI
cytochrome oxidase inhibitor
ChEBI
cytochrome oxidase inhibitors
ChEBI
cytochrome-c oxidase inhibitor
ChEBI
cytochrome-c oxidase inhibitors
ChEBI
ferrocytochrome c oxidase inhibitor
ChEBI
ferrocytochrome c oxidase inhibitors
ChEBI
ferrocytochrome-c:oxygen oxidoreductase inhibitor
ChEBI
ferrocytochrome-c:oxygen oxidoreductase inhibitors
ChEBI
indophenol oxidase inhibitor
ChEBI
indophenol oxidase inhibitors
ChEBI
indophenolase inhibitor
ChEBI
indophenolase inhibitors
ChEBI
mitochondrial complex IV inhibitor
ChEBI
mitochondrial complex IV inhibitors
ChEBI
mitochondrial cytochrome-c oxidase inhibitors
ChEBI
chebi_ontology
inorganic sodium salts
CHEBI:38702
inorganic sodium salt
inorganic sodium salts
ChEBI
Substance which produces loss of feeling or sensation.
anaesthetic
chebi_ontology
Anaesthetika
Anaesthetikum
anaesthetics
anesthetic agent
anesthetic drug
anesthetics
CHEBI:38867
anaesthetic
anaesthetic
IUPAC
Anaesthetika
ChEBI
Anaesthetikum
ChEBI
anaesthetics
ChEBI
anesthetic agent
ChEBI
anesthetic drug
ChEBI
anesthetics
ChEBI
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
Bronsted acid
chebi_ontology
Bronsted-Saeure
acide de Bronsted
donneur d'hydron
hydron donor
CHEBI:39141
Bronsted acid
Bronsted acid
IUPAC
Bronsted-Saeure
ChEBI
acide de Bronsted
IUPAC
donneur d'hydron
IUPAC
hydron donor
IUPAC
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
Bronsted base
chebi_ontology
Bronsted-Base
accepteur d'hydron
base de Bronsted
hydron acceptor
CHEBI:39142
Bronsted base
Bronsted base
IUPAC
Bronsted-Base
ChEBI
accepteur d'hydron
IUPAC
base de Bronsted
IUPAC
hydron acceptor
IUPAC
0
HO
17.00734
17.00274
*O[H]
CHEBI:24706
CHEBI:43171
PDBeChem:OH
HYDROXY GROUP
hydroxy
hydroxy group
chebi_ontology
-OH
hydroxyl
hydroxyl group
CHEBI:43176
hydroxy group
HYDROXY GROUP
PDBeChem
hydroxy
IUPAC
hydroxy group
UniProt
-OH
IUPAC
hydroxyl
ChEBI
hydroxyl group
ChEBI
0
O
15.99940
15.99491
O=*
CHEBI:29353
CHEBI:44607
PDBeChem:O
OXO GROUP
oxo
chebi_ontology
=O
CHEBI:46629
oxo group
OXO GROUP
PDBeChem
oxo
IUPAC
=O
IUPAC
In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').
mineral
chebi_ontology
Minerale
minerales
minerals
mineraux
CHEBI:46662
mineral
mineral
ChEBI
Minerale
ChEBI
minerales
ChEBI
minerals
ChEBI
mineraux
ChEBI
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Wikipedia:Solvent
chebi_ontology
Loesungsmittel
solvant
solvents
CHEBI:46787
solvent
Loesungsmittel
ChEBI
solvant
ChEBI
solvents
ChEBI
0
CHO2
45.01744
44.99765
*C(=O)O
CHEBI:23025
CHEBI:41420
PDBeChem:FMT
CARBOXY GROUP
carboxy
chebi_ontology
-C(O)OH
-CO2H
-COOH
carboxyl group
CHEBI:46883
carboxy group
CARBOXY GROUP
PDBeChem
carboxy
IUPAC
-C(O)OH
IUPAC
-CO2H
ChEBI
-COOH
IUPAC
carboxyl group
ChEBI
Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
chebi_ontology
Indikator
CHEBI:47867
indicator
Indikator
ChEBI
macrocyclic polypyrroles
chebi_ontology
cyclic polypyrroles
polypyrrole macrocycles
CHEBI:47882
cyclic polypyrrole
macrocyclic polypyrroles
IUPAC
cyclic polypyrroles
ChEBI
polypyrrole macrocycles
ChEBI
A nitrogen oxoacid of formula HNO3 in which the nitrogen atom is bonded to a hydroxy group and by equivalent bonds to the remaining two oxygen atoms.
0
HNO3
InChI=1S/HNO3/c2-1(3)4/h(H,2,3,4)
GRYLNZFGIOXLOG-UHFFFAOYSA-N
63.01280
62.99564
O[N+]([O-])=O
CHEBI:25545
CHEBI:7580
CAS:7697-37-2
Gmelin:1576
KEGG:C00244
KEGG:D02313
MetaCyc:CPD-15028
PMID:22285512
PMID:23402861
Reaxys:3587310
Wikipedia:Nitric_acid
Nitric acid
hydrogen trioxonitrate(1-)
hydroxidodioxidonitrogen
trioxonitric acid
chebi_ontology
HNO3
HONO2
Salpetersaeure
[NO2(OH)]
acide azotique
acide nitrique
azotic acid
hydrogen nitrate
CHEBI:48107
nitric acid
CAS:7697-37-2
ChemIDplus
CAS:7697-37-2
NIST Chemistry WebBook
Gmelin:1576
Gmelin
PMID:22285512
Europe PMC
PMID:23402861
Europe PMC
Reaxys:3587310
Reaxys
Nitric acid
KEGG_COMPOUND
hydrogen trioxonitrate(1-)
IUPAC
hydroxidodioxidonitrogen
IUPAC
trioxonitric acid
IUPAC
HNO3
IUPAC
HONO2
NIST_Chemistry_WebBook
Salpetersaeure
ChemIDplus
[NO2(OH)]
IUPAC
acide azotique
ChEBI
acide nitrique
ChemIDplus
azotic acid
ChemIDplus
hydrogen nitrate
NIST_Chemistry_WebBook
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
polar solvent
chebi_ontology
polar solvents
CHEBI:48354
polar solvent
polar solvent
IUPAC
polar solvents
ChEBI
A polar solvent that is capable of acting as a hydron (proton) donor.
protogenic solvent
chebi_ontology
CHEBI:48356
protic solvent
protogenic solvent
IUPAC
chebi_ontology
CHEBI:48359
protophilic solvent
chebi_ontology
CHEBI:48360
amphiprotic solvent
Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances.
antagonist
chebi_ontology
antagonista
antagoniste
antagonists
CHEBI:48706
antagonist
antagonist
IUPAC
antagonista
ChEBI
antagoniste
ChEBI
antagonists
ChEBI
0
Ar
InChI=1S/Ar
XKRFYHLGVUSROY-UHFFFAOYSA-N
39.94800
39.96238
[Ar]
CHEBI:33311
CAS:7440-37-1
WebElements:Ar
argon
chebi_ontology
18Ar
Ar
argon
CHEBI:49475
argon atom
CAS:7440-37-1
ChemIDplus
argon
IUPAC
18Ar
IUPAC
Ar
IUPAC
argon
ChEBI
0
H
InChI=1S/H
YZCKVEUIGOORGS-UHFFFAOYSA-N
1.00794
1.00783
[H]
CHEBI:24634
CHEBI:49636
WebElements:H
hydrogen
chebi_ontology
1H
H
Wasserstoff
hidrogeno
hydrogen
hydrogene
CHEBI:49637
hydrogen atom
hydrogen
IUPAC
1H
IUPAC
H
IUPAC
Wasserstoff
ChEBI
hidrogeno
ChEBI
hydrogen
ChEBI
hydrogene
ChEBI
An enzyme inhibitor that interferes with the activity of cytochrome P450 involved in catalysis of organic substances.
chebi_ontology
CYP2D6 inhbitor
CYP2D6 inhbitors
P450 inhibitors
cytochrome P450 inhibitor
cytochrome P450 inhibitors
CHEBI:50183
P450 inhibitor
CYP2D6 inhbitor
ChEBI
CYP2D6 inhbitors
ChEBI
P450 inhibitors
ChEBI
cytochrome P450 inhibitor
ChEBI
cytochrome P450 inhibitors
ChEBI
chebi_ontology
CHEBI:50312
onium compound
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
onium cations
chebi_ontology
onium cations
onium ion
onium ions
CHEBI:50313
onium cation
onium cations
IUPAC
onium cations
ChEBI
onium ion
ChEBI
onium ions
ChEBI
+1
ClH2
InChI=1S/ClH2/h1H2/q+1
IGJWHVUMEJASKV-UHFFFAOYSA-N
37.46858
36.98395
[H][Cl+][H]
Gmelin:331
chloranium
chloronium
chebi_ontology
H2Cl(+)
[ClH2](+)
CHEBI:50315
chloronium
Gmelin:331
Gmelin
chloranium
IUPAC
chloronium
IUPAC
H2Cl(+)
IUPAC
[ClH2](+)
IUPAC
A role played by a molecular entity used to study the microscopic environment.
chebi_ontology
CHEBI:50406
probe
An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
CHEBI:22937
CHEBI:50581
chebi_ontology
alkyl alcohols
hydroxyalkane
hydroxyalkanes
CHEBI:50584
alkyl alcohol
alkyl alcohols
ChEBI
hydroxyalkane
ChEBI
hydroxyalkanes
ChEBI
Any molecular entity that contains carbon.
CHEBI:25700
CHEBI:33244
chebi_ontology
organic compounds
organic entity
organic molecular entities
CHEBI:50860
organic molecular entity
organic compounds
ChEBI
organic entity
ChEBI
organic molecular entities
ChEBI
A role is particular behaviour which a material entity may exhibit.
chebi_ontology
CHEBI:50906
role
A poison that interferes with the functions of the nervous system.
CHEBI:50911
Wikipedia:Neurotoxin
chebi_ontology
agente neurotoxico
nerve poison
nerve poisons
neurotoxic agent
neurotoxic agents
neurotoxicant
neurotoxins
CHEBI:50910
neurotoxin
agente neurotoxico
ChEBI
nerve poison
ChEBI
nerve poisons
ChEBI
neurotoxic agent
ChEBI
neurotoxic agents
ChEBI
neurotoxicant
ChEBI
neurotoxins
ChEBI
A role played by the molecular entity or part thereof within a chemical context.
chebi_ontology
CHEBI:51086
chemical role
CHEBI:25556
CHEBI:7594
KEGG:C06061
chebi_ontology
Nitrogenous compounds
nitrogen compounds
nitrogen molecular entities
CHEBI:51143
nitrogen molecular entity
Nitrogenous compounds
KEGG_COMPOUND
nitrogen compounds
ChEBI
nitrogen molecular entities
ChEBI
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
chebi_ontology
organodiyl groups
CHEBI:51422
organodiyl group
organodiyl groups
ChEBI
chebi_ontology
CHEBI:51446
organic divalent group
chebi_ontology
CHEBI:51447
organic univalent group
An organic anion that is the conjugate base of methanol.
-1
CH3O
InChI=1S/CH3O/c1-2/h1H3/q-1
NBTOZLQBSIZIKS-UHFFFAOYSA-N
31.03390
31.01894
C[O-]
Reaxys:1839368
chebi_ontology
methoxide ion
CHEBI:52090
methoxide
Reaxys:1839368
Reaxys
Reaxys:1839368
Reaxys
methoxide ion
ChEBI
A biological role played by the molecular entity or part thereof within a biochemical context.
chebi_ontology
CHEBI:52206
biochemical role
A role played by the molecular entity or part thereof which causes the development of a pathological process.
chebi_ontology
etiopathogenetic agent
etiopathogenetic role
CHEBI:52209
aetiopathogenetic role
etiopathogenetic agent
ChEBI
etiopathogenetic role
ChEBI
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
chebi_ontology
CHEBI:52210
pharmacological role
chebi_ontology
CHEBI:52211
physiological role
Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
Wikipedia:Ligand
chebi_ontology
ligands
CHEBI:52214
ligand
ligands
ChEBI
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
CHEBI:33293
CHEBI:33294
chebi_ontology
farmaco
medicament
pharmaceuticals
CHEBI:52217
pharmaceutical
farmaco
ChEBI
medicament
ChEBI
pharmaceuticals
ChEBI
chebi_ontology
inorganic hydroxides
CHEBI:52625
inorganic hydroxy compound
inorganic hydroxides
ChEBI
A cyclic compound having as ring members atoms of at least two different elements.
Heterocyclic compound
chebi_ontology
compuesto heterociclico
compuestos heterociclicos
heterocycle
heterocyclic compounds
CHEBI:5686
heterocyclic compound
Heterocyclic compound
KEGG_COMPOUND
compuesto heterociclico
IUPAC
compuestos heterociclicos
IUPAC
heterocycle
ChEBI
heterocyclic compounds
ChEBI
A cyclic tetrapyrrole anion that is the conjugate base of chlorophyllide a arising from deprotonation of the carboxy group; major species at pH 7.3.
-1
C35H33MgN4O5
InChI=1S/C35H36N4O5.Mg/c1-8-19-15(3)22-12-24-17(5)21(10-11-28(40)41)32(38-24)30-31(35(43)44-7)34(42)29-18(6)25(39-33(29)30)14-27-20(9-2)16(4)23(37-27)13-26(19)36-22;/h8,12-14,17,21,31H,1,9-11H2,2-7H3,(H3,36,37,38,39,40,41,42);/q;+2/p-3/t17-,21-,31+;/m0./s1
ANWUQYTXRXCEMZ-NYABAGMLSA-K
613.96600
613.23069
CCC1=C(C)C2=[N+]3C1=Cc1c(C)c4C(=O)[C@H](C(=O)OC)C5=C6[C@@H](CCC([O-])=O)[C@H](C)C7=[N+]6[Mg--]3(n1c45)n1c(=C7)c(C)c(C=C)c1=C2
chebi_ontology
chlorophyllide a anion
CHEBI:57942
chlorophyllide a(1-)
chlorophyllide a anion
ChEBI
Conjugate acid of carbon monoxide arising from protonation of the carbon; major species at pH 7.3.
+1
CHO
InChI=1S/CHO/c1-2/h1H/q+1
XPRMKTHGXOVKEH-UHFFFAOYSA-N
29.01800
29.00219
C#[O+]
methylidyneoxonium
chebi_ontology
CO(1+)
methylidyneoxidanium
CHEBI:58072
carbon monoxide(1+)
methylidyneoxonium
IUPAC
CO(1+)
ChEBI
methylidyneoxidanium
ChEBI
A cyclic tetrapyrrole anion arising from deprotonation at the 21-position of chlorophyll a.
-1
C55H71MgN4O5
InChI=1S/C55H72N4O5.Mg/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42;/h13,26,28-33,37,41H,1,14-25,27H2,2-12H3,(H-,56,57,58,59,61);/q-2;+2/p-1/b34-26+;/t32-,33-,37+,41+;/m1./s1
VSRAJQZEEBBURZ-ONWAGYJKSA-M
892.48100
891.52804
CCC1=C(C)C2=Cc3c(C=C)c(C)c4C=C5[C@@H](C)[C@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C6=[N+]5[Mg--]5(n34)n3c(=CC1=[N+]25)c(C)c1C(=O)[C-](C(=O)OC)C6=c31
chebi_ontology
chlorophyll a
CHEBI:58416
chlorophyll a(1-)
chlorophyll a
UniProt
An organic anion arising from deprotonation of a cyclic tetrapyrrole compound.
chebi_ontology
cyclic tetrapyrrole anions
CHEBI:58941
cyclic tetrapyrrole anion
cyclic tetrapyrrole anions
ChEBI
A substance used as an indicator of a biological state.
chebi_ontology
biological marker
CHEBI:59163
biomarker
biological marker
ChEBI
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
chebi_ontology
Chemische Substanz
CHEBI:59999
chemical substance
Chemische Substanz
ChEBI
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
chebi_ontology
a monovalent cation
CHEBI:60242
monovalent inorganic cation
a monovalent cation
UniProt
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.
chebi_ontology
signal molecule
signal molecules
signaling molecule
signaling molecules
signalling molecules
CHEBI:62488
signalling molecule
signal molecule
ChEBI
signal molecules
ChEBI
signaling molecule
ChEBI
signaling molecules
ChEBI
signalling molecules
ChEBI
A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively.
PMID:12076975
PMID:17667957
PMID:9741578
Wikipedia:Reactive_nitrogen_species
chebi_ontology
RNI
RNS
CHEBI:62764
reactive nitrogen species
PMID:12076975
SUBMITTER
PMID:17667957
SUBMITTER
PMID:9741578
SUBMITTER
RNI
SUBMITTER
RNS
SUBMITTER
A substance that removes electrons from another reactant in a redox reaction.
chebi_ontology
oxidant
oxidants
oxidiser
oxidisers
oxidising agents
oxidizer
oxidizers
oxidizing agent
oxidizing agents
CHEBI:63248
oxidising agent
oxidant
ChEBI
oxidants
ChEBI
oxidiser
ChEBI
oxidisers
ChEBI
oxidising agents
ChEBI
oxidizer
ChEBI
oxidizers
ChEBI
oxidizing agent
ChEBI
oxidizing agents
ChEBI
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
Wikipedia:Food_additive
chebi_ontology
food additives
CHEBI:64047
food additive
food additives
ChEBI
An organic molecular entity containing a single carbon atom (C1).
chebi_ontology
one-carbon compounds
CHEBI:64708
one-carbon compound
one-carbon compounds
ChEBI
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
chebi_ontology
organic acids
CHEBI:64709
organic acid
organic acids
ChEBI
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.
Wikipedia:Poison
chebi_ontology
poisonous agent
poisonous agents
poisonous substance
poisonous substances
poisons
toxic agent
toxic agents
toxic substance
toxic substances
CHEBI:64909
poison
poisonous agent
ChEBI
poisonous agents
ChEBI
poisonous substance
ChEBI
poisonous substances
ChEBI
poisons
ChEBI
toxic agent
ChEBI
toxic agents
ChEBI
toxic substance
ChEBI
toxic substances
ChEBI
Any compound that has anti-inflammatory effects.
chebi_ontology
anti-inflammatory agents
antiinflammatory agent
antiinflammatory agents
CHEBI:67079
anti-inflammatory agent
anti-inflammatory agents
ChEBI
antiinflammatory agent
ChEBI
antiinflammatory agents
ChEBI
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
chebi_ontology
organic compound
organic compounds
organic molecules
CHEBI:72695
organic molecule
organic compound
ChEBI
organic compounds
ChEBI
organic molecules
ChEBI
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
chebi_ontology
eukaryotic metabolites
CHEBI:75763
eukaryotic metabolite
eukaryotic metabolites
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
CHEBI:77721
CHEBI:77743
chebi_ontology
animal metabolites
CHEBI:75767
animal metabolite
animal metabolites
ChEBI
Any animal metabolite produced during a metabolic reaction in mammals.
CHEBI:77464
CHEBI:77744
chebi_ontology
mammalian metabolites
CHEBI:75768
mammalian metabolite
mammalian metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
chebi_ontology
Mus musculus metabolite
Mus musculus metabolites
mouse metabolites
CHEBI:75771
mouse metabolite
Mus musculus metabolite
ChEBI
Mus musculus metabolites
ChEBI
mouse metabolites
ChEBI
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
CHEBI:76949
CHEBI:76951
chebi_ontology
S. cerevisiae metabolite
S. cerevisiae metabolites
S. cerevisiae secondary metabolite
S. cerevisiae secondary metabolites
Saccharomyces cerevisiae metabolites
Saccharomyces cerevisiae secondary metabolites
baker's yeast metabolite
baker's yeast metabolites
baker's yeast secondary metabolite
baker's yeast secondary metabolites
CHEBI:75772
Saccharomyces cerevisiae metabolite
S. cerevisiae metabolite
ChEBI
S. cerevisiae metabolites
ChEBI
S. cerevisiae secondary metabolite
ChEBI
S. cerevisiae secondary metabolites
ChEBI
Saccharomyces cerevisiae metabolites
ChEBI
Saccharomyces cerevisiae secondary metabolites
ChEBI
baker's yeast metabolite
ChEBI
baker's yeast metabolites
ChEBI
baker's yeast secondary metabolite
ChEBI
baker's yeast secondary metabolites
ChEBI
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
chebi_ontology
prokaryotic metabolites
CHEBI:75787
prokaryotic metabolite
prokaryotic metabolites
ChEBI
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
Wikipedia:Greenhouse_gas
chebi_ontology
greenhouse gases
CHEBI:76413
envoPolar
greenhouse gas
greenhouse gases
ChEBI
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.
PMID:22519407
PMID:24001847
chebi_ontology
propellants
CHEBI:76414
propellant
PMID:22519407
Europe PMC
PMID:24001847
Europe PMC
propellants
ChEBI
An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
Wikipedia:Oxidoreductase
chebi_ontology
EC 1.* (oxidoreductase) inhibitors
EC 1.* inhibitor
EC 1.* inhibitors
oxidoreductase (EC 1.*) inhibitor
oxidoreductase (EC 1.*) inhibitors
oxidoreductase inhibitor
oxidoreductase inhibitors
CHEBI:76725
EC 1.* (oxidoreductase) inhibitor
EC 1.* (oxidoreductase) inhibitors
ChEBI
EC 1.* inhibitor
ChEBI
EC 1.* inhibitors
ChEBI
oxidoreductase (EC 1.*) inhibitor
ChEBI
oxidoreductase (EC 1.*) inhibitors
ChEBI
oxidoreductase inhibitor
ChEBI
oxidoreductase inhibitors
ChEBI
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).
chebi_ontology
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors
EC 1.9.* inhibitor
EC 1.9.* inhibitors
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
CHEBI:76736
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor
ChEBI
EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors
ChEBI
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors
ChEBI
EC 1.9.* inhibitor
ChEBI
EC 1.9.* inhibitors
ChEBI
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
ChEBI
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
ChEBI
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on hydrogen as donors (EC 1.14.*.*).
chebi_ontology
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors
EC 1.14.* inhibitor
EC 1.14.* 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
CHEBI:76741
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor
EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors
ChEBI
EC 1.14.* inhibitor
ChEBI
EC 1.14.* inhibitors
ChEBI
inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
ChEBI
inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
ChEBI
inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
ChEBI
inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*)
ChEBI
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor
ChEBI
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors
ChEBI
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor
ChEBI
oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors
ChEBI
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.*).
chebi_ontology
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
EC 1.14.14.* inhibitor
EC 1.14.14.* 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
CHEBI:76838
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor
EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors
ChEBI
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
ChEBI
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
ChEBI
EC 1.14.14.* inhibitor
ChEBI
EC 1.14.14.* inhibitors
ChEBI
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
ChEBI
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
ChEBI
An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).
chebi_ontology
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors
EC 1.9.3.* inhibitor
EC 1.9.3.* inhibitors
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors
CHEBI:76870
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors
ChEBI
EC 1.9.3.* inhibitor
ChEBI
EC 1.9.3.* inhibitors
ChEBI
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor
ChEBI
oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors
ChEBI
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).
chebi_ontology
EC 1.14.14.1 (unspecific monooxygenase) inhibitors
EC 1.14.14.1 inhibitor
EC 1.14.14.1 inhibitors
aryl hydrocarbon hydroxylase inhibitor
aryl hydrocarbon hydroxylase inhibitors
aryl-4-monooxygenase inhibitor
aryl-4-monooxygenase inhibitors
flavoprotein monooxygenase inhibitor
flavoprotein monooxygenase inhibitors
flavoprotein-linked monooxygenase inhibitor
flavoprotein-linked monooxygenase inhibitors
microsomal P-450 inhibitor
microsomal P-450 inhibitors
microsomal monooxygenase inhibitor
microsomal 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
unspecific monooxygenase inhibitor
unspecific monooxygenase inhibitors
xenobiotic monooxygenase inhibitor
xenobiotic monooxygenase inhibitors
CHEBI:76898
EC 1.14.14.1 (unspecific monooxygenase) inhibitor
EC 1.14.14.1 (unspecific monooxygenase) inhibitors
ChEBI
EC 1.14.14.1 inhibitor
ChEBI
EC 1.14.14.1 inhibitors
ChEBI
aryl hydrocarbon hydroxylase inhibitor
ChEBI
aryl hydrocarbon hydroxylase inhibitors
ChEBI
aryl-4-monooxygenase inhibitor
ChEBI
aryl-4-monooxygenase inhibitors
ChEBI
flavoprotein monooxygenase inhibitor
ChEBI
flavoprotein monooxygenase inhibitors
ChEBI
flavoprotein-linked monooxygenase inhibitor
ChEBI
flavoprotein-linked monooxygenase inhibitors
ChEBI
microsomal P-450 inhibitor
ChEBI
microsomal P-450 inhibitors
ChEBI
microsomal monooxygenase inhibitor
ChEBI
microsomal monooxygenase inhibitors
ChEBI
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitor
ChEBI
substrate,reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating or -epoxidising) inhibitors
ChEBI
unspecific monooxygenase (EC 1.14.14.1) inhibitor
ChEBI
unspecific monooxygenase (EC 1.14.14.1) inhibitors
ChEBI
unspecific monooxygenase inhibitor
ChEBI
unspecific monooxygenase inhibitors
ChEBI
xenobiotic monooxygenase inhibitor
ChEBI
xenobiotic monooxygenase inhibitors
ChEBI
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
chebi_ontology
metabolic pathway inhibitor
metabolic pathway inhibitors
pathway inhibitors
CHEBI:76932
pathway inhibitor
metabolic pathway inhibitor
ChEBI
metabolic pathway inhibitors
ChEBI
pathway inhibitors
ChEBI
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
CHEBI:75765
CHEBI:76947
chebi_ontology
fungal metabolites
CHEBI:76946
fungal metabolite
fungal metabolites
ChEBI
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
CHEBI:75760
CHEBI:76970
chebi_ontology
CHEBI:76969
bacterial metabolite
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
chebi_ontology
E.coli metabolite
E.coli metabolites
Escherichia coli metabolites
CHEBI:76971
Escherichia coli metabolite
E.coli metabolite
ChEBI
E.coli metabolites
ChEBI
Escherichia coli metabolites
ChEBI
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
CHEBI:75770
CHEBI:77123
chebi_ontology
H. sapiens metabolite
H. sapiens metabolites
Homo sapiens metabolite
Homo sapiens metabolites
CHEBI:77746
human metabolite
H. sapiens metabolite
ChEBI
H. sapiens metabolites
ChEBI
Homo sapiens metabolite
ChEBI
Homo sapiens metabolites
ChEBI
A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container.
Wikipedia:Packaging_gas
chebi_ontology
food packaging gases
CHEBI:77974
food packaging gas
food packaging gases
ChEBI
A propellant that is used to expel foods from an aerosol container.
chebi_ontology
food propellants
CHEBI:78017
food propellant
food propellants
ChEBI
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.
chebi_ontology
dietary component
dietary components
food components
CHEBI:78295
food component
dietary component
ChEBI
dietary components
ChEBI
food components
ChEBI
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.
Wikipedia:Refrigerant
chebi_ontology
refrigerants
CHEBI:78433
refrigerant
refrigerants
ChEBI
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.
chebi_ontology
carbohydrates and derivatives
carbohydrates and their derivatives
CHEBI:78616
carbohydrates and carbohydrate derivatives
carbohydrates and derivatives
ChEBI
carbohydrates and their derivatives
ChEBI
Any compound that is added to manufactured materials to inhibit, suppress, or delay the production of flames and so prevent the spread of fire.
Wikipedia:Flame_retardant
chebi_ontology
flame retardants
CHEBI:79314
flame retardant
flame retardants
ChEBI
Any inorganic anion with a valency of one.
chebi_ontology
monovalent inorganic anions
CHEBI:79389
monovalent inorganic anion
monovalent inorganic anions
ChEBI
A cyclic tetrapyrrole anion arising from deprotonation of the carboxy group and the C-21 posiiton of chlorophyllide a. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
-2
C35H32MgN4O5
InChI=1S/C35H35N4O5.Mg/c1-8-19-15(3)22-12-24-17(5)21(10-11-28(40)41)32(38-24)30-31(35(43)44-7)34(42)29-18(6)25(39-33(29)30)14-27-20(9-2)16(4)23(37-27)13-26(19)36-22;/h8,12-14,17,21H,1,9-11H2,2-7H3,(H3,36,37,38,39,40,41,42);/q-1;+2/p-3/t17-,21-;/m0./s1
IZOAGQOHKWGYKF-PVMVIUQGSA-K
612.95800
612.22341
CCC1=C(C)C2=[N+]3C1=Cc1c(C)c4C(=O)[C-](C(=O)OC)C5=C6[C@@H](CCC([O-])=O)[C@H](C)C7=[N+]6[Mg--]3(n1c45)n1c(=C7)c(C)c(C=C)c1=C2
chebi_ontology
chlorophyllide a
CHEBI:83348
chlorophyllide a(2-)
chlorophyllide a
UniProt
cell
A system in which living entities consume living, dead, or non-living entities or are consumed by other living entities through trophic interactions.
consumer-resource system
trophic system
topological web
web of life
food web
A system in which living entities consume living, dead, or non-living entities or are consumed by other living entities through trophic interactions.
https://en.wikipedia.org/wiki/Food_web
A food web in which the outputs of a trophic interaction are consumed by organisms acting in a lower trophic level relative to the initial interaction.
Definition needs revision, but core intention is captured.
food cycle
A system in which a series of living entities consume living, dead, or non-living entities in successively higher trophic levels.
consumer-resource chain
trophic chain
food chain
A system in which a series of living entities consume living, dead, or non-living entities in successively higher trophic levels.
https://en.wikipedia.org/wiki/Food_web
A function which inheres in a living entity by virtue of that entity being able to feed on a material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
trophic function
A function which inheres in a living entity by virtue of that entity being able to feed on living or once-living (dead) material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
heterotrophic function
A function which inheres in a living entity by virtue of that entity being able to harvest energy and create biomass from non-living materials.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
autotrophic function
A function which inheres in a living entity by virtue of that entity being able to realize autotrophic and heterotrophic functions.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
mixotrophic function
A process during which a living entity acquires or generates food and energy from a living, dead, or non-living entity.
All categories of interaction partners should be indentified in subclasses.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
trophic interaction
A trophic interaction process during which a living entity acquires energy and generates biomass from non-living entities.
This should be axiomatised and made a defined class: any trophic interaction which has as input some inorganic material (non-living) that is the only source of carbon or reducing equivalents source is a autotrophic process.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
autotrophy
An organism that obtains carbon for growth and development by metabolizing biogenic organic compounds derived from living or dead material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
consumer
heterotroph
A trophic interaction process during which a living entity acquires food and energy by consuming another organism or organism part, living or dead.
This should be axiomatised and made a defined class: any trophic interaction which has as input some organic material (living or dead) that is the only source of carbon or reducing equivalents source is a autotrophic process.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
consumption
heterotrophy
An organism which is capable of heterotrophic and autotrophic trophic processes.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
mixotroph
A process during which a living entity generates food from abiotic sources and captures energy from light.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
photoautotrophy
A process during which a living entity generates food from abiotic sources and captures energy from light.
https://en.wikipedia.org/wiki/Phototroph
A process during which a living entity acquires reducing equivalents from inorganic chemicals for use in biosynthesis or energy conservation via aerobic or anaerobic respiration.
http://orcid.org/0000-0002-4366-3088
lithotrophy
A process during which a living entity acquires reducing equivalents from inorganic chemicals for use in biosynthesis or energy conservation via aerobic or anaerobic respiration.
https://en.wikipedia.org/wiki/Lithotroph
A heterotroph which consumes fungi.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
mycophage
fungivore
A heterotrophic process during which a living entity acquires food and energy by consuming living fungal material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
mycophagy
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a fungi-heavy diet: this is a functional defintion, referencing the act of eating, primarily, a fungi-based diet.
fungivory
A process during which a living entity generates food from abiotic sources or through consumption of living or dead material, and captures energy from light.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
phototrophy
A process during which a living entity generates food from abiotic sources or through consumption of living or dead material, and captures energy from light.
https://en.wikipedia.org/wiki/Phototroph
A history which includes all the processes during which resources are used by an organism to grow, survive, and reproduce over its lifetime.
http://orcid.org/0000-0002-4364-7715
http://orcid.org/0000-0002-4366-3088
life history
A history which includes all the processes during which resources are used by an organism to grow, survive, and reproduce over its lifetime.
ISBN:130596733X
ISBN:9781305967335
A heterotroph which consumes plants or macroalgae via ingestion through a type of "mouth". Plant or algal matter is broken down through an internal digestion process.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
primary consumer
plant eater
There is some debate over whether herbivores should be restricted to plants and macroalgae or generalsed to more photoautotrophs. We welcome input on our issue tracker: https://github.com/EcologicalSemantics/ecocore
herbivore
A heterotrophic process during which a living entity acquires food and energy by consuming living plant- or macro-algal material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
plant trophism
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a herbivorous diet: this is a functional defintion, referencing the act of eating, primarily, a plant- or macroalga-based diet.
herbivory
A heterotrophic process during which a living entity acquires food and energy from consuming living metazoan (animal) material.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
In this class, we make no commitment to whether the organism belongs to a taxon which has adapted to a carnivorous diet: this is a functional defintion, referencing the act of eating, primarily, an animal-based diet.
carnivory
An organism which is capable of incorporating abiogenic (inorganic) carbon into its biomass.
http://orcid.org/0000-0002-2908-3327
http://orcid.org/0000-0002-4366-3088
primary producer
autotroph
Quotient (or ratio) of surface area of an organism divided by the mass of the same organism
http://orcid.org/0000-0002-2908-3327
area to mass ratio
The duration of the development from fertilized, deposited or implanted egg to hatching/birth. Corresponds to egg incubation duration in oviparous animals and to gestation period duration in viviparous animals.
http://orcid.org/0000-0002-2908-3327
gestation
incubation
prenatal development
Type of food comprising the majority of the diet of an organism
http://orcid.org/0000-0002-2908-3327
primary diet
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that develop inside a shelled egg, with a large food supply in yolk, after internal fertilization
http://orcid.org/0000-0002-2908-3327
oviparous
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that are born live, or where the development of the offspring is supported by either parent in or on any part of their body
http://orcid.org/0000-0002-2908-3327
viviparous
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that are born live after retaining the eggs inside the body of the female
http://orcid.org/0000-0002-2908-3327
ovoviviparous
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilization, the oocytes being released and fertilized outside the female's body by the male
http://orcid.org/0000-0002-2908-3327
ovuliparous
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce zygotes that develop in the female's oviducts, but find their nutriments from other tissues, whether skin or glandular tissue
http://orcid.org/0000-0002-2908-3327
histrotrophic viviparity
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring that receive nutriments from the female during prenatal development via a specialized structure, such as a placenta
http://orcid.org/0000-0002-2908-3327
hemotrophic viviparity
The second post-naupliar life stage of a copepod
http://orcid.org/0000-0002-2908-3327
copepodid stage 2
The third post-naupliar life stage of a copepod
http://orcid.org/0000-0002-2908-3327
copepodid stage 3
The fourth post-naupliar life stage of a copepod
http://orcid.org/0000-0002-2908-3327
copepodid stage 4
The sixth post-naupliar life stage of a copepod
http://orcid.org/0000-0002-2908-3327
copepodid stage 6
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for running
http://orcid.org/0000-0002-2908-3327
cursorial
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for digging and living underground
http://orcid.org/0000-0002-2908-3327
fossorial
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for living in trees
http://orcid.org/0000-0002-2908-3327
arboreal
a reproductive quality inhering in the bearer by virtue of the bearer having reproductive organs normally associated with both male and female sexes at the same time
http://orcid.org/0000-0002-2908-3327
monoecious
hermaphroditic
a reproductive quality inhering in the bearer by virtue of the bearer having female reproductive organs at the beginning of its life and then switching to male reproductive organs
http://orcid.org/0000-0002-2908-3327
protogynous
The process by which a larvae transforms into an adult wherein the larvae looks like a smaller adult form
http://orcid.org/0000-0002-2908-3327
direct development
heterotroph that acquires nutrition from a symbiont
http://orcid.org/0000-0002-2908-3327
symbiotroph
An organism bearing a symbiont role and capable of living within a plant for at least part of its life cycle without causing apparent disease
http://orcid.org/0000-0002-2908-3327
endophyte
anatomical entity that comprises the organism in a distinct juvenile form that is provided with a source of nutrition, usually a yolk sac, to use before metamorphosing into an adult
lecithotrophic larva
a community of microscopic, unicellular eukaryotic algae and the prokaryotic Cyanobacteria which live on sediment surfaces
http://orcid.org/0000-0002-2908-3327
algae
microphytobenthos
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water.
https://orcid.org/0000-0002-2908-3327
deposit feeder
A heterotroph that acquires nutrition by consuming particles suspended in water or air.
https://orcid.org/0000-0002-2908-3327
suspension feeder
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water. The organism lives beneath the surface of the bottom sediment and retrieves food particles without coming into direct contact with the sediment surface.
https://orcid.org/0000-0002-2908-3327
subsurface deposit feeder
Organism that acquires nutrition by consuming particles of organic matter that have settled to the bottom of a body of water. The organism lives on or in the bottom sediment and uses a part of its body to retrieve the food particles directly from the surface.
https://orcid.org/0000-0002-2908-3327
surface deposit feeder
heterotroph that obtains nutrition by breaking down dead or decaying organisms or other organic matter
https://orcid.org/0000-0002-2908-3327
decomposer
A decomposer which obtains nutrition by consuming detritus.
https://orcid.org/0000-0002-2908-3327
detritivore
A decomposer that obtains nutrition through extracellular digestion of decaying organic matter
https://orcid.org/0000-0002-2908-3327
saprotroph
A decomposition process during which a living entity acquires food and energy by consuming detritus.
https://orcid.org/0000-0002-2908-3327
detritivory
A heterotrophic process during which a living entity acquires food and energy by breaking down organic substances into simpler matter.
https://orcid.org/0000-0002-2908-3327
decomposition
A decomposition process during which a living entity acquires food and energy through extracellular digestion of decaying organic matter.
https://orcid.org/0000-0002-2908-3327
saprotrophy
A heterotrophic process during which a living entity acquires food and energy through a symbiotic relationship with another organism.
https://orcid.org/0000-0002-2908-3327
symbiotrophy
An organismal quality inhering in a bearer by virtue of the organization of the systems of organs involved with sexual reproduction amongst the bearer's conspecifics.
https://orcid.org/0000-0002-2908-3327
sexual system
An organismal quality inhering in a bearer by virtue of the structure of the bearer's conspecifics in relation to sexual behavior.
https://orcid.org/0000-0002-2908-3327
mating system
One male and one female have an exclusive mating relationship
https://orcid.org/0000-0002-2908-3327
monogamous
One female has an exclusive mating relationship with two or more males
https://orcid.org/0000-0002-2908-3327
polyandrous
One male has an exclusive mating relationship with two or more females
https://orcid.org/0000-0002-2908-3327
polygynous
Two or more males have an exclusive mating relationship with two or more females
https://orcid.org/0000-0002-2908-3327
polygynandrous
a member of one sex mates with any member of the opposite sex
https://orcid.org/0000-0002-2908-3327
promiscuity
The ecological state of a species being unique to a defined geographic location, such as an island, nation, or other defined zone or habitat type.
https://orcid.org/0000-0002-2908-3327
endemic
The ecological state of a species or population wherein all individuals are dead.
https://orcid.org/0000-0002-2908-3327
extinct
The ecological state of a species living in a region where its presence is the result of only natural process, with no human intervention
https://orcid.org/0000-0002-2908-3327
native
indigenous
The ecological state of a species living outside its native distributional range, which has arrived there by human activity, either deliberate or accidental.
https://orcid.org/0000-0002-2908-3327
exotic
introduced
The ecological state that is not the extinct state
https://orcid.org/0000-0002-2908-3327
extant
The ecological state of a species being found across all or most of the world in appropriate habitats.
https://orcid.org/0000-0002-2908-3327
cosmopolitan
The ecological state of a species being unique to a very small and specific location, such as the side of a mountain or a single lake.
https://orcid.org/0000-0002-2908-3327
microendemic
The estimated proportion of members of a population alive in year t that is still alive in year t + 1
https://orcid.org/0000-0002-2908-3327
annual survival rate
A polyphyletic group of diverse photosynthetic organisms that excludes vascular plants and mosses and includes cyanobacteria, seaweed, and some single-celled organisms.
https://orcid.org/0000-0002-2908-3327
algae
Bacteria that are able to obtain their energy through photosynthesis
https://orcid.org/0000-0002-2908-3327
cyanobacteria
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active primarily during dawn and dusk
https://orcid.org/0000-0002-2908-3327
crepuscular
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active during the hours of darkness
https://orcid.org/0000-0002-2908-3327
nocturnal
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for being active during the hours of daylight
https://orcid.org/0000-0002-2908-3327
diurnal
An evolutionary quality inhering in a bearer by virtue of the bearer's morphological and physiological adaptation for participating in long-distance movement of conspecifics, usually on a seasonal basis
https://orcid.org/0000-0002-2908-3327
migratory
An herbivore that primarily consumes grasses.
http://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Graminivore
grass eater
graminivore
An herbivore that primarily consumes leaves
http://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Folivore
leaf eater
folivore
An herbivore that primarily consumes roots
http://orcid.org/0000-0002-2908-3327
root eater
root herbivore
rhizovore
An herbivore that primarily consumes algae
http://orcid.org/0000-0002-2908-3327
algae eater
algivore
A heterotroph with a temporary parasitic association with another organism that leads to the death of the host. After which, the parasitoid can continue without the host or can move on to a new host. These organisms are considered partly parasites and partly predators.
http://orcid.org/0000-0002-2908-3327
parasitoid
A heterotroph that consumes animals in whole or in part via ingestion through a type of "mouth". Animal matter is broken down through an internal digestion process.
http://orcid.org/0000-0002-2908-3327
carnivore
A carnivore that actively captures and consumes other animals, causing their immediate or immenent death
http://orcid.org/0000-0002-2908-3327
predator
A carnivore that feeds on dead and decaying animal matter
http://orcid.org/0000-0002-2908-3327
scavenger
A predator that primarily eats insects
http://orcid.org/0000-0002-2908-3327
insectivore
http://orcid.org/0000-0002-2908-3327
A predator that eats primary consumers or herbivores
secondary consumer
A predator that eats secondary consumers
http://orcid.org/0000-0002-2908-3327
tertiary consumer
A predator that eats tertiary consumers
http://orcid.org/0000-0002-2908-3327
quaternary consumer
a predator residing at the top of a food chain upon which no other creatures prey.
http://orcid.org/0000-0002-2908-3327
top predator
apex predator
a predator that captures or traps prey by stealth or strategy, rather than by speed or strength.
http://orcid.org/0000-0002-2908-3327
ambush predator
a detritivore that consumes leaf litter
https://orcid.org/0000-0002-2908-3327
litter transformer
a heterotroph that consumes bacteria
bacterivore
A herbivorous process during which a living entity acquires food and energy by consuming grasses, leaves, and other soft plant material.
http://orcid.org/0000-0002-2908-3327
herbivorous grazing
A herbivorous process during which a living entity acquires food and energy by consuming seeds of a plant.
http://orcid.org/0000-0002-2908-3327
seed predation
A herbivorous process during which a living entity acquires food and energy by consuming twigs, leaves, and bark of trees and shrubs.
http://orcid.org/0000-0002-2908-3327
herbivorous browsing
A carnivorous process during which a living entity acquires food and energy by consuming other animals while they are stil alive. Predation leads directly to the imminent death of the prey organism(s).
https://orcid.org/0000-0002-2908-3327
The definition of predation can be controversial.
predation
A predation process during which a living entity acquires food and energy by consuming all or part of another individual of the same species as food.
https://orcid.org/0000-0002-2908-3327
cannibalism
A cannibalistic process during which an embryo obtains food and energy by consuming a less-developed sibling while both are still in the uterus.
https://orcid.org/0000-0002-2908-3327
intrauterine cannibalism
A cannibalistic process during which an embryo obtains food and energy by consuming a less-developed sibling embryo while both are still in the uterus.
https://orcid.org/0000-0002-2908-3327
embryophagy
adelphophagy
A cannibalistic process during which an embryo obtains food and energy by consuming less-developed sibling eggs while both are still in the uterus.
https://orcid.org/0000-0002-2908-3327
oophagy
A predation process during which a living entity acquires food and energy by consuming insects.
https://orcid.org/0000-0002-2908-3327
insectivory
A predation process during which a living entity acquires food and energy by consuming eggs.
https://orcid.org/0000-0002-2908-3327
egg predation
A predation process during which a group of predators cooperates to kill creatures larger than those they could overpower singly.
https://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Predation#Social_predation
social predation
A heterotrophic process during which a living entity acquires food and energy by consuming a very narrow range of food items, sometimes only one.
http://orcid.org/0000-0002-2908-3327
monophagy
A heterotrophic process during which a living entity acquires food and energy by consuming a few, very specific food items.
http://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Oligophagy
oligophagy
A heterotrophic process during which a living entity acquires food and energy by consuming a wide range of food items.
http://orcid.org/0000-0002-2908-3327
polyphagy
A heterotrophic process during which a living entity acquires food and energy from consuming bacteria.
http://orcid.org/0000-0002-2908-3327
bactivory
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilisation, the oocytes being scattered into the environment and fertilised outside the female's body by the male.
http://orcid.org/0000-0002-2908-3327
broadcast spawn
A reproductive quality inhering in a bearer by virtue of the bearer's ability to produce offspring via external fertilisation, the oocytes being released in an ovigerous sac and fertilised outside the female's body by the male.
http://orcid.org/0000-0002-2908-3327
sac spawn
a reproductive quality inhering in the bearer by virtue of the bearer having male reproductive organs at the beginning of its life and then switching to female reproductive organs
http://orcid.org/0000-0002-2908-3327
protandrous
a reproductive quality inhering in the bearer by virtue of the bearer having female reproductive organs at the beginning of its life and then switching to being a hermaphrodite
http://orcid.org/0000-0002-2908-3327
protogynous hermaphroditism
a reproductive quality inhering in the bearer by virtue of the bearer having male reproductive organs at the beginning of its life and then switching to being a hermaphrodite
http://orcid.org/0000-0002-2908-3327
protandrous hermaphroditism
Sequential hermaphroditism occurs when the individual changes sex at some point in its life.
a reproductive quality inhering in the bearer by virtue of the bearer changing sex at some point in its life
http://orcid.org/0000-0002-2908-3327
dichogamy
sequentially hermaphroditic
A photoautotroph which is capable of using a biogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
photoorganoautotroph
A photoautotroph which is capable of using an abiogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
photolithoautotroph
A chemoautotroph which is capable of using a biogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
chemoorganoautotroph
A chemoautotroph which is capable of using an abiogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
chemolithoautotroph
A photoheterotroph which is capable of using a biogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
photoorganoheterotroph
A photoheterotroph which is capable of using an abiogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
photolithoheterotroph
A chemoheterotroph which is capable of using a biogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
chemoorganoheterotroph
A chemoheterotroph which is capable of using an abiogenic organic compound as an electron donor.
http://orcid.org/0000-0002-2908-3327
chemolithoheterotroph
An autotroph which is capable of obtaining energy from the bonds in a chemical compound.
http://orcid.org/0000-0002-2908-3327
chemoautotroph
An autotroph which is capable of transforming light into chemical energy.
http://orcid.org/0000-0002-2908-3327
photoautotroph
A heterotroph which is capable of transforming light into chemical energy.
http://orcid.org/0000-0002-2908-3327
photoheterotroph
A heterotroph which is capable of obtaining energy from the bonds in a chemical compound.
http://orcid.org/0000-0002-2908-3327
chemoheterotroph
An organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth
http://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Extremophile
extremophile
An organismal quality inhering in a bearer by virtue of the bearer's ability to live on the surface of the soil and in leaf litter
http://orcid.org/0000-0002-2908-3327
https://orcid.org/0000-0002-1434-9495
surface dwelling
epigeic
An herbivore that primarily consumes fruits or fruit-like vegetables
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q1470764
fruit eater
frugivore
An herbivore that primarily consumes pollen
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q3805698
pollen eater
palynivore
A heterotrophic process during which a living entity acquires food and energy by eating food off of a surface while slowly moving through the environment.
http://orcid.org/0000-0002-2908-3327
grazing
An herbivore that primarily consumes nectar
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entry/Q120880
nectar eater
nectarivore
An organismal quality inhering in a bearer by virtue of the bearer's ability to live in the top 20 cm of soil and make temporary, horizontal burrows.
http://orcid.org/0000-0002-2908-3327
https://orcid.org/0000-0002-1434-9495
endogeic
An organismal quality inhering in a bearer by virtue of the bearer's ability to burrow more than 20 cm deep into the soil and make permanent, vertical burrows.
http://orcid.org/0000-0002-2908-3327
https://orcid.org/0000-0002-1434-9495
anecic
An herbivore that primarily consumes seeds
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q1974986
seed eater
granivore
An herbivore that primarily consumes wood
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q2072826
xylophage
An herbivore that primarily consumes plant exudates - gums, saps, and resins
http://orcid.org/0000-0002-2908-3327
J.G. Fleagle 1988 Primate Adaptations and Evolution. Academic Press. NY
https://www.wikidata.org/entity/Q17020010
gumivore
gummivore
gumnivore
A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q10253316
parasite
A symbiotrophic process during which a living entity acquires food and energy from another living entity via a close association. The entity providing the food and energy is harmed by this process.
http://orcid.org/0000-0002-2908-3327
parasitism
An organism that is consumed in whole or in part by a predator
http://orcid.org/0000-0002-2908-3327
prey
Prey that is successfully captured and consumed at a higher frequency than other types of prey. The predator may be specially adapted for capturing or consuming its preferred prey or have special nutritional requirements that are only met by the preferred prey.
http://orcid.org/0000-0002-2908-3327
preferred prey
Prey that is consumed only if the preferred prey are unavailable.
http://orcid.org/0000-0002-2908-3327
alternative prey
alternate prey
A parasite that lives entirely within the body of its host
https://www.wikidata.org/entity/Q9300235
endoparasite
internal parasite
A parasite that lives on the exterior surface of its host
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q7880449
ectoparasite
external parasite
A parasite that enters the body of the host, but remains partially outside
http://orcid.org/0000-0002-2908-3327
mesoparasite
A predation process during which a living entity acquires food and energy by consuming snakes.
https://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q2746753
snake eating
ophiophagy
A heterotrophic process during which a living entity acquires food and energy from consuming hard organisms or hard parts of organisms. This can include plants, such as bamboo, animals with hard shells, such as corals, or the hard parts of organisms, such as bone. Durophagy requires special adaptions, such as blunt, strong teeth and a heavy jaw.
http://orcid.org/0000-0002-2908-3327
https://en.wikipedia.org/wiki/Durophagy
https://www.wikidata.org/entity/Q5316712
durophagy
A predator that primarily eats fish
http://orcid.org/0000-0002-2908-3327
https://www.wikidata.org/entity/Q1420208
fish eater
piscivore
A suspension feeder that acquires nutrition by consuming particles using a filtering apparatus.
filter feeder
A suspension feeder that acquires nutrition by consuming planktonic organisms.
planktivore
A heterotroph that obtains dissolved organic compounds by osmosis for nutrition. An osmotroph is not directly involved in breaking down organic material to create the organic compounds it uses.
http://orcid.org/0000-0002-2908-3327
osmotroph
A form of symbiosis in which a bacterium provides chemically-derived energy and nutrients, often via the oxidation of hydrogen sulfide, to a higher organism.
https://orcid.org/0000-0002-2908-3327
chemosymbiosis
A symbiosis in which a photosynthetic organism provides energy and nutrients to a heterotrophic organism.
https://orcid.org/0000-0002-2908-3327
photosymbiosis
A process during which a living entity acquires reducing equivalents from organic chemicals for use in biosynthesis or energy conservation via aerobic or anaerobic respiration.
organotrophy
A process during which a living entity generates food from abiotic sources or through consumption of living or dead material, and captures energy from preformed molecules.
chemotrophy
A carnivore that consumes blood, during a brief, temporary interaction.
http://orcid.org/0000-0002-2908-3327
blood eater
sanguivore
A carnivorous process during which a living entity acquires food and energy from consuming blood.
http://orcid.org/0000-0002-2908-3327
hematophagy
A reproductive process wherein a virus uses another cell for reproduction. This process causes the mortality of the host cell via lysis.
http://orcid.org/0000-0002-2908-3327
viral predation
a folivore that lives in and eats the leaf tissue of plants
http://orcid.org/0000-0002-2908-3327
leaf miner
an herbivore that primarily consumes grasses, leaves, and other soft plant material
http://orcid.org/0000-0002-2908-3327
https://orcid.org/0000-0002-9943-2342
herbivorous grazer
An herbivore that primarily consumes twigs, leaves, and bark of trees and shrubs.
http://orcid.org/0000-0002-2908-3327
herbivorous browser
a carnivore that primarily eats organisms less than 1 cm in their longest dimension
http://orcid.org/0000-0002-2908-3327
https://orcid.org/0000-0002-9943-2342
microcarnivore
an organism that uses inorganic sulfur compounds as a terminal electron acceptor during cellular respiration
http://orcid.org/0000-0002-2908-3327
sulfur reducing organism
sulphur reducer
sulphur reducing organism
sulfur reducer
an organism that does not require oxygen for growth
http://orcid.org/0000-0002-2908-3327
anaerobic organism
anaerobe
an organism that can survive and grow in an oxygenated environment
http://orcid.org/0000-0002-2908-3327
aerobic organism
aerobe
an organism capable of producing all amino acids required for its growth
http://orcid.org/0000-0002-2908-3327
prototrophic organism
prototroph
an organism that is unable to synthesize a particular organic compound required for its growth
http://orcid.org/0000-0002-2908-3327
auxotrophic organism
auxotroph
a decomposer which obtains nutrition by consuming feces
http://orcid.org/0000-0002-2908-3327
coprophage
https://en.wikipedia.org/wiki/Geographic_feature
macroscopic spatial feature
envoPolar
May appear on a map.
geographic feature
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
FTT:78
TGN:50001
man-made feature
manmade feature
anthropogenic geographic feature
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
ORCID:0000-0002-4366-3088
A geographical feature associated with water.
FTT:131
FTT:280
FTT:711
FTT:761
FTT:824
FTT:825
FTT:826
FTT:827
FTT:828
FTT:829
Geonames:H.OVF
fluvial feature
envoPolar
hydrographic feature
A geographical feature associated with water.
MA:ma
fluvial feature
ADL:FTT
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
LTER:695
EcoLexicon:ocean
FTT:1019
FTT:943
Geonames:H.OCN
SWEETRealm:Ocean
TGN:21102
https://en.wikipedia.org/wiki/Ocean
Ocean
ocean
ocean region
envoMarine
envoPolar
ocean
LTER:695
http://129.24.124.196/vocab/vocab/index.php?tema=127&/coral-reefs
Ocean
NASA:earthrealm
ocean
Geonames:feature
ocean region
ADL:FTT
A large expanse of saline water usually connected with an ocean.
EcoLexicon:sea
FTT:233
FTT:830
Geonames:H.SEA
TGN:21103
https://en.wikipedia.org/wiki/Sea
Sea
sea
channel
closed sea
marginal sea
open sea
open sound
open water
ENVO
ENVO:00000016
envoMarine
envoPolar
sea
A large expanse of saline water usually connected with an ocean.
https://en.wikipedia.org/wiki/Sea
Sea
NASA:earthrealm
sea
ADL:FTT
sea
Geonames:feature
closed sea
USGS:SDTS
marginal sea
USGS:SDTS
open sea
USGS:SDTS
open sound
USGS:SDTS
open water
USGS:SDTS
A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L).
ENVO
ENVO:00000017
saline hydrographic feature
A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L).
https://en.wikipedia.org/wiki/Salinity
A lake whose water contains a considerable concentration of dissolved salts.
FTT:221
FTT:907
Geonames:H.LKN
Geonames:H.LKSN
TGN:21116
https://en.wikipedia.org/wiki/Saline_lake
salt lake
salina
soda lake
saline lake
A lake whose water contains a considerable concentration of dissolved salts.
MA:ma
salt lake
USGS:SDTS
salina
USGS:SDTS
A body of water or other liquid of considerable size contained in a depression on a landmass.
LTER:278
EcoLexicon:lake
FTT:221
FTT:704
FTT:909
Geonames:H.LK
Geonames:H.LKS
SPIRE:Lake_or_pond
SWEETRealm:Lake
TGN:21114
TGN:21115
catch basin
open water
tarn
broad
llyn
loch
lochan
lough
mere
mortlake
pasteuer lake
envoPolar
lake
A body of water or other liquid of considerable size contained in a depression on a landmass.
https://en.wikipedia.org/wiki/Lake
LTER:278
http://129.24.124.196/vocab/vocab/index.php?tema=278&/lakes
catch basin
USGS:SDTS
open water
USGS:SDTS
tarn
ADL:FTT
lochan
ADL:FTT
mortlake
USGS:SDTS
pasteuer lake
USGS:SDTS
An vegetated area which overlaps a wetland ecosystem.
WetlandRegion
wetland area
An vegetated area which overlaps a wetland ecosystem.
https://en.wikipedia.org/wiki/Wetland
WetlandRegion
NASA:earthrealm
An accumulation of water of varying size.
hydrographic feature
EcoLexicon:waterbody
FTT:131
FTT:280
FTT:827
SWEETRealm:BodyOfWater
TGN:21100
TGN:21101
https://en.wikipedia.org/wiki/Water_body
aquatic feature
bodies of water
body of water
waterbody
https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.
water body
An accumulation of water of varying size.
https://en.wikipedia.org/wiki/Body_of_water
hydrographic feature
ADL:FTT
bodies of water
Getty:TGN
body of water
ADL:FTT
body of water
Getty:TGN
A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate.
EcoLexicon:valley
FTT:158
FTT:166
FTT:418
FTT:761
FTT:811
FTT:949
Geonames:T.GRGE
Geonames:T.VAL
Geonames:T.VALS
SWEETRealm:Valley
TGN:21425
TGN:21451
TGN:21452
TGN:21453
chasm
coulee
dale
glacial gorge
glacial trough
gulch
gully
median valley
shelf valley
glen
goe
gorge
graben
hollow
lavaka
moat
ravine
re-entrant
seachannel
strath
trench
vale
water gap
Valleys are typically located between hills our mountains.
valley
A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate.
ADL:FTT
https://en.wikipedia.org/wiki/Valley
chasm
USGS:SDTS
coulee
USGS:SDTS
dale
USGS:SDTS
glacial gorge
USGS:SDTS
glacial trough
USGS:SDTS
gulch
USGS:SDTS
gully
Getty:TGN
gully
USGS:SDTS
median valley
ADL:FTT
median valley
Geonames:feature
shelf valley
Geonames:feature
glen
ADL:FTT
glen
USGS:SDTS
goe
USGS:SDTS
gorge
Geonames:feature
gorge
USGS:SDTS
graben
USGS:SDTS
hollow
ADL:FTT
hollow
Getty:TGN
hollow
USGS:SDTS
moat
USGS:SDTS
ravine
USGS:SDTS
re-entrant
USGS:SDTS
seachannel
USGS:SDTS
strath
USGS:SDTS
trench
USGS:SDTS
water gap
USGS:SDTS
A hydrographic feature characterized by the dominance of snow or ice.
EcoLexicon:ice
FTT:648
SWEETRealm:LandIce
TGN:21410
glacer
Ice
LandIce
glacial landform
glacier feature
envoPolar
Likely to be depopulated and "glacial" made into a quality or similar.
glacial feature
A hydrographic feature characterized by the dominance of snow or ice.
MA:ma
glacer
ADL:FTT
Ice
NASA:earthrealm
LandIce
NASA:earthrealm
glacial landform
Getty:TGN
glacier feature
ADL:FTT
Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.
EcoLexicon:permafrost
LTER:408
https://en.wikipedia.org/wiki/Permafrost
Permafrost
envoPolar
Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.
permafrost
Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.
https://en.wikipedia.org/wiki/Permafrost
Permafrost
NASA:earthrealm
A landform elevated above the surrounding area.
LTER:177
SWEETRealm:Elevation
https://en.wikipedia.org/wiki/Elevation
elevation
A landform elevated above the surrounding area.
MA:ma
A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.
EcoLexicon:landform
EcoLexicon:landforms
FTT:754
FTT:96
SWEETRealm:Landform
TGN:21400
TGN:21401
geological feature
physiographic feature
solid astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.
https://en.wikipedia.org/wiki/Landform
geological feature
ADL:FTT
ENVO
ENVO:00000240
It would be more correct to say that this has_quality salty or has_part ((soil and water) and has_increased_levels_of salt.
saline wetland
A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section.
https://en.wikipedia.org/wiki/Glacial_valley
ENVO
valley
ENVO:00000248
envoPolar
glacial valley
A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section.
MA:ma
valley
USGS:SDTS
That part of the land in immediate contact with a body of water including the area between high and low water lines.
coastal zone
EcoLexicon:shore
FTT:240
FTT:503
FTT:504
Geonames:T.SHOR
SWEETRealm:Shore
TGN:21481
https://en.wikipedia.org/wiki/Shore
SHORE
shore
shoreface
beach face
foreshore
inshore
rivage
seashore
strand
shore
That part of the land in immediate contact with a body of water including the area between high and low water lines.
USGS:SDTS
coastal zone
ADL:FTT
SHORE
USGS:SDTS
shore
Geonames:feature
shoreface
USGS:SDTS
beach face
USGS:SDTS
foreshore
USGS:SDTS
inshore
USGS:SDTS
rivage
USGS:SDTS
seashore
USGS:SDTS
strand
USGS:SDTS
A landform sunken or depressed below the surrounding area.
Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486
EcoLexicon:depression
FTT:175
FTT:215
FTT:216
Geonames:T.DPR
Geonames:T.PAN
Geonames:T.PANS
SWEETRealm:Depression
TGN:21454
TGN:21497
TGN:21521
barrier basin
depression
non tidal basin
pan
pan (geologic)
pans
tidal basin
depression
A landform sunken or depressed below the surrounding area.
https://en.wikipedia.org/wiki/Depression_%28geology%29
barrier basin
USGS:SDTS
depression
Geonames:feature
non tidal basin
USGS:SDTS
pan
Geonames:feature
pan
Getty:TGN
pan (geologic)
ADL:FTT
pans
Geonames:feature
tidal basin
USGS:SDTS
2
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
LTER:809
EcoLexicon:biome
major habitat type
EcosytemType
There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar.
biome
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
DOI:10.1186/2041-1480-4-43
https://en.wikipedia.org/wiki/Biome
LTER:809
http://129.24.124.196/vocab/vocab/index.php?tema=809&/biomes
major habitat type
WWF:Biome
EcosytemType
NASA:earthrealm
A biome that applies to the terrestrial realm.
LTER:798
SPIRE:Terrestrial
ENVO
terrestrial realm
ENVO:00000446
terrestrial biome
A biome that applies to the terrestrial realm.
https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes
An aquatic biome that comprises systems of open-ocean and unprotected coastal habitats, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt.
SPIRE:Marine
marine realm
envoPolar
marine biome
An aquatic biome that comprises systems of open-ocean and unprotected coastal habitats, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt.
ISBN-10:0618455043
MA:ma
ORCID:0000-0002-4366-3088
https://en.wikipedia.org/wiki/Ocean
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
EcoLexicon:rock
FTT:1010
FTT:145
Geonames:T.RK
Geonames:T.RKS
SWEETRealm:Rock
TGN:21444
https://en.wikipedia.org/wiki/Rock
ENVO
ENVO:00001995
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
rock
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
MA:ma
https://en.wikipedia.org/wiki/Rock_(geology)
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]
regolith
LTER:535
SPIRE:Soil
SWEETRealm:Soil
https://en.wikipedia.org/wiki/Soil
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil
" The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants.
The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
soil
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
https://en.wikipedia.org/wiki/Soil
A significant accumulation of water which is part of a marine biome.
body of marine water
marine waterbody
Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review.
marine water body
A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land.
EcoLexicon:slope
SWEETRealm:Slope
https://en.wikipedia.org/wiki/Slope
flank
side
slope
A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land.
MA:ma
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
EcoLexicon:air
LTER:18
SWEETRealm:Air
https://en.wikipedia.org/wiki/Air
envoPolar
air
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
https://en.wikipedia.org/wiki/Air
An environmental material primarily composed of dihydrogen oxide in its liquid form.
water
EcoLexicon:water
LTER:617
https://en.wikipedia.org/wiki/Water
liquid water
An environmental material primarily composed of dihydrogen oxide in its liquid form.
MA:ma
Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.
EcoLexicon:sediment
EcoLexicon:sedimentation
LTER:492
LTER:493
SWEETRealm:Sediment
https://en.wikipedia.org/wiki/Sediment
envoPolar
It is recommended to use a combination of sediment terms to describe a more specific sediment type.
sediment
Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.
https://en.wikipedia.org/wiki/Sediment
Water which contains a significant concentration of dissolved salts.
EcoLexicon:saltwater
SWEETRealm:SalineWater
SWEETRealm:SaltWater
https://en.wikipedia.org/wiki/Saline_water
salt water
The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.
saline water
A biome which has its properties and composition determined by a water body and within which most members of resident ecological communities have adapted to life in or on water.
LTER:41
aquatic biome
EcoLexicon:wood
LTER:637
SWEETRealm:Wood
https://en.wikipedia.org/wiki/Wood
ENVO
ENVO:00002040
wood
Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean.
When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class.
EcoLexicon:sea_water
LTER:701
SWEETRealm:SeaWater
https://en.wikipedia.org/wiki/Sea_water
ocean water
seawater
This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels.
sea water
A material entity which determines an environmental system.
ENVO
ENVO:00002297
A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
environmental feature
A material entity which determines an environmental system.
DOI:10.1186/2041-1480-4-43
NM:nm
ORCID:0000-0002-4366-3088
A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water.
EcoLexicon:clay
SWEETRealm:Clay
https://en.wikipedia.org/wiki/Clay
clay
A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water.
https://en.wikipedia.org/wiki/Clay
A portion of enriched soil is a portion of soil with elevated levels of some material entity.
ENVO
ENVO:00003082
This could be demoted to an inferred class if issues with double inheritance arise.
enriched soil
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
portion of environmental material
Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
environmental material
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
DOI:10.1186/2041-1480-4-43
MA:ma
ORCID:0000-0002-4366-3088
URL:http://ontology.buffalo.edu/smith/articles/niches.html
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
EcoLexicon:surface
http://sweetontology.net/reprSpaceGeometry/Surface
https://en.wikipedia.org/wiki/Surface
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
surface layer
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
URL:http://www.merriam-webster.com/dictionary/surface
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
EcoLexicon:aerosol
SWEETRealm:Aerosol
envoAtmo
Should connect to PATO as "quality of an aerosol"
aerosol
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
https://en.wikipedia.org/wiki/Aerosol
Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar.
EcoLexicon:silt
SWEETRealm:Silt
https://en.wikipedia.org/wiki/Silt
https://en.wikipedia.org/wiki/ In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
silt
Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar.
https://en.wikipedia.org/wiki/Silt
A naturally occurring granular material composed of finely divided rock and mineral particles.
EcoLexicon:sand
LTER:484
SWEETRealm:Sand
https://en.wikipedia.org/wiki/Sand
ENVO
ENVO:01000017
sand
A naturally occurring granular material composed of finely divided rock and mineral particles.
https://en.wikipedia.org/wiki/Sand
The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths.
ORCID:0000-0002-4366-3088
2010-03-15T11:17:06Z
ENVO
ENVO:01000023
envoPolar
marine pelagic biome
The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths.
ISBN:0750633840
The neritic epipelagic zone biome comprises the marine water column above a continental shelf.
ORCID:0000-0002-4366-3088
2010-03-15T11:19:19Z
ENVO
ENVO:01000032
neritic pelagic zone biome
The neritic epipelagic zone biome comprises the marine water column above a continental shelf.
ISBN:044482619X
ISBN:0750633840
ORCID:0000-0002-4366-3088
The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf.
ORCID:0000-0002-4366-3088
2010-03-15T11:19:19Z
ENVO
ENVO:01000033
oceanic pelagic zone biome
The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf.
ISBN:044482619X
ISBN:0750633840
ORCID:0000-0002-4366-3088
The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
ORCID:0000-0002-4366-3088
2010-03-15T11:21:03Z
ENVO
ENVO:01000034
oceanic sea surface microlayer biome
The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
ORCID:0000-0002-4366-3088
https://en.wikipedia.org/wiki/Sea_surface_microlayer
The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
ORCID:0000-0002-4366-3088
2010-03-15T11:22:09Z
ENVO
ENVO:01000041
neritic sea surface microlayer biome
The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath.
ORCID:0000-0002-4366-3088
https://en.wikipedia.org/wiki/Sea_surface_microlayer
A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column.
ORCID:0000-0002-4366-3088
2010-03-16T12:10:50Z
envoPolar
marine pelagic feature
A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column.
ISBN-10:0618455043
ORCID:0000-0002-4366-3088
Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material.
Subclasses should be assigned by inference.
envoAtmo
envoPolar
particulate matter
A portion of planktonic material is a portion of environmental material primarily composed of plankton.
See Issue #251. Awaiting class creation in PCO to attempt logical definitions.
algae
envoPolar
planktonic material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
ORCID:0000-0002-4366-3088
2010-03-20T08:40:04Z
EcoLexicon:organic_material
biomass
organic material
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
ISBN-10:0618455043
ORCID:0000-0002-4366-3088
A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs.
ORCID:0000-0002-4366-3088
2013-04-07T14:26:46Z
Preliminary definition.
shrubland biome
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
ORCID:0000-0002-4366-3088
2013-04-07T14:35:18Z
envoPolar
A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
environmental condition
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
DOI:10.1186/2041-1480-4-43
A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
ORCID:0000-0002-4366-3088
2013-04-07T14:40:32Z
wwfBiome
Preliminary definition.
montane shrubland biome
A system which has the disposition to environ one or more material entities.
2013-09-23T16:04:08Z
EcoLexicon:environment
environment
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
environmental system
A system which has the disposition to environ one or more material entities.
DOI:10.1186/2041-1480-4-43
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
ORCID:0000-0002-4366-3088
2013-10-05T12:37:41Z
LTER:341
mineral material
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
https://en.wikipedia.org/wiki/Mineral
Water vapour is a vapour which is the gas phase of water.
ORCID:0000-0002-4366-3088
2013-10-10T07:58:18Z
aqueous vapor
aqueous vapour
water vapor
ENVO
ENVO:01000266
Perhaps a better relation between water vapour and water can be found in or added to RO?
water vapour
Water vapour is a vapour which is the gas phase of water.
https://en.wikipedia.org/wiki/Water_vapor
aqueous vapor
https://en.wikipedia.org/wiki/Water_vapor
aqueous vapour
https://en.wikipedia.org/wiki/Water_vapor
water vapor
https://en.wikipedia.org/wiki/Water_vapor
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
ORCID:0000-0002-4366-3088
2013-10-10T08:14:50Z
LTER:48
atmosphere
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
https://en.wikipedia.org/wiki/Atmosphere
https://en.wikipedia.org/wiki/Physical_geography
Atmospheric water vapour is water vapour that is part of an atmosphere.
ORCID:0000-0002-4366-3088
2013-10-10T08:22:07Z
atmospheric water vapor
ENVO
ENVO:01000268
envoPolar
atmospheric water vapour
Atmospheric water vapour is water vapour that is part of an atmosphere.
https://en.wikipedia.org/wiki/Water_vapor
atmospheric water vapor
https://en.wikipedia.org/wiki/Water_vapor
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
ORCID:0000-0002-4366-3088
2013-10-12T17:21:09Z
envoPolar
Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO.
ecoregion
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2
URL:http://worldwildlife.org/biomes
Ice is water frozen into a solid state. It can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.
ORCID:0000-0002-4366-3088
2013-10-13T12:01:28Z
LTER:262
ice
envoPolar
water ice
Ice is water frozen into a solid state. It can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.
https://en.wikipedia.org/wiki/Ice
ice
http://www.eionet.europa.eu/gemet/concept/4131
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
ORCID:0000-0002-4366-3088
2013-10-13T18:32:46Z
envoPolar
ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO.
https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories.
ecozone
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
https://en.wikipedia.org/wiki/ecozone
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
ORCID:0000-0002-4366-3088
2013-10-15T16:42:02Z
envoPolar
Preliminary definition.
layer
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
Wiktionary:layer
A layer which is part of a lake.
ORCID:0000-0002-4366-3088
2013-10-15T16:57:43Z
ENVO
ENVO:01000283
envoPolar
Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline.
lake layer
A mass of ice.
Class should be populated by inference and asserted subclasses redistributed.
ORCID:0000-0002-4366-3088
2013-10-15T19:49:11Z
envoPolar
ice mass
A layer that is part of a marine water body.
ORCID:0000-0002-4366-3088
envoMarine
envoPolar
marine layer
A layer that is part of a marine water body.
ORCID:0000-0002-4366-3088
An endolithic environment is an environment that exists within solid rock.
endolithic environment
A high temperature environment is an environment in which material entities are exposed to increased levels of heat radiation or which have molecules or atoms moving randomly with increased levels of average kinietic energy.
high temperature environment
An environmental system which has its properties and dynamics determined by saline water.
Water (saline)
envoEmpo
envoOmics
envoPolar
saline water environment
Water (saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environment which has a lower temperature than some local or global average.
envoPolar
The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'.
cold environment
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
anthropogenic environment
A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes.
high osmolarity environment
An environment whose dynamics are strongly influenced by water.
aquatic environment
A rocky slope is a slope which has a surface primarily composed of rock.
rocky slope
A marine environment and enviroment which is determined by a marine water body.
envoPolar
marine environment
A marine environment and enviroment which is determined by a marine water body.
NM:nm
An environmental system determined by seawater.
ocean water environment
envoPolar
sea water environment
A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
planetary surface
A layer in a water mass, itself composed primarily of water.
envoPolar
This class will eventually be populated by inference, and its asserted subclasses removed.
aquatic layer
A montane condition is an environmental condition in which an altitude range falls between mid-altitude forests and the tree line.
ORCID:0000-0002-4366-3088
LTER:350
envoPolar
The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate.
montane
A montane condition is an environmental condition in which an altitude range falls between mid-altitude forests and the tree line.
https://en.wikipedia.org/wiki/Altitudinal_zonation
The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate.
https://en.wikipedia.org/wiki/Altitudinal_zonation
An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude.
ORCID:0000-0002-4366-3088
envoPolar
Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change.
altitudinal condition
An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude.
https://en.wikipedia.org/wiki/Altitudinal_zonation
An organic material primarily composed of a portion of plant root.
Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.
root matter
A layer which is determined by a form of vegetation.
forest layer
forest stratum
woodland layer
woodland stratum
Usually found in woodlands and forests.
vegetation layer
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
envoPolar
snow
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
http://www.eionet.europa.eu/gemet/concept/7769
https://en.wikipedia.org/wiki/Snow
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
environmental area
envoPolar
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
environmental zone
A gas that is primarily composed of hydrocarbon molecules.
envoPolar
hydrocarbon gas
A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow.
lentic water body
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
condensation
envoPolar
"process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog)
hydrological condensation process
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
https://en.wikipedia.org/wiki/Condensation
Land is a planetary surface that is not covered by liquid.
ground
Land may more properly be represented as part of a planetary surface rather than a sublcass.
land
Land is a planetary surface that is not covered by liquid.
Adpated from https://en.wikipedia.org/wiki/Planetary_surface
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
space
envoAstro
outer space
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
https://en.wikipedia.org/wiki/Outer_space
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
crust
This class is meant to be applicable accross planets. Earth's crust would be an instance.
planetary crust
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
https://en.wikipedia.org/wiki/Crust_(geology)
A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition.
Label should be improved to match definition.
planetary structural layer
A mass of water.
water mass
A coast is the area where land meets the sea, ocean, or lake.
Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore'
coast
A coast is the area where land meets the sea, ocean, or lake.
https://en.wikipedia.org/wiki/Coast
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
precipitation
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
https://en.wikipedia.org/wiki/Precipitation
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
Condensation is a process during which a gas undergoes a phase transition into a liquid.
https://en.wikipedia.org/wiki/Condensation
An environmental system which can sustain and allow the growth of an ecological population.
EcoLexicon:habitat
LTER:238
SWEETRealm:Habitat
https://en.wikipedia.org/wiki/Habitat
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
An environmental system which can sustain and allow the growth of an ecological population.
EnvO:EnvO
A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes.
This may not need to be in the atmosphere, also note that "meteor" will do much of the same work.
envoAtmo
Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas.
aeroform
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gas
gaseous environmental material
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
http://www.merriam-webster.com/dictionary/gas
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
celestial body
envoAstro
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
https://en.wikipedia.org/wiki/Astronomical_object
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
envoAstro
envoPolar
Considerable debate on the definition of planet exists.
planet
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
http://solarsystem.nasa.gov/planets/whatisaplanet
https://en.wikipedia.org/wiki/Planet
1
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
celestial object
envoAstro
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
https://en.wikipedia.org/wiki/Astronomical_object
A material part of an astronomical body.
envoAstro
envoPolar
astronomical body part
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
envoPolar
This is a defined class: its subclasses will not be asserted, but filled by inference.
liquid environmental material
A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
envoAstro
envoPolar
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
http://www.biology-online.org/dictionary/Biosphere
https://en.wikipedia.org/wiki/Biosphere
A cryosphere is that part of a planet which is primarily composed of water is in solid form.
envoAstro
envoPolar
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
cryosphere
A cryosphere is that part of a planet which is primarily composed of water is in solid form.
https://en.wikipedia.org/wiki/Cryosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
envoAstro
envoPolar
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
hydrosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
https://en.wikipedia.org/wiki/Hydrosphere
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29
https://en.wikipedia.org/wiki/Precipitation
A hydrological process in which irregular aggregates of snow fall to a planetary surface.
snow fall
environmental_hazards
envoPolar
snowfall
An ecosystem which bridges two or more adjoining ecosystems and through which organisms may move or propagate.
animal corridor
green corridor
habitat corridor
wildlife corridor
Ecological corridors may or may not provide habitats for the organisms which move through them. They serve to mitigate the effects of habitat fragmentation by allowing genetic exchange between populations that would otherwise be separated by, e.g., human activity.
ecological corridor
An ecosystem which bridges two or more adjoining ecosystems and through which organisms may move or propagate.
http://www.eionet.europa.eu/gemet/concept/10510
https://www.eionet.europa.eu/gemet/concept/3756
2
An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions.
There are many subtypes of ecotone, some with sharp transitions and others with gradual, patchy transitions between communities. From Wikipedia:Ecotone - The word ecotone was coined from a combination of eco(logy) plus -tone, from the Greek tonos or tension – in other words, a place where ecologies are in tension.
ecotone
An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions.
ISBN:0030584140 9780030584145
https://en.wikipedia.org/wiki/Ecotone
https://github.com/EnvironmentOntology/envo/issues/501
https://www.merriam-webster.com/dictionary/ecotone
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
non-anthropised environment
non-anthropized environment
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
https://en.wikipedia.org/wiki/Anthropization
https://en.wikipedia.org/wiki/Natural_environment
A process during which a natural environmental system is altered by human action.
anthropization
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A process during which a natural environmental system is altered by human action.
https://en.wikipedia.org/wiki/Anthropization
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
https://en.wikipedia.org/wiki/Anthropization
A planet that is composed primarily of silicate rocks or metals.
rocky planet
telluric planet
Earth-like planet
envoAstro
terrestrial planet
A planet that is composed primarily of silicate rocks or metals.
https://en.wikipedia.org/wiki/Terrestrial_planet
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
envoPolar
This class can refer to the flow of any material in a liquid phase.
mass liquid flow
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
https://en.wikipedia.org/wiki/Wind
A process during which a volume of water is transported due to a disequilibria in physical forces.
environmental_hazards
water flow process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump).
environmental system determined by a material
An environmental system which is determined by a living organism.
host-associated environment
envoEmpo
envoOmics
environmental system determined by an organism
An environmental system determined by a green plant.
Plant
plant environment
Viridiplantae-associated environment
envoEmpo
envoOmics
plant-associated environment
Plant
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system determined by an animal.
Animal
animal environment
Metazoan-associated environment
envoEmpo
envoMeo
envoOmics
animal-associated environment
Animal
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body.
envoAtmo
meteor
A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body.
https://cloudatlas.wmo.int/other-meteors.html
A meteor which is primarily composed of water.
envoAtmo
hydrometeor
A meteor which is primarily composed of water.
https://cloudatlas.wmo.int/other-meteors.html
A meteor which is primarily composed of rock.
envoAtmo
lithometeor
A lake which has formed as the result of processes that are not or are only minimally driven by human activity.
This class is to be filled by inference.
natural lake
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions).
environmental_hazards
envoAstro
radiation
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
https://en.wikipedia.org/wiki/Radiation
An environmental system which has its properties and dynamics determined by a bodily secretion of a metazoan.
Animal secretion
envoEmpo
envoMeo
envoOmics
environment determined by a metazoan secretion
Animal secretion
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system which has its properties and dynamics determined by a digestive tract.
Animal proximal gut
envoEmpo
envoMeo
envoOmics
digestive tract environment
Animal proximal gut
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
This EMPO class includes examples of microbial environments determined by the "gut intestine, gizzard, crop, lumen, [and] mucosa".
An environment which is determined by materials which bear significant concentrations of salts.
Saline
envoEmpo
The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request.
saline environment
Saline
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system determined by a fungal structure.
Fungus
fungus environment
fungus-associated environment
envoEmpo
envoMeo
envoOmics
fungi-associated environment
Fungus
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system which has its properties and dynamics determined by soil.
Soil (non-saline)
envoEmpo
envoOmics
soil environment
Soil (non-saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system which has its properties and dynamics determined by sediment.
envoEmpo
envoOmics
sediment environment
An environmental system which has its properties and dynamics determined by an aerosol.
Aerosol (saline)
envoEmpo
envoOmics
aerosol environment
Aerosol (saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system which has its properties and dynamics determined by a saline aerosol.
Aerosol (saline)
envoEmpo
envoOmics
saline aerosol environment
Aerosol (saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
seaspray or other aerosolized saline material (>5 psu)
An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes.
Aerosol (non-saline)
envoEmpo
envoOmics
non-saline aerosol environment
Aerosol (non-saline)
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
aerosolized dust or liquid
An environmental system determined by part of a living or dead animal, or a whole small animal.
Animal corpus
envoEmpo
envoMeo
envoOmics
environment associated with an animal part or small animal
Animal corpus
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system determined by part of a living or dead plant, or a whole small plant.
Plant corpus
envoEmpo
envoMeo
envoOmics
environment associated with a plant part or small plant
Plant corpus
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An environmental system determined by part of a living or dead fungus.
Fungus corpus
envoEmpo
envoMeo
envoOmics
environment associated with a fungal tissue
Fungus corpus
http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids.
envoAstro
meteoroid
An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids.
https://en.wikipedia.org/wiki/Meteoroid
A material which is composed primarily of one or more pure metals and which shows their properties.
Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.
metal
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
A material which is composed primarily of one or more pure metals and which shows their properties.
https://en.wikipedia.org/wiki/Metal
An aerosol which has non-gaseous parts that are primarily composed of liquid droplets.
SWEETRealm:Aerosol
liquid aerosol
envoAtmo
aerosolised liquids
An aerosol which has non-gaseous parts that are primarily composed of liquid droplets.
https://en.wikipedia.org/wiki/Aerosol
An aerosol which has non-gaseous parts that are primarily composed of solid particles.
SWEETRealm:Aerosol
solid aerosol
envoAtmo
aerosolised solids
An aerosol which has non-gaseous parts that are primarily composed of solid particles.
https://en.wikipedia.org/wiki/Aerosol
An organic material which is primarily composed of dead particulate matter.
detritus
An organic material which is primarily composed of dead particulate matter.
https://en.wikipedia.org/wiki/Detritus
An environmental system which includes both living and non-living components.
LTER:173
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
An environmental system which includes both living and non-living components.
https://en.wikipedia.org/wiki/Ecosystem
LTER:173
http://129.24.124.196/vocab/vocab/index.php?tema=173&/ecosystems
A planet which is primarily composed of hydrogen and helium.
envoAstro
Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants.
gas planet
A planet which is primarily composed of hydrogen and helium.
http://solarsystem.nasa.gov/planets/whatisaplanet
https://en.wikipedia.org/wiki/List_of_planet_types
https://en.wikipedia.org/wiki/Planet
An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
This class is defined logically - any material that is frozen is considered a subclass. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.
ice
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class.
aquaplanet
panthalassic planet
water world
envoAstro
While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b.
ocean planet
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
https://en.wikipedia.org/wiki/Ocean_planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
cryoplanet
envoAstro
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
ice planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
https://en.wikipedia.org/wiki/Ice_planet
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
https://en.wikipedia.org/wiki/Ice_planet
A gas planet which has an atmosphere composed primarily of helium.
The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated.
envoAstro
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
helium planet
A gas planet which has an atmosphere composed primarily of helium.
https://en.wikipedia.org/wiki/Helium_planet
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
https://en.wikipedia.org/wiki/Helium_planet
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
Add and axiomatise with moon and lunar crust
volatile
envoAstro
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
volatile astrogeological material
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
https://en.wikipedia.org/wiki/Volatiles
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
https://en.wikipedia.org/wiki/Volatiles
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
gas
envoAstro
This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin.
astrogeological gas
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
https://en.wikipedia.org/wiki/Volatiles
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
https://en.wikipedia.org/wiki/Geodiversity
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system.
http://purl.jp/bio/11/meo/MEO_0000871
envoMeo
envoOmics
environment associated with an aquatic invertebrate
http://purl.jp/bio/11/meo/MEO_0000871
Not currently live, may need to be switched to alternative PURLs.
An organic material which is primarily composed of living or dead algae, along with their exudates.
This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO.
algal material
An organic material which is primarily composed of living or dead algae, along with their exudates.
https://en.wikipedia.org/wiki/Algae
The surface layer of a volume of water.
EcoLexicon:surface_water
SWEETRealm:SurfaceWater
https://en.wikipedia.org/wiki/Surface_water
surface of a body of water
water body surface
water surface
The surface layer of a mass of sediment.
surface of a sedimentary mass
surface sediment
sediment surface
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
An environmental zone which is bounded by material parts of a marine environment.
This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density.
marine environmental zone
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
EcoLexicon:wetland
FTT:1001
FTT:1060
FTT:1061
FTT:1118
FTT:1180
FTT:1190
FTT:1206
FTT:1207
FTT:1226
FTT:184
FTT:185
FTT:228
FTT:281
FTT:480
FTT:716
FTT:883
FTT:934
FTT:945
FTT:983
Geonames:H.WTLD
LTER:630
SPIRE:Bog
SWEETRealm:Wetland
TGN:21301
TGN:21304
TGN:21305
https://en.wikipedia.org/wiki/Wetland
WETLAND
Wetland
EstuarineWetland
LacustrineWetland
MarineWetland
PalustrineWetland
RiparianWetland
TerrestialWetland
back marsh
backswamp
backwater
barrier flat
blanket bog
bog
cienaga
dismal
everglade
floating marsh
forested wetland
marsh
mire
mud flat
peat cutting area
peatland
quagmire
quaking bog
riparian area
slash
slough
slue
swamp forest
tulelands
moor
morass
muskeg
wetland ecosystem
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
https://en.wikipedia.org/wiki/Wetland
WETLAND
USGS:SDTS
Wetland
NASA:earthrealm
EstuarineWetland
NASA:earthrealm
LacustrineWetland
NASA:earthrealm
MarineWetland
NASA:earthrealm
PalustrineWetland
NASA:earthrealm
RiparianWetland
NASA:earthrealm
TerrestialWetland
NASA:earthrealm
back marsh
USGS:SDTS
backswamp
USGS:SDTS
backwater
ADL:FTT
barrier flat
USGS:SDTS
blanket bog
USGS:SDTS
bog
ADL:FTT
bog
Getty:TGN
cienaga
ADL:FTT
dismal
USGS:SDTS
everglade
USGS:SDTS
floating marsh
USGS:SDTS
forested wetland
ADL:FTT
marsh
ADL:FTT
mire
ADL:FTT
mire
USGS:SDTS
mud flat
ADL:FTT
peat cutting area
ADL:FTT
peatland
ADL:FTT
quagmire
ADL:FTT
quagmire
USGS:SDTS
quaking bog
USGS:SDTS
riparian area
ADL:FTT
slash
USGS:SDTS
slough
ADL:FTT
slough
Getty:TGN
slough
USGS:SDTS
slue
ADL:FTT
swamp forest
USGS:SDTS
tulelands
USGS:SDTS
moor
USGS:SDTS
morass
USGS:SDTS
muskeg
USGS:SDTS
A natural environment which is located on a land mass.
terrestrial natural environment
A natural environment which is within a water body.
aquatic natural environment
A layer which is primarily composed of some liquid material.
liquid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
water ice layer
An environmental zone which is part of an atmosphere.
atmospheric area
atmospheric zone
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
ORCID:0000-0002-4366-3088
envoPolar
vegetated area
A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process.
Should create links to envrionmental process with new relation like "sustained_by"
Similar, in spirit, to landform.
hydroform
Should create links to envrionmental process with new relation like "sustained_by"
ORCID:0000-0002-4366-3088
A liquid surface layer which is in contact with air.
liquid air-water interface layer
A liquid surface layer which is in contact with air.
liquid surface layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A body of water which is primarily composed of saline water.
saline body of water
This class has its subclasses populated by inference.
saline water body
A biogeochemical cycle which has nitrogen-bearing chemical entities as participants.
nitrogen cycle
envoPolar
nitrogen cycling
A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged.
advective transport
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged.
https://en.wikipedia.org/wiki/Advection
https://en.wikipedia.org/wiki/Intensive_and_extensive_properties
An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited.
erosion
An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited.
https://en.wikipedia.org/wiki/Erosion
A material transport process during which solid or liquid particles are directly introduced into a volume of gas.
primary aerosol formation
primary aerosol formation process
A material transport process during which solid or liquid particles are directly introduced into a volume of gas.
https://en.wikipedia.org/wiki/Aerosol
https://en.wikipedia.org/wiki/Particulates
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
http://orcid.org/0000-0002-4366-3088
anthropogenic ecosystem conversion process
http://orcid.org/0000-0002-4366-3088
body of liquid
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
http://orcid.org/0000-0002-4366-3088
liquid astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
https://en.wikipedia.org/wiki/Landform
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
http://orcid.org/0000-0002-4366-3088
gaseous astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
https://en.wikipedia.org/wiki/Landform
A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes.
http://orcid.org/0000-0002-4366-3088
2018-10-04T13:59:22Z
fluid astronomical body part
A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes.
https://en.wikipedia.org/wiki/Landform
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
http://orcid.org/0000-0002-4366-3088
2018-10-04T16:55:57Z
a useful class: this can be used to define sub-terrestrial and sub-marine entities
surface of an astronomical body
A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions.
http://orcid.org/0000-0002-4366-3088
2019-01-14T18:47:32Z
congelation
congelation process
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions.
https://en.wikipedia.org/wiki/Congelation
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
https://en.wikipedia.org/wiki/Congelation
Land which is below the freezing point of water.
http://orcid.org/0000-0002-4366-3088
2019-01-14T21:18:19Z
http://sweetontology.net/realmCryo/FrozenGround
frozen ground
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
frozen land
Land which is below the freezing point of water.
https://orcid.org/0000-0003-4808-4736
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
https://orcid.org/0000-0003-4808-4736
Soil which is below the freezing point of water.
http://orcid.org/0000-0002-4366-3088
2019-01-14T21:26:59Z
frozen soil
A water surface that is part of a water body.
http://orcid.org/0000-0002-4366-3088
2019-02-27T21:22:13Z
surface layer of a water body
An ecoregion which is located on a landmass.
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:40:44Z
https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions
terrestrial ecoregion
A surface layer of a water body which is part of an ocean or sea.
http://orcid.org/0000-0002-4366-3088
2019-03-06T01:22:01Z
envoMarine
At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases.
sea surface layer
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
A biogeochemical process during which one or more chemical compounds are sequentially converted into a series of related compounds in a regularly repeating, periodic fashion.
envoPolar
biogeochemical cycling
A biogeochemical cycle which has carbon-bearing chemical entities as participants.
carbon cycle
envoPolar
carbon cycling
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
Relabel the obo foundry unique label to be generic process
anthropogenic modulatory intervention process
An environmental process which is driven by the action of humans.
anthropogenic environmental process
An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited.
envoPolar
planetary erosion
An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited.
https://en.wikipedia.org/wiki/Erosion
1
1
A process during which chemicals that are involved in natural ecosystem processes are transported or transformed, and which impact the activity of biological entities
envoPolar
biogeochemical process
A process during which chemicals that are involved in natural ecosystem processes are transported or transformed, and which impact the activity of biological entities
https://en.wikipedia.org/wiki/Biogeochemistry
An environmental process which has water - in any of its states - as a participant.
This classes asserted subclasses will be moved away as it should be an inferred class.
hydrological process
A process during which the mass of one or more materials, present within a given site, increases.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process.
material accumulation process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
Experimental class for structural purposes not recommended for annotation.
material transport process
A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed.
The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
geographic basin
A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed.
https://en.wikipedia.org/wiki/Basin
Sediment which has been transported through the marine water column, settling on the seafloor.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
marine sediments
envoPolar
Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.
marine sediment
Sediment which has been transported through the marine water column, settling on the seafloor.
https://en.wikipedia.org/wiki/Pelagic_sediment#_note-8
A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
sedimentation in a water body
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A geographic feature which is primarily composed of a continuous mass of snow and/or ice.
Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
cryoform
A mass of snow.
http://orcid.org/0000-0002-3410-4655
http://orcid.org/0000-0002-4366-3088
envoPolar
snow mass
An environment that is determined by a mouth.
TermGenie
2015-04-10T23:34:03Z
envoMeo
mouth environment
true
true
An environment that is determined by a mouth.
GOC:TermGenie
The concentration of a carbon atom when measured in environmental material.
environmental material carbon atom concentration
concentration of carbon atom in environmental material
The concentration of a carbon atom when measured in soil.
soil carbon atom concentration
concentration of carbon atom in soil
The concentration of a carbon atom when measured in water.
water carbon atom concentration
concentration of carbon atom in water
The concentration of a nitrogen atom when measured in environmental material.
environmental material nitrogen atom concentration
concentration of nitrogen atom in environmental material
The concentration of a nitrogen atom when measured in soil.
soil nitrogen atom concentration
concentration of nitrogen atom in soil
The concentration of a nitrogen atom when measured in water.
water nitrogen atom concentration
concentration of nitrogen atom in water
The concentration of a chloride when measured in water.
water chloride concentration
concentration of chloride in water
The temperature of some environmental material.
environmental material temperature
temperature of environmental material
The temperature of some air.
air temperature
temperature of air
The porosity of some soil.
soil porosity
porosity of soil
The concentration of a nitrate when measured in soil.
soil nitrate concentration
concentration of nitrate in soil
The composition of some soil.
soil composition
composition of soil
The structure of some soil.
soil structure
structure of soil
The temperature of some soil.
soil temperature
temperature of soil
The wetness of some soil.
soil wetness
wetness of soil
The temperature of some water.
water temperature
temperature of water
The composition of some water.
water composition
composition of water
The concentration of a oxygen when measured in water.
water oxygen concentration
concentration of oxygen in water
cjm
2018-11-03T21:35:24Z
hydrocarbon-based environmental material
A biogeochemical cycle which has oxygen as participant.
cjm
2018-11-03T22:06:08Z
global carbon cycling
oxygen cycling
An environment which is determined by an anatomical entity.
anatomical entity environment
An environment determined by an area or zone of skin tissue.
envoMeo
skin environment
integumental system environment
envoMeo
face skin environment
The concentration of chlorophyll a when measured in water.
water chlorophyll a concentration
concentration of chlorophyll a in water
The concentration of chlorophyllide a when measured in water.
water chlorophyllide a concentration
concentration of chlorophyllide a in water
The concentration of dioxygen when measured in water.
water dioxygen concentration
concentration of dioxygen in water
The concentration of methane when measured in water.
water methane concentration
concentration of methane in water
The concentration of nitrate when measured in water.
water nitrate concentration
concentration of nitrate in water
The concentration of chlorophyll when measured in water.
water chlorophyll concentration
concentration of chlorophyll in water
An anatomical structure that forms all or part of a fungus.
fungal structure ontology
fungal structure
A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
Damion Dooley
https://en.wikipedia.org/wiki/Food
food product
The FoodOn product type class is provided as a food product category tree under which new food product categories and food products themselves can be placed. This tree has upper level categories inspired from other product type schemes like the US Code of Federal Regulations. However it has a much greater depth to it than the other product type schemes in an effort to group related products together. The basis of this tree was inherited from the environment ontology (ENVO).
foodon product type
This food product type includes food products which are derived from or produced by a plant.
plant food product
A food preserved by soaking and storing it in vinegar or brine.
SUBSET_SIREN:F1302
SUBSET_SIREN:F16510
pickled
subset_siren
subset_siren
SIREN DB annotation:
* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)
* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190)
food (pickled)
Damion Dooley
http://langual.org
2019-06-11T07:25:19Z
SUBSET_SIREN:F5644
alcoholic beverage
subset_siren
SIREN DB annotation:
* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)
* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)
* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)
fermented beverage
Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked.
prepared
prepared food product
Damion Dooley
cooked
food (cooked)
plant derived beverage
plant derived fermented beverage
Are all fermented foods considered preserved to some extent?
Damion Dooley
food (fermented)
Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food.
vegetable food product
Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food.
http://www.fao.org/es/faodef/fdef07e.htm#7.01
An alcoholic drink (or alcoholic beverage) is a drink that contains ethanol, a type of alcohol produced by fermentation of grains, fruits, or other sources of sugar.
Damion Dooley
https://en.m.wikipedia.org/wiki/Alcoholic_drink
alcoholic beverage
food component
Damion Dooley
preserved
food (preserved)
vegetable pickle food product
A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition)
Damion Dooley
food product by meal type
food product by organism
food
food material
A process involving the physical transformation of a food source or food product into some derived organic material or food product
Damion Dooley
food transformation process
The food product by quality class provides descriptors for describing food visually or via other senses, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process.
Damion Dooley
food product by quality
Damion Dooley
2019-05-23T23:02:07Z
food product by process
A liquid prepared for consumption, or a product that can be combined with water or milk to make one.
Damion Dooley
http://langual.org
2019-09-12T00:00:00
beverage food product
Fruits and vegetables in all forms. [FDA CFSAN 1995]
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=A0257
fruit or vegetable product (us cfr)
Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995]
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=A0289
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
product type, USA
A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories.
Damion Dooley
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=A0361
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
food product type
Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=A1270
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
product type, U.S. code of federal regulations, title 21
https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=B1041
LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds).
chemical food component
A multicellular eukaryote organism of the kingdom Plantae.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=B1347
obsolete: plant
http://purl.obolibrary.org/obo/PO_0000003
true
order=
obolibrary:FOODON_03411297 # vertebrate
obolibrary:FOODON_00002452 # invertebrate
obolibrary:FOODON_03411347 # plant
obolibrary:FOODON_03411301 # algae
obolibrary:FOODON_03411261 # fungae
obolibrary:FOODON_03412345 # lichen
A food source is a plant or animal from which a food product or component is derived.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=B1564
This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995].
food source
This section and its narrover terms refer to the European Commission food additive regulation according to COMMISSION REGULATION (EU) No 1129/2011 of 11 November 2011 amending Annex II to Regulation (EC) No 1333/2008 of the European Parliament and of the Council by establishing a Union list of food additives [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:295:0001:0177:EN:PDF] and its basis, the four Food Additive Directives: the EEC Framework Directive on Food Additives (89/107/EEC), the Directive on colours (94/36/EC), the Directive on sweeteners (94/35/EC) and the 'miscellaneous' Directive (95/2/EC) plus amendments [http://ec.europa.eu/food/fs/sfp/flav_index_en.html]
and/or Codex Alimentarius Commission General Standard for Food Additives (CODEX STAN 192, revised 2011) [http://www.codexalimentarius.net/download/standards/4/CXS_192e.pdf].
If used for food supplement substances, thissection and its narrover terms refer to the European Commission regulation in general [http://ec.europa.eu/food/food/labellingnutrition/supplements/index_en.htm] and specifically to the EC Directive on the approximation of the laws of the Members States relating to food supplements (2002/46/EC) [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF].
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=B2972
Damion Dooley's note: manysubclasses here are currently originating from LanguaL additives that have not yet been matched to CHEBI ontology terms. If matches are possible they will be implemented over time, at which point the corresponding FoodOn id's will be deprecated.
food additive
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=B3357
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
plant according to family
Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=C0152
carbohydrate extract, concentrate, or isolate
A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=C0228
Damion Dooley's note: Items in this branch will be merged into foodon food product branch.
extract, concentrate or isolate of plant or animal
A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*.
http://langual.org
SUBSET_SIREN:F5105
http://www.langual.org/langual_thesaurus.asp?termid=E0130
fluid
SIREN DB annotation:
* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)
food (liquid)
Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned.
http://langual.org
http://www.langual.org/langual_thesaurus.asp?termid=H0111
LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.
food treatment process
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GO:0019952
GO:0050876
Wikipedia:Reproduction
reproductive physiological process
biological_process
GO:0000003
reproduction
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GOC:go_curators
GOC:isa_complete
GOC:jl
ISBN:0198506732
The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
glycan biosynthesis
glycan biosynthetic process
polysaccharide anabolism
polysaccharide biosynthesis
polysaccharide formation
polysaccharide synthesis
biological_process
GO:0000271
polysaccharide biosynthetic process
The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
GOC:go_curators
The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters.
biological_process
GO:0002164
larval development
The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters.
GOC:jid
ISBN:0877795088
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Wikipedia:Immune_system
biological_process
GO:0002376
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
GOC:add
GO_REF:0000022
Any process that modulates the frequency, rate, or extent of an immune system process.
biological_process
GO:0002682
regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune system process.
GOC:add
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
down regulation of immune system process
down-regulation of immune system process
downregulation of immune system process
inhibition of immune system process
biological_process
GO:0002683
negative regulation of immune system process
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
GOC:add
Any process that activates or increases the frequency, rate, or extent of an immune system process.
up regulation of immune system process
up-regulation of immune system process
upregulation of immune system process
activation of immune system process
stimulation of immune system process
biological_process
GO:0002684
positive regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
GOC:add
A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.
puberty
biological_process
reproductive developmental process
GO:0003006
developmental process involved in reproduction
A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.
GOC:dph
GOC:isa_complete
puberty
GOC:dph
reproductive developmental process
GOC:dph
GOC:tb
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular process
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
true
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
receptor binding
Wikipedia:Ligand_(biochemistry)
receptor ligand
molecular_function
receptor-associated protein activity
GO:0005102
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
signaling receptor binding
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
GOC:bf
GOC:ceb
ISBN:0198506732
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Wikipedia:Binding_(molecular)
ligand
molecular_function
GO:0005488
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
GOC:ceb
GOC:mah
ISBN:0198506732
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO:0001948
GO:0045308
MIPS_funcat:16.01
MIPS_funcat:18.01.07
Reactome:R-HSA-170835
Reactome:R-HSA-170846
protein amino acid binding
glycoprotein binding
molecular_function
GO:0005515
protein binding
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GOC:go_curators
Reactome:R-HSA-170835
An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3
Reactome:R-HSA-170846
TGFBR2 recruits TGFBR1
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GOC:pdt
NIF_Subcellular:sao1337158144
subcellular entity
NIF_Subcellular:nlx_subcell_100315
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Wikipedia:Intracellular
internal to cell
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
MIPS_funcat:70.10
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
jl
2012-10-23T15:40:34Z
GO:0044261
GO:0044723
Wikipedia:Carbohydrate_metabolism
carbohydrate metabolism
multicellular organismal carbohydrate metabolic process
biological_process
single-organism carbohydrate metabolic process
GO:0005975
carbohydrate metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
GOC:mah
ISBN:0198506732
The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
GO:0044263
polysaccharide metabolism
glycan metabolic process
glycan metabolism
multicellular organismal polysaccharide metabolic process
biological_process
GO:0005976
polysaccharide metabolic process
The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
ISBN:0198547684
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
glycogen metabolism
biological_process
GO:0005977
glycogen metabolic process
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
ISBN:0198506732
The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
starch metabolism
biological_process
GO:0005982
starch metabolic process
The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
ISBN:0198506732
The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
monosaccharide metabolism
biological_process
GO:0005996
monosaccharide metabolic process
The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
ISBN:0198506732
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
cellular glucose metabolic process
glucose metabolism
biological_process
GO:0006006
glucose metabolic process
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
ISBN:0198506732
cellular glucose metabolic process
GOC:vw
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
cellular glucan metabolism
biological_process
GO:0006073
cellular glucan metabolic process
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
ISBN:0198547684
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
energy pathways
biological_process
intermediary metabolism
metabolic energy generation
GO:0006091
generation of precursor metabolites and energy
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
GOC:jl
intermediary metabolism
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
regulation of carbohydrate metabolism
biological_process
GO:0006109
regulation of carbohydrate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
GOC:go_curators
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
energy reserve metabolism
biological_process
GO:0006112
energy reserve metabolic process
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
GOC:mah
The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
MetaCyc:FERMENTATION-PWY
Wikipedia:Fermentation_(biochemistry)
biological_process
GO:0006113
fermentation
The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
GOC:curators
ISBN:0201090910
MetaCyc:Fermentation
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
phosphorus metabolism
biological_process
GO:0006793
phosphorus metabolic process
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
GOC:ai
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
MIPS_funcat:01.04
phosphate metabolism
biological_process
phosphate metabolic process
GO:0006796
phosphate-containing compound metabolic process
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
GOC:ai
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
nitrogen compound metabolism
biological_process
GO:0006807
nitrogen compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GOC:jl
ISBN:0198506732
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
janelomax
jl
2012-12-13T16:25:32Z
GO:0015457
GO:0015460
GO:0044765
MIPS_funcat:20
small molecule transport
solute:solute exchange
biological_process
single-organism transport
GO:0006810
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
transport
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
GOC:dos
GOC:dph
GOC:jl
GOC:mah
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
Wikipedia:Chemotaxis
taxis in response to chemical stimulus
biological_process
GO:0006935
chemotaxis
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
ISBN:0198506732
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
biological_process
GO:0006955
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
GOC:add
GO_REF:0000022
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Wikipedia:Cell_signaling
biological_process
GO:0007154
cell communication
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:mah
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GO:0023033
MIPS_funcat:30
Wikipedia:Signal_transduction
signaling cascade
signalling cascade
biological_process
signaling pathway
signalling pathway
GO:0007165
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
signal transduction
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GOC:go_curators
GOC:mtg_signaling_feb11
signalling pathway
GOC:mah
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
biological_process
GO:0007275
Note that this term was 'developmental process'.
multicellular organism development
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:dph
GOC:ems
GOC:isa_complete
GOC:tb
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
janelomax
jl
2012-09-20T14:06:08Z
GO:0023032
GO:0044708
GO:0044709
Wikipedia:Behavior
behavioral response to stimulus
behaviour
behavioural response to stimulus
biological_process
single-organism behavior
GO:0007610
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.
2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
behavior
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
GOC:ems
GOC:jl
ISBN:0395448956
PMID:20160973
Behavior associated with the intake of food.
https://github.com/geneontology/go-ontology/issues/18547
jl
2011-10-27T03:53:33Z
GO:0044366
GO:0044367
GO:0044368
GO:0044369
GO:0044370
GO:0044371
GO:0044372
MIPS_funcat:36.03
Wikipedia:List_of_feeding_behaviours
behavioral response to food
behavioural response to food
feeding behaviour
drinking
eating
feeding from phloem of other organism
feeding from plant phloem
feeding from tissue of other organism
feeding from vascular tissue of another organism
feeding from xylem of other organism
feeding on blood of other organism
feeding on or from other organism
feeding on plant sap
hematophagy
injection of substance into other organism during feeding on blood of other organism
taking of blood meal
biological_process
GO:0007631
See also the biological process term 'behavior ; GO:0007610'.
feeding behavior
Behavior associated with the intake of food.
GOC:mah
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
janelomax
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
janelomax
jl
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
MIPS_funcat:01
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
multicellular organism metabolic process
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GOC:go_curators
ISBN:0198547684
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
jl
2012-10-17T15:52:18Z
GO:0044274
GO:0044711
formation
Wikipedia:Anabolism
anabolism
biosynthesis
synthesis
multicellular organismal biosynthetic process
biological_process
single-organism biosynthetic process
GO:0009058
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GOC:curators
ISBN:0198547684
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GO:0043284
biopolymer biosynthetic process
macromolecule anabolism
macromolecule biosynthesis
macromolecule formation
macromolecule synthesis
biological_process
GO:0009059
macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:mah
biopolymer biosynthetic process
GOC:mtg_chebi_dec09
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
MetaCyc:PWY-3781
Wikipedia:Cellular_respiration#Aerobic_respiration
biological_process
GO:0009060
aerobic respiration
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
GOC:das
GOC:jl
ISBN:0140513590
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
MetaCyc:ANARESP1-PWY
Wikipedia:Anaerobic_respiration
Wikipedia:Cellular_respiration#Anaerobic_respiration
biological_process
GO:0009061
anaerobic respiration
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
GOC:das
GOC:jl
ISBN:0140513590
The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
glucan anabolism
glucan biosynthesis
glucan formation
glucan synthesis
biological_process
GO:0009250
glucan biosynthetic process
The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
GOC:go_curators
The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
biological_process
virulence
GO:0009405
Note that this term should not be used to annotate gene products that are involved in the host response to pathogenesis. It should only be used to annotate those gene products involved in the generation of pathogenesis by the pathogen itself.
pathogenesis
The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
GOC:go_curators
The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates.
energytaxis
taxis in response to energy source
biological_process
GO:0009453
energy taxis
The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates.
GOC:jl
PMID:11029423
The directed movement of a motile cell or organism in response to environmental oxygen.
taxis in response to atmospheric oxygen
biological_process
GO:0009454
aerotaxis
The directed movement of a motile cell or organism in response to environmental oxygen.
GOC:jl
ISBN:0192801023
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
MIPS_funcat:36.20.35
response to environmental stimulus
biological_process
GO:0009605
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to external stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
GOC:hb
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
biological_process
GO:0009791
post-embryonic development
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
regulation of anabolism
regulation of biosynthesis
regulation of formation
regulation of synthesis
biological_process
GO:0009889
regulation of biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
GOC:go_curators
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
down regulation of biosynthetic process
down-regulation of biosynthetic process
downregulation of biosynthetic process
negative regulation of anabolism
negative regulation of biosynthesis
negative regulation of formation
negative regulation of synthesis
inhibition of biosynthetic process
biological_process
GO:0009890
negative regulation of biosynthetic process
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of anabolism
positive regulation of biosynthesis
positive regulation of formation
positive regulation of synthesis
up regulation of biosynthetic process
up-regulation of biosynthetic process
upregulation of biosynthetic process
activation of biosynthetic process
stimulation of biosynthetic process
biological_process
GO:0009891
positive regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044252
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
negative regulation of organismal metabolism
inhibition of metabolic process
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
biological_process
GO:0009892
negative regulation of metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044253
positive regulation of metabolism
up regulation of metabolic process
up-regulation of metabolic process
upregulation of metabolic process
activation of metabolic process
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of metabolic process
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
biological_process
GO:0009893
positive regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that modulates the frequency, rate or extent of signal transduction.
GO:0035466
biological_process
regulation of signaling pathway
regulation of signalling pathway
GO:0009966
regulation of signal transduction
Any process that modulates the frequency, rate or extent of signal transduction.
GOC:sm
regulation of signalling pathway
GOC:mah
Any process that activates or increases the frequency, rate or extent of signal transduction.
GO:0035468
up regulation of signal transduction
up-regulation of signal transduction
upregulation of signal transduction
activation of signal transduction
stimulation of signal transduction
biological_process
positive regulation of signaling pathway
positive regulation of signalling pathway
GO:0009967
positive regulation of signal transduction
Any process that activates or increases the frequency, rate or extent of signal transduction.
GOC:sm
positive regulation of signalling pathway
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GO:0035467
down regulation of signal transduction
down-regulation of signal transduction
downregulation of signal transduction
inhibition of signal transduction
biological_process
negative regulation of signaling pathway
negative regulation of signalling pathway
GO:0009968
negative regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GOC:sm
negative regulation of signalling pathway
GOC:mah
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
janelomax
jl
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
Any process that modulates the frequency, rate or extent of photosynthesis.
biological_process
GO:0010109
regulation of photosynthesis
Any process that modulates the frequency, rate or extent of photosynthesis.
GOC:sm
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
regulation of receptor activity
biological_process
GO:0010469
regulation of signaling receptor activity
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010556
regulation of macromolecule biosynthetic process
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010557
positive regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010558
negative regulation of macromolecule biosynthetic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010562
positive regulation of phosphorus metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010563
negative regulation of phosphorus metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
An process which modulate the frequency, rate or extent of starch biosynthesis, the chemical reactions and pathways resulting in the formation of starch.
biological_process
GO:0010581
regulation of starch biosynthetic process
An process which modulate the frequency, rate or extent of starch biosynthesis, the chemical reactions and pathways resulting in the formation of starch.
GOC:tb
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010604
positive regulation of macromolecule metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0010605
negative regulation of macromolecule metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010646
regulation of cell communication
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010647
positive regulation of cell communication
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
biological_process
GO:0010648
negative regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
GOC:dph
GOC:tb
Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
biological_process
GO:0010675
regulation of cellular carbohydrate metabolic process
Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
GOC:dph
GOC:tb
Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
biological_process
GO:0010676
positive regulation of cellular carbohydrate metabolic process
Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
GOC:dph
GOC:tb
Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
biological_process
GO:0010677
negative regulation of cellular carbohydrate metabolic process
Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
regulation of glucose metabolism
biological_process
GO:0010906
regulation of glucose metabolic process
Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
GOC:BHF
GOC:tb
regulation of glucose metabolism
GOC:tb
Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
positive regulation of glucose metabolism
biological_process
GO:0010907
positive regulation of glucose metabolic process
Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
GOC:BHF
GOC:tb
positive regulation of glucose metabolism
GOC:tb
Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
tb
2009-05-11T12:17:53Z
biological_process
GO:0010962
regulation of glucan biosynthetic process
Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
GOC:dph
GOC:tb
The chemical reactions and pathways by which a cell derives energy from inorganic compounds; results in the oxidation of the compounds from which energy is released.
Wikipedia:Lithotrophy
chemolithotrophie
chemolithotrophy
lithotrophy
biological_process
GO:0015975
energy derivation by oxidation of reduced inorganic compounds
The chemical reactions and pathways by which a cell derives energy from inorganic compounds; results in the oxidation of the compounds from which energy is released.
GOC:mah
lithotrophy
Wikipedia:Lithotrophy
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
Wikipedia:Photosynthesis
biological_process
GO:0015979
envoPolar
photosynthesis
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
ISBN:0198547684
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
chemoorganotrophy
biological_process
GO:0015980
energy derivation by oxidation of organic compounds
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
GOC:mah
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0006093
anabolic carbohydrate metabolic process
anabolic carbohydrate metabolism
carbohydrate anabolism
carbohydrate biosynthesis
carbohydrate formation
carbohydrate synthesis
biological_process
GO:0016051
carbohydrate biosynthetic process
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
ISBN:0198506732
OBSOLETE. A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
GO:0008219
GO:0012501
Wikipedia:Death
biological_process
GO:0016265
This term was made obsolete because it refers to a phenotype. When death of a cell or tissue is a result of a true biological process, this should be captured using 'programmed cell death' or one of its descendants.
obsolete death
true
OBSOLETE. A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
GOC:mah
GOC:mtg_apoptosis
ISBN:0877797099
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Wikipedia:Phosphorylation
biological_process
GO:0016310
phosphorylation
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
ISBN:0198506732
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-6787403
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-6787403
GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA
Reactome:R-HSA-8868783
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
EC:2.7
molecular_function
GO:0016772
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
The specific behavior of an organism that is associated with reproduction.
janelomax
jl
2012-09-19T16:01:37Z
GO:0033057
GO:0044704
reproductive behavior in a multicellular organism
reproductive behaviour
multicellular organism reproductive behavior
biological_process
single-organism reproductive behavior
GO:0019098
reproductive behavior
The specific behavior of an organism that is associated with reproduction.
GOC:jl
GOC:pr
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolism
biological_process
GO:0019220
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044246
regulation of metabolism
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
biological_process
GO:0019222
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
regulation of organismal metabolic process
GOC:tb
The chemical reactions and pathways resulting in the formation of starch, the most important reserve polysaccharide in plants.
MetaCyc:PWY-622
starch anabolism
starch biosynthesis
starch formation
starch synthesis
biological_process
GO:0019252
starch biosynthetic process
The chemical reactions and pathways resulting in the formation of starch, the most important reserve polysaccharide in plants.
GOC:ai
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
hexose metabolism
biological_process
GO:0019318
hexose metabolic process
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
ISBN:0198506732
The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons.
biological_process
GO:0019329
ammonia oxidation
The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons.
GOC:mah
MetaCyc:AMMOXID-PWY
MetaCyc:P303-PWY
MetaCyc:PWY-2242
The oxidation of ammonium (NH4) to nitrogen (N2) in the absence of oxygen, using nitrite (NO2) as the electron acceptor. It is suggested that hydroxylamine and ammonium are combined to yield hydrazine, which is subsequently oxidized to N2.
anaerobic ammonium oxidation
MetaCyc:P303-PWY
Wikipedia:Anammox
anammox
biological_process
GO:0019331
envoPolar
anaerobic respiration, using ammonium as electron donor
The oxidation of ammonium (NH4) to nitrogen (N2) in the absence of oxygen, using nitrite (NO2) as the electron acceptor. It is suggested that hydroxylamine and ammonium are combined to yield hydrazine, which is subsequently oxidized to N2.
MetaCyc:P303-PWY
The oxidation of nitrite (NO2) to nitrate (NO3), using oxygen (O2) as the electron acceptor. Nitrite oxidation is the final step in nitrification, the oxidation of ammonia to nitrate, and nitrite oxidoreductase (NOR) is the key enzyme complex that catalyzes the conversion of nitrite to nitrate in nitrite oxidizing species.
nitrite oxidation
MetaCyc:P282-PWY
biological_process
GO:0019332
envoPolar
aerobic respiration, using nitrite as electron donor
The oxidation of nitrite (NO2) to nitrate (NO3), using oxygen (O2) as the electron acceptor. Nitrite oxidation is the final step in nitrification, the oxidation of ammonia to nitrate, and nitrite oxidoreductase (NOR) is the key enzyme complex that catalyzes the conversion of nitrite to nitrate in nitrite oxidizing species.
MetaCyc:P282-PWY
The metabolic process in which ammonia (NH3) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite.
MetaCyc:AMMOXID-PWY
aerobic ammonia oxidation to nitrite via hydrazine
biological_process
GO:0019409
envoPolar
aerobic respiration, using ammonia as electron donor
The metabolic process in which ammonia (NH3) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite.
MetaCyc:AMMOXID-PWY
aerobic ammonia oxidation to nitrite via hydrazine
GOC:mah
The metabolic process in which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation.
biological_process
GO:0019410
aerobic respiration, using carbon monoxide as electron donor
The metabolic process in which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation.
PMID:18024677
The oxidation of hydrogen (H2) to water (H2O), using oxygen (O2) as the electron acceptor. A hydrogenase enzyme binds H2 and the hydrogen atoms are passed through an electron transfer chain to O2 to form water.
hydrogen oxidation
MetaCyc:P283-PWY
biological_process
GO:0019412
envoPolar
aerobic respiration, using hydrogen as electron donor
The oxidation of hydrogen (H2) to water (H2O), using oxygen (O2) as the electron acceptor. A hydrogenase enzyme binds H2 and the hydrogen atoms are passed through an electron transfer chain to O2 to form water.
MetaCyc:P283-PWY
An aerobic respiration process in which a sulfur-containing molecule (hydrogen sulfide, sulfur, sulfite, thiosulfate, and various polythionates) is oxidized.
aerobic respiration, using sulphur or sulphate as electron donor
biological_process
GO:0019414
envoPolar
aerobic respiration, using sulfur or sulfate as electron donor
An aerobic respiration process in which a sulfur-containing molecule (hydrogen sulfide, sulfur, sulfite, thiosulfate, and various polythionates) is oxidized.
PMID:11425697
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
reproductive cellular process in multicellular organism
biological_process
GO:0022412
cellular process involved in reproduction in multicellular organism
A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism.
GOC:isa_complete
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
janelomax
jl
2012-09-19T15:56:06Z
GO:0044702
biological_process
single organism reproductive process
GO:0022414
reproductive process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:dph
GOC:isa_complete
Any process that modulates the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
regulation of signaling process
regulation of signalling process
GO:0023051
regulation of signaling
Any process that modulates the frequency, rate or extent of a signaling process.
GOC:mtg_signal
regulation of signaling process
GOC:bf
regulation of signalling process
GOC:mah
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
janelomax
jl
2010-02-16T09:30:50Z
GO:0023046
GO:0044700
biological signaling
signaling process
signalling
biological_process
signalling process
single organism signaling
GO:0023052
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
signaling
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
GOC:mtg_signal
GOC:mtg_signaling_feb11
GOC:signaling
signalling process
GOC:mah
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
positive regulation of signalling process
biological_process
positive regulation of signaling process
GO:0023056
positive regulation of signaling
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
GOC:mtg_signal
positive regulation of signalling process
GOC:mah
positive regulation of signaling process
GOC:bf
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
negative regulation of signaling process
negative regulation of signalling process
GO:0023057
negative regulation of signaling
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
GOC:mtg_signal
negative regulation of signaling process
GOC:bf
negative regulation of signalling process
GOC:mah
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
MIPS_funcat:18.02.07
molecular_function
GO:0030545
receptor regulator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
GOC:ceb
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
receptor activator activity
molecular_function
GO:0030546
signaling receptor activator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
GOC:ceb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolism
biological_process
GO:0031323
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
biological_process
GO:0031324
negative regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
biological_process
GO:0031325
positive regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
regulation of cellular anabolism
regulation of cellular biosynthesis
regulation of cellular formation
regulation of cellular synthesis
biological_process
GO:0031326
regulation of cellular biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
down regulation of cellular biosynthetic process
down-regulation of cellular biosynthetic process
downregulation of cellular biosynthetic process
negative regulation of cellular anabolism
negative regulation of cellular biosynthesis
negative regulation of cellular formation
negative regulation of cellular synthesis
inhibition of cellular biosynthetic process
biological_process
GO:0031327
negative regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
activation of cellular biosynthetic process
stimulation of cellular biosynthetic process
biological_process
GO:0031328
positive regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
down regulation of protein binding
down-regulation of protein binding
downregulation of protein binding
inhibition of protein binding
biological_process
GO:0032091
negative regulation of protein binding
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
GOC:mah
Any process that activates or increases the frequency, rate or extent of protein binding.
up regulation of protein binding
up-regulation of protein binding
upregulation of protein binding
activation of protein binding
stimulation of protein binding
biological_process
GO:0032092
positive regulation of protein binding
Any process that activates or increases the frequency, rate or extent of protein binding.
GOC:mah
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
biological_process
GO:0032101
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to external stimulus
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
down regulation of response to external stimulus
down-regulation of response to external stimulus
downregulation of response to external stimulus
inhibition of response to external stimulus
biological_process
GO:0032102
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
negative regulation of response to external stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
GOC:mah
Any process that activates, maintains or increases the rate of a response to an external stimulus.
up regulation of response to external stimulus
up-regulation of response to external stimulus
upregulation of response to external stimulus
activation of response to external stimulus
stimulation of response to external stimulus
biological_process
GO:0032103
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
positive regulation of response to external stimulus
Any process that activates, maintains or increases the rate of a response to an external stimulus.
GOC:mah
Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.
biological_process
GO:0032386
regulation of intracellular transport
Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells.
down regulation of intracellular transport
down-regulation of intracellular transport
downregulation of intracellular transport
inhibition of intracellular transport
biological_process
GO:0032387
negative regulation of intracellular transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells.
GOC:mah
Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells.
up regulation of intracellular transport
up-regulation of intracellular transport
upregulation of intracellular transport
activation of intracellular transport
stimulation of intracellular transport
biological_process
GO:0032388
positive regulation of intracellular transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells.
GOC:mah
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
janelomax
jl
2012-09-19T16:07:47Z
GO:0044707
GO:0050874
organismal physiological process
biological_process
single-multicellular organism process
GO:0032501
multicellular organismal process
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
GOC:curators
GOC:dph
GOC:isa_complete
GOC:tb
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
jl
2012-12-19T12:21:31Z
GO:0044767
development
biological_process
single-organism developmental process
GO:0032502
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
GOC:isa_complete
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
biological_process
GO:0032504
multicellular organism reproduction
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
GOC:isa_complete
GOC:jid
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
regulation of localisation
biological_process
GO:0032879
regulation of localization
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
GOC:mah
regulation of localisation
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides.
biological_process
GO:0032881
regulation of polysaccharide metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides.
GOC:mah
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides.
biological_process
GO:0032885
regulation of polysaccharide biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
down regulation of kinase activity
down-regulation of kinase activity
downregulation of kinase activity
inhibition of kinase activity
kinase inhibitor
biological_process
GO:0033673
negative regulation of kinase activity
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
up regulation of kinase activity
up-regulation of kinase activity
upregulation of kinase activity
kinase activator
stimulation of kinase activity
biological_process
GO:0033674
positive regulation of kinase activity
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:mah
The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell.
cellular glycan biosynthesis
cellular glycan biosynthetic process
cellular polysaccharide anabolism
cellular polysaccharide biosynthesis
cellular polysaccharide formation
cellular polysaccharide synthesis
biological_process
GO:0033692
cellular polysaccharide biosynthetic process
The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell.
GOC:go_curators
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells.
biological_process
GO:0034637
cellular carbohydrate biosynthetic process
The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells.
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
GO:0034961
cellular biopolymer biosynthetic process
cellular macromolecule anabolism
cellular macromolecule biosynthesis
cellular macromolecule formation
cellular macromolecule synthesis
biological_process
GO:0034645
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
GOC:mah
cellular biopolymer biosynthetic process
GOC:mtg_chebi_dec09
cellular macromolecule anabolism
GOC:mah
cellular macromolecule biosynthesis
GOC:mah
cellular macromolecule formation
GOC:mah
cellular macromolecule synthesis
GOC:mah
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
bf
rfoulger
2010-05-14T01:14:37Z
GO:0007242
GO:0007243
GO:0023013
GO:0023034
intracellular signaling chain
intracellular protein kinase cascade
intracellular signal transduction pathway
protein kinase cascade
signal transmission via intracellular cascade
biological_process
intracellular signaling cascade
intracellular signaling pathway
signal transduction via intracellular signaling cascade
GO:0035556
intracellular signal transduction
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
GOC:bf
GOC:jl
GOC:signaling
ISBN:3527303782
intracellular signaling chain
ISBN:3527303782
intracellular protein kinase cascade
GOC:signaling
protein kinase cascade
GOC:signaling
intracellular signaling cascade
GOC:signaling
OBSOLETE. The transfer of information between living organisms.
bf
2011-01-14T10:11:25Z
multi-organism signalling
signaling between organisms
signaling with other organism
pheromone signaling
biological_process
GO:0035636
This term was obsoleted because it was a grouping term but had no subclasses.
obsolete multi-organism signaling
true
OBSOLETE. The transfer of information between living organisms.
GOC:go_curators
multi-organism signalling
GOC:bf
signaling between organisms
GOC:bf
signaling with other organism
GOC:bf
pheromone signaling
GOC:bf
The process in which an organism effects a change in the structure or processes of another organism.
https://github.com/geneontology/go-ontology/issues/18605
bf
2011-04-21T01:31:51Z
modification of morphology or physiology of other organism
regulation of morphology of other organism
regulation of physiological process of other organism
regulation of physiology of other organism
biological_process
regulation of morphology or physiology of other organism
GO:0035821
modulation of process of other organism
The process in which an organism effects a change in the structure or processes of another organism.
GOC:bf
regulation of morphology of other organism
GOC:bf
regulation of physiological process of other organism
GOC:bf
regulation of physiology of other organism
GOC:bf
regulation of morphology or physiology of other organism
GOC:bf
A form of mutualism between a fungus and the roots of a vascular plant, where hyphae of the fungus penetrate the plant cell wall and invaginate its cell membrane. Once inside, the fungus forms highly branched structures for nutrient exchange with the plant called arbuscules. Aids in the acquisition by the plant of nutrients such as phosphorus from the soil.
bf
2013-05-07T15:07:32Z
arbuscular mycorrhizae formation
arbuscular mycorrhizas formation
biological_process
arbuscular mycorrhizal symbiosis
GO:0036377
arbuscular mycorrhizal association
A form of mutualism between a fungus and the roots of a vascular plant, where hyphae of the fungus penetrate the plant cell wall and invaginate its cell membrane. Once inside, the fungus forms highly branched structures for nutrient exchange with the plant called arbuscules. Aids in the acquisition by the plant of nutrients such as phosphorus from the soil.
GOC:sk
Wikipedia:Arbuscular_mycorrhiza
arbuscular mycorrhizae formation
Wikipedia:Arbuscular_mycorrhiza
arbuscular mycorrhizas formation
Wikipedia:Arbuscular_mycorrhiza
arbuscular mycorrhizal symbiosis
Wikipedia:Arbuscular_mycorrhiza
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
bf
rfoulger
2011-08-01T02:45:27Z
GO:0004872
GO:0019041
receptor activity
receptor activity involved in signal transduction
molecular_function
GO:0038023
signaling receptor activity
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
GOC:bf
GOC:signaling
receptor activity involved in signal transduction
GOC:bf
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO:0048590
biological_process
growth pattern
non-developmental growth
GO:0040007
See also the biological process term 'cell growth ; GO:0016049'.
growth
The increase in size or mass of an entire organism, a part of an organism or a cell.
GOC:bf
GOC:ma
non-developmental growth
GOC:mah
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
biological_process
GO:0040008
regulation of growth
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
GOC:ems
GOC:mah
Self-propelled movement of a cell or organism from one location to another.
MIPS_funcat:02.45.11
biological_process
GO:0040011
locomotion
Self-propelled movement of a cell or organism from one location to another.
GOC:dgh
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
biological_process
GO:0040012
regulation of locomotion
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
GOC:ems
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
down regulation of locomotion
down-regulation of locomotion
downregulation of locomotion
inhibition of locomotion
biological_process
GO:0040013
negative regulation of locomotion
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
up regulation of locomotion
up-regulation of locomotion
upregulation of locomotion
activation of locomotion
stimulation of locomotion
biological_process
GO:0040017
positive regulation of locomotion
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
GOC:go_curators
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
MIPS_funcat:34.11.03
MIPS_funcat:34.11.03.05
MIPS_funcat:36.20.35.09
response to chemical stimulus
response to chemical substance
biological_process
GO:0042221
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to chemical
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
GOC:jl
response to chemical stimulus
GOC:dos
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
biological_process
GO:0042325
regulation of phosphorylation
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
GOC:jl
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
down regulation of phosphorylation
down-regulation of phosphorylation
downregulation of phosphorylation
inhibition of phosphorylation
biological_process
GO:0042326
negative regulation of phosphorylation
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
up regulation of phosphorylation
up-regulation of phosphorylation
upregulation of phosphorylation
activation of phosphorylation
stimulation of phosphorylation
biological_process
GO:0042327
positive regulation of phosphorylation
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
GOC:jl
The directed movement of a motile cell or organism in response to an external stimulus.
Wikipedia:Taxis
directed movement in response to stimulus
biological_process
GO:0042330
taxis
The directed movement of a motile cell or organism in response to an external stimulus.
GOC:jl
ISBN:0192801023
Any process that activates or increases the activity of an enzyme.
GO:0048554
MIPS_funcat:18.02.01.01
positive regulation of enzyme activity
up regulation of enzyme activity
up-regulation of enzyme activity
upregulation of enzyme activity
activation of enzyme activity
activation of metalloenzyme activity
positive regulation of metalloenzyme activity
stimulation of enzyme activity
stimulation of metalloenzyme activity
up regulation of metalloenzyme activity
up-regulation of metalloenzyme activity
upregulation of metalloenzyme activity
biological_process
GO:0043085
positive regulation of catalytic activity
Any process that activates or increases the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
positive regulation of enzyme activity
GOC:tb
Any process that stops or reduces the activity of an enzyme.
GO:0048553
down regulation of enzyme activity
down-regulation of enzyme activity
down-regulation of metalloenzyme activity
downregulation of enzyme activity
negative regulation of enzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
inhibition of enzyme activity
inhibition of metalloenzyme activity
negative regulation of metalloenzyme activity
biological_process
GO:0043086
negative regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
negative regulation of enzyme activity
GOC:tb
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GO:0043283
GO:0044259
biopolymer metabolic process
macromolecule metabolism
organismal macromolecule metabolism
multicellular organismal macromolecule metabolic process
biological_process
GO:0043170
macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:mah
biopolymer metabolic process
GOC:mtg_chebi_dec09
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
NIF_Subcellular:sao414196390
membrane-enclosed organelle
cellular_component
GO:0043227
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
cellular_component
GO:0043229
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
cellular_component
GO:0043231
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates.
regulation of carbohydrate anabolism
regulation of carbohydrate biosynthesis
regulation of carbohydrate formation
regulation of carbohydrate synthesis
biological_process
GO:0043255
regulation of carbohydrate biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates.
GOC:jl
Any process that modulates the frequency, rate or extent of protein binding.
biological_process
GO:0043393
regulation of protein binding
Any process that modulates the frequency, rate or extent of protein binding.
GOC:go_curators
Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
biological_process
GO:0043457
regulation of cellular respiration
Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
GOC:jl
Any process that modulates the frequency, rate or extent of fermentation, the anaerobic enzymatic conversion of organic compounds, especially carbohydrates, to other compounds, especially to ethyl alcohol, resulting in energy in the form of adenosine triphosphate (ATP).
biological_process
GO:0043465
regulation of fermentation
Any process that modulates the frequency, rate or extent of fermentation, the anaerobic enzymatic conversion of organic compounds, especially carbohydrates, to other compounds, especially to ethyl alcohol, resulting in energy in the form of adenosine triphosphate (ATP).
GOC:jl
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances.
biological_process
GO:0043467
regulation of generation of precursor metabolites and energy
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances.
GOC:jl
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological_process
GO:0043549
regulation of kinase activity
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GOC:bf
The oxidation of arsenite to arsenate, using oxygen (O2) as the electron acceptor. Arsenite oxidase provides electrons to an electron carrier which transfers them to oxygen utilizing respiratory systems.
biological_process
GO:0043554
aerobic respiration, using arsenite as electron donor
The oxidation of arsenite to arsenate, using oxygen (O2) as the electron acceptor. Arsenite oxidase provides electrons to an electron carrier which transfers them to oxygen utilizing respiratory systems.
GOC:mlg
Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
biological_process
GO:0043900
regulation of multi-organism process
Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
GOC:jl
Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
biological_process
GO:0043901
negative regulation of multi-organism process
Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
GOC:jl
Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
biological_process
GO:0043902
positive regulation of multi-organism process
Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
GOC:jl
Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.
https://github.com/geneontology/go-ontology/issues/19222
biological_process
regulation of symbiosis, encompassing mutualism through parasitism
GO:0043903
regulation of interspecies interactions between organisms
Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.
GOC:jl
Any process in which an organism activates, maintains or increases the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
activation of enzyme activity in other organism
activation of enzyme activity in other organism during symbiotic interaction
biological_process
positive regulation of catalytic activity in other organism during symbiotic interaction
up regulation of enzyme activity in other organism during symbiotic interaction
up-regulation of enzyme activity in other organism during symbiotic interaction
upregulation of enzyme activity in other organism during symbiotic interaction
GO:0043946
positive regulation of catalytic activity in other organism involved in symbiotic interaction
Any process in which an organism activates, maintains or increases the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
GOC:tb
positive regulation of catalytic activity in other organism during symbiotic interaction
GOC:dph
Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
positive regulation by symbiont of host catalytic activity
positive regulation by symbiont of host enzyme activity
up regulation by symbiont of host enzyme activity
up-regulation by symbiont of host enzyme activity
upregulation by symbiont of host enzyme activity
activation by symbiont of host enzyme activity
activation of host enzyme activity
biological_process
GO:0043948
induction by symbiont of host catalytic activity
Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
The process in which a symbiont organism effects a change in the structure or processes of its host organism.
https://github.com/geneontology/go-ontology/issues/18719
GO:0044004
GO:0044055
modulation by symbiont of host system process
regulation by symbiont of host system process
biological_process
disruption by symbiont of host cell
modification by symbiont of host biological process
modification by symbiont of host morphology or physiology
GO:0044003
modulation by symbiont of host process
The process in which a symbiont organism effects a change in the structure or processes of its host organism.
GOC:cc
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism.
multi-organism metabolism
multi-organismal metabolic process
multi-organismal metabolism
biological_process
GO:0044033
multi-organism metabolic process
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism.
GOC:jl
OBSOLETE. A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - which involves more than one organism.
https://github.com/geneontology/go-ontology/issues/18787
multi-organism biosynthesis
multi-organismal biosynthesis
multi-organismal biosynthetic process
biological_process
GO:0044034
This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism biosynthetic process
true
OBSOLETE. A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - which involves more than one organism.
GOC:jl
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
glucan metabolism
biological_process
GO:0044042
glucan metabolic process
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
GOC:jl
Any process in which a symbiont organism modulates the frequency, rate or extent of a cellular process, any process that is carried out at the cellular level, but not necessarily restricted to a single cell, in its host organism.
modulation of host cellular process by symbiont
regulation by symbiont of host cellular process
regulation of host cellular process by symbiont
biological_process
GO:0044068
modulation by symbiont of host cellular process
Any process in which a symbiont organism modulates the frequency, rate or extent of a cellular process, any process that is carried out at the cellular level, but not necessarily restricted to a single cell, in its host organism.
MITRE:tk
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jane
jl
2009-04-21T04:07:27Z
biological_process
GO:0044092
negative regulation of molecular function
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
jane
jl
2009-04-21T04:11:06Z
biological_process
GO:0044093
positive regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GO:jl
The increase in size or mass of an organism occurring when the organism is in a symbiotic interaction.
jl
2009-07-30T02:22:33Z
GO:0044153
biological_process
growth during symbiotic interaction
growth on or near surface of other organism during symbiotic interaction
growth on or near surface of other organism involved in symbiotic interaction
GO:0044110
This term partially replaces the obsolete term 'growth or development during symbiotic interaction ; GO:0052171'. See also 'development during symbiotic interaction ; GO:0044111'.
growth involved in symbiotic interaction
The increase in size or mass of an organism occurring when the organism is in a symbiotic interaction.
GO:jl
GOC:pamgo_curators
growth during symbiotic interaction
GOC:dph
growth on or near surface of other organism during symbiotic interaction
GOC:tb
The progression of an organism from an initial condition to a later condition, occurring when the organism is in a symbiotic interaction.
jl
2009-07-30T02:26:46Z
GO:0044152
development on or near surface of other organism involved in symbiotic interaction
biological_process
development during symbiotic interaction
development on or near surface of other organism during symbiotic interaction
GO:0044111
This term partially replaces the obsolete term 'growth or development during symbiotic interaction ; GO:0052171'. See also 'growth during symbiotic interaction ; GO:0044110'.
development involved in symbiotic interaction
The progression of an organism from an initial condition to a later condition, occurring when the organism is in a symbiotic interaction.
GO:jl
GOC:pamgo_curators
development during symbiotic interaction
gOC:dph
development on or near surface of other organism during symbiotic interaction
GOC:dph
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolism
biological_process
GO:0044238
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
GOC:go_curators
http://www.metacyc.org
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular anabolism
cellular biosynthesis
cellular formation
cellular synthesis
biological_process
GO:0044249
cellular biosynthetic process
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:jl
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GO:0034960
cellular biopolymer metabolic process
cellular macromolecule metabolism
biological_process
GO:0044260
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
GOC:mah
cellular biopolymer metabolic process
GOC:mtg_chebi_dec09
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
GO:0006092
cellular carbohydrate metabolism
main pathways of carbohydrate metabolic process
main pathways of carbohydrate metabolism
biological_process
GO:0044262
cellular carbohydrate metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
GOC:jl
The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells.
cellular glycan metabolic process
cellular glycan metabolism
cellular polysaccharide metabolism
biological_process
GO:0044264
cellular polysaccharide metabolic process
The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells.
GOC:jl
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
jl
2010-01-26T12:05:20Z
small molecule metabolism
biological_process
GO:0044281
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule metabolic process
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:vw
The process in which an organism effects a change in the function of proteins in a second organism.
jl
2011-10-27T01:28:16Z
biological_process
GO:0044359
modulation of molecular function in other organism
The process in which an organism effects a change in the function of proteins in a second organism.
GOC:jl
Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the function of proteins in a second organism.
jl
2011-10-27T02:12:49Z
biological_process
GO:0044362
negative regulation of molecular function in other organism
Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the function of proteins in a second organism.
GOC:jl
OBSOLETE. Any process in which an organism within a multispecies community gains an advantage in growth or survival over another organism of a different species in that community.
https://github.com/geneontology/go-ontology/issues/18568
interspecies competition
competition with another organism
biological_process
GO:0044402
This term was obsoleted because it is outside the scope of GO.
obsolete competition with other organism
true
OBSOLETE. Any process in which an organism within a multispecies community gains an advantage in growth or survival over another organism of a different species in that community.
GOC:cc
competition with another organism
GOC:bf
true
A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
https://github.com/geneontology/go-ontology/issues/14807
GO:0043298
GO:0044404
GO:0072519
GO:0085031
commensalism
host-pathogen interaction
parasitism
biological_process
symbiosis
symbiosis, encompassing mutualism through parasitism
symbiotic interaction
symbiotic interaction between host and organism
symbiotic interaction between organisms
symbiotic interaction between species
GO:0044403
symbiosis, encompassing mutualism through parasitism
symbiotic process
A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
GOC:cc
https://study.com/academy/lesson/symbiont-definition-lesson-quiz.html
Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
https://github.com/geneontology/go-ontology/issues/18563
GO:0030260
GO:0044411
GO:0051806
GO:0051828
GO:0051830
GO:0075052
GO:0085027
GO:0085028
host invasion
host penetration
invasion into host
invasion of host
penetration into host
entry into cell of other organism during symbiotic interaction
entry into host cell
entry into host cell via penetration peg
entry into host via a specialized structure during symbiotic interaction
entry into host via enzymatic degradation of host anatomical structure
entry into host via enzymatic degradation of host cuticle
host cell invasion
other organism cell invasion
penetration into host via a specialized structure
penetration into host via a specialized structure during symbiotic interaction
biological_process
entry into cell of other organism involved in symbiotic interaction
entry into host through host barriers
entry into other organism during symbiotic interaction
entry into other organism involved in symbiotic interaction
invasion into other organism
invasion of other organism
invasive growth
other organism invasion
GO:0044409
entry into host
Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:vw
host penetration
GOC:vw
penetration into host
GOC:vw
entry into cell of other organism during symbiotic interaction
GOC:tb
penetration into host via a specialized structure
GOC:vw
penetration into host via a specialized structure during symbiotic interaction
GOC:vw
entry into other organism during symbiotic interaction
GOC:tb
true
Any process in which an organism has an effect on an organism of a different species.
interaction with another species
interspecies interaction
interspecies interaction with other organisms
biological_process
GO:0044419
interspecies interaction between organisms
Any process in which an organism has an effect on an organism of a different species.
GOC:cc
OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms.
CL:0000000
NIF_Subcellular:sao628508602
cellular subcomponent
cellular_component
protoplast
GO:0044464
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
cell part
obsolete cell part
true
OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms.
GOC:jl
cellular subcomponent
NIF_Subcellular:sao628508602
protoplast
GOC:mah
true
true
true
Any process that is carried out at the cellular level which involves another organism of the same or different species.
jl
2012-12-11T17:00:50Z
biological_process
GO:0044764
multi-organism cellular process
Any process that is carried out at the cellular level which involves another organism of the same or different species.
GOC:jl
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism.
jl
2012-12-13T16:25:50Z
biological_process
GO:0044766
multi-organism transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism.
GOC:jl
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
respiration
Wikipedia:Cellular_respiration
oxidative metabolic process
oxidative metabolism
biological_process
GO:0045333
cellular respiration
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
GOC:das
ISBN:0140513590
ISBN:0198506732
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
down regulation of carbohydrate metabolic process
down-regulation of carbohydrate metabolic process
downregulation of carbohydrate metabolic process
negative regulation of carbohydrate metabolism
inhibition of carbohydrate metabolic process
biological_process
GO:0045912
negative regulation of carbohydrate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
positive regulation of carbohydrate metabolism
up regulation of carbohydrate metabolic process
up-regulation of carbohydrate metabolic process
upregulation of carbohydrate metabolic process
activation of carbohydrate metabolic process
stimulation of carbohydrate metabolic process
biological_process
GO:0045913
positive regulation of carbohydrate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
GOC:go_curators
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
down regulation of growth
down-regulation of growth
downregulation of growth
inhibition of growth
biological_process
GO:0045926
negative regulation of growth
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
GOC:go_curators
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
up regulation of growth
up-regulation of growth
upregulation of growth
activation of growth
stimulation of growth
biological_process
GO:0045927
positive regulation of growth
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GOC:go_curators
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
down regulation of phosphate metabolic process
down-regulation of phosphate metabolic process
downregulation of phosphate metabolic process
negative regulation of phosphate metabolism
inhibition of phosphate metabolic process
biological_process
GO:0045936
negative regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
biological_process
GO:0045937
positive regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
The directed movement of substances within a cell.
jl
2013-12-18T14:04:50Z
GO:1902582
biological_process
single organism intracellular transport
single-organism intracellular transport
GO:0046907
intracellular transport
The directed movement of substances within a cell.
GOC:ai
single organism intracellular transport
GOC:TermGenie
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
https://github.com/geneontology/go-ontology/issues/14220
mah
midori
2010-09-13T04:51:59Z
GO:0071884
receptor agonist activity
signaling molecule
signaling receptor ligand activity
vitamin D receptor activator activity
molecular_function
GO:0048018
Definition discussed in https://github.com/geneontology/go-ontology/issues/14220
receptor ligand activity
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
GOC:kv
GOC:molecular_function_refactoring
GOC:pdt
receptor agonist activity
GOC:molecular_function_refactoring
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0043119
positive regulation of physiological process
up regulation of biological process
up-regulation of biological process
upregulation of biological process
activation of biological process
stimulation of biological process
biological_process
GO:0048518
positive regulation of biological process
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0043118
down regulation of biological process
down-regulation of biological process
downregulation of biological process
negative regulation of physiological process
inhibition of biological process
biological_process
GO:0048519
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:jid
Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
up regulation of behavior
up-regulation of behavior
upregulation of behavior
activation of behavior
stimulation of behavior
biological_process
GO:0048520
positive regulation of behavior
Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:jid
GOC:pr
Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
down regulation of behavior
down-regulation of behavior
downregulation of behavior
inhibition of behavior
biological_process
GO:0048521
negative regulation of behavior
Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:jid
GOC:pr
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051242
positive regulation of cellular physiological process
up regulation of cellular process
up-regulation of cellular process
upregulation of cellular process
activation of cellular process
stimulation of cellular process
biological_process
GO:0048522
positive regulation of cellular process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051243
down regulation of cellular process
down-regulation of cellular process
downregulation of cellular process
negative regulation of cellular physiological process
inhibition of cellular process
biological_process
GO:0048523
negative regulation of cellular process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:jid
Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
biological_process
GO:0048580
regulation of post-embryonic development
Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
down regulation of post-embryonic development
down-regulation of post-embryonic development
downregulation of post-embryonic development
inhibition of post-embryonic development
biological_process
GO:0048581
negative regulation of post-embryonic development
Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
GOC:jid
Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
up regulation of post-embryonic development
up-regulation of post-embryonic development
upregulation of post-embryonic development
activation of post-embryonic development
stimulation of post-embryonic development
biological_process
GO:0048582
positive regulation of post-embryonic development
Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure.
GOC:jid
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
biological_process
GO:0048583
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
regulation of response to stimulus
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
up regulation of response to stimulus
up-regulation of response to stimulus
upregulation of response to stimulus
activation of response to stimulus
stimulation of response to stimulus
biological_process
GO:0048584
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
positive regulation of response to stimulus
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
down regulation of response to stimulus
down-regulation of response to stimulus
downregulation of response to stimulus
inhibition of response to stimulus
biological_process
GO:0048585
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
negative regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
GOC:jid
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
organismal reproductive process
reproductive process in a multicellular organism
biological_process
GO:0048609
multicellular organismal reproductive process
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
GOC:dph
GOC:jid
GOC:tb
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
development of an anatomical structure
biological_process
GO:0048856
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GO_REF:0000021
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
biological_process
GO:0050776
regulation of immune response
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
down regulation of immune response
down-regulation of immune response
downregulation of immune response
inhibition of immune response
biological_process
GO:0050777
negative regulation of immune response
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
up regulation of immune response
up-regulation of immune response
upregulation of immune response
stimulation of immune response
biological_process
GO:0050778
positive regulation of immune response
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GO:0050791
regulation of physiological process
biological_process
GO:0050789
regulation of biological process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
GOC:ai
GOC:go_curators
Any process that modulates the activity of an enzyme.
GO:0048552
MIPS_funcat:18.02.01
regulation of enzyme activity
regulation of metalloenzyme activity
biological_process
GO:0050790
regulation of catalytic activity
Any process that modulates the activity of an enzyme.
GOC:ai
GOC:ebc
GOC:vw
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
biological_process
GO:0050793
regulation of developmental process
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:go_curators
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GO:0051244
regulation of cellular physiological process
biological_process
GO:0050794
regulation of cellular process
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
regulation of behaviour
biological_process
GO:0050795
regulation of behavior
Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
GOC:go_curators
GOC:pr
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GO:0051869
MIPS_funcat:34.11
physiological response to stimulus
biological_process
GO:0050896
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GOC:ai
GOC:bf
Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
biological_process
GO:0050920
regulation of chemotaxis
Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
GOC:ai
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
up regulation of chemotaxis
up-regulation of chemotaxis
upregulation of chemotaxis
activation of chemotaxis
stimulation of chemotaxis
biological_process
GO:0050921
positive regulation of chemotaxis
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
down regulation of chemotaxis
down-regulation of chemotaxis
downregulation of chemotaxis
inhibition of chemotaxis
biological_process
GO:0050922
negative regulation of chemotaxis
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
GOC:ai
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
biological_process
GO:0051049
regulation of transport
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GOC:ai
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
up regulation of transport
up-regulation of transport
upregulation of transport
activation of transport
stimulation of transport
biological_process
GO:0051050
positive regulation of transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of transport
down-regulation of transport
downregulation of transport
inhibition of transport
biological_process
GO:0051051
negative regulation of transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GOC:ai
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
down regulation of developmental process
down-regulation of developmental process
downregulation of developmental process
inhibition of developmental process
biological_process
GO:0051093
negative regulation of developmental process
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:ai
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
up regulation of developmental process
up-regulation of developmental process
upregulation of developmental process
activation of developmental process
stimulation of developmental process
biological_process
GO:0051094
positive regulation of developmental process
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
GOC:ai
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
biological_process
GO:0051098
regulation of binding
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
up regulation of binding
up-regulation of binding
upregulation of binding
activation of binding
stimulation of binding
biological_process
GO:0051099
positive regulation of binding
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
down regulation of binding
down-regulation of binding
downregulation of binding
inhibition of binding
biological_process
GO:0051100
negative regulation of binding
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
GOC:ai
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
regulation of nitrogen metabolism
biological_process
GO:0051171
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
regulation of nitrogen metabolic process
GOC:tb
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
down regulation of nitrogen metabolic process
down-regulation of nitrogen metabolic process
downregulation of nitrogen metabolic process
negative regulation of nitrogen metabolic process
negative regulation of nitrogen metabolism
inhibition of nitrogen metabolic process
biological_process
GO:0051172
negative regulation of nitrogen compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
negative regulation of nitrogen metabolic process
GOC:tb
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
activation of nitrogen metabolic process
stimulation of nitrogen metabolic process
biological_process
GO:0051173
positive regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
GOC:ai
GOC:tb
positive regulation of nitrogen metabolic process
GOC:tb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolism
biological_process
GO:0051174
regulation of phosphorus metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:ai
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
jl
2013-12-18T13:51:04Z
GO:1902578
establishment and maintenance of localization
establishment and maintenance of position
localisation
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
biological_process
single organism localization
single-organism localization
GO:0051179
localization
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
GOC:ai
GOC:dos
localisation
GOC:mah
single organism localization
GOC:TermGenie
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of localisation
biological_process
GO:0051234
establishment of localization
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
GOC:ai
GOC:dos
establishment of localisation
GOC:mah
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
biological_process
GO:0051239
regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
GOC:dph
GOC:tb
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
biological_process
GO:0051240
positive regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
biological_process
GO:0051241
negative regulation of multicellular organismal process
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
GOC:ai
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
transferase regulator
biological_process
GO:0051338
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
regulation of transferase activity
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
EC:2.-.-.-
GOC:ai
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
transferase activator
up regulation of transferase activity
up-regulation of transferase activity
upregulation of transferase activity
activation of transferase activity
stimulation of transferase activity
biological_process
GO:0051347
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
positive regulation of transferase activity
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
down regulation of transferase activity
down-regulation of transferase activity
downregulation of transferase activity
transferase inhibitor
inhibition of transferase activity
biological_process
GO:0051348
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
negative regulation of transferase activity
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
GOC:ai
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
jl
2013-12-18T14:04:32Z
GO:1902580
cellular localisation
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
single organism cellular localization
intracellular localization
localization within cell
biological_process
single-organism cellular localization
GO:0051641
cellular localization
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
GOC:tb
GOC:vw
cellular localisation
GOC:mah
single organism cellular localization
GOC:TermGenie
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of localisation in cell
establishment of intracellular localization
establishment of localization within cell
positioning within cell
biological_process
establishment of cellular localization
GO:0051649
establishment of localization in cell
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
GOC:ai
GOC:dos
GOC:dph
GOC:tb
establishment of localisation in cell
GOC:mah
establishment of cellular localization
GOC:dph
GOC:tb
An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
biological_process
GO:0051701
interaction with host
An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
GOC:cc
Any process in which an organism has an effect on an organism of the same species.
intraspecies interaction with other organisms
biological_process
GO:0051703
intraspecies interaction between organisms
Any process in which an organism has an effect on an organism of the same species.
GOC:ai
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
biological_process
GO:0051716
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
cellular response to stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
GOC:bf
GOC:jl
The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction.
https://github.com/geneontology/go-ontology/issues/18605
regulation of morphology of other organism during symbiotic interaction
regulation of physiological process in other organism during symbiotic interaction
regulation of physiology of other organism during symbiotic interaction
biological_process
modification of morphology or physiology of other organism during symbiotic interaction
modification of morphology or physiology of other organism involved in symbiotic interaction
modulation of biological process of other organism involved in symbiotic interaction
modulation of morphology or physiology of other organism during symbiotic interaction
regulation of morphology or physiology of other organism during symbiotic interaction
GO:0051817
modulation of process of other organism involved in symbiotic interaction
The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction.
GOC:cc
modification of morphology or physiology of other organism during symbiotic interaction
GOC:dph
true
true
The chemical reactions and pathways performed by an organism in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
biological_process
GO:0052002
metabolism by symbiont of substance in host
The chemical reactions and pathways performed by an organism in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
modulation of host intracellular trafficking
biological_process
GO:0052038
modulation by symbiont of host intracellular transport
Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
down regulation by symbiont of host enzyme activity
down-regulation by symbiont of host enzyme activity
downregulation by symbiont of host enzyme activity
inhibition of host enzyme activity
negative regulation by symbiont of host enzyme activity
inhibition by symbiont of host enzyme activity
biological_process
GO:0052053
negative regulation by symbiont of host catalytic activity
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
The process in which an organism effects a change in the function of a host protein via a direct interaction. The host is defined as the larger of the organisms involved in a symbiotic interaction.
modification by symbiont of host molecular function
modification by symbiont of host protein function
biological_process
GO:0052055
modulation by symbiont of host molecular function
The process in which an organism effects a change in the function of a host protein via a direct interaction. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:dph
GOC:mtg_pamgo_17jul06
GOC:tb
modification by symbiont of host protein function
GOC:dph
GOC:tb
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of host proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
down regulation by symbiont of host protein function
down-regulation by symbiont of host protein function
downregulation by symbiont of host protein function
inhibition of host protein function
negative regulation by symbiont of host protein function
inhibition by symbiont of host protein function
biological_process
GO:0052056
negative regulation by symbiont of host molecular function
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of host proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:dph
GOC:mtg_pamgo_17jul06
GOC:tb
negative regulation by symbiont of host protein function
GOC:dph
GOC:tb
The directed movement of an organism or motile cell on, within or near its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
movement in response to host
biological_process
GO:0052126
movement in host environment
The directed movement of an organism or motile cell on, within or near its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
The process in which an organism effects a change in host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
modulation by symbiont of host enzyme activity
modulation of catalytic activity of host by symbiont
regulation by symbiont of host catalytic activity
regulation of catalytic activity of host by symbiont
regulation of host catalytic activity by symbiont
biological_process
GO:0052148
modulation by symbiont of host catalytic activity
The process in which an organism effects a change in host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
GOC:tb
modulation by symbiont of host enzyme activity
GOC:tb
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
inhibition of enzyme activity in other organism
negative regulation of enzyme activity in other organism during symbiotic interaction
inhibition of enzyme activity in other organism during symbiotic interaction
biological_process
down regulation of enzyme activity in other organism during symbiotic interaction
down-regulation of enzyme activity in other organism during symbiotic interaction
downregulation of enzyme activity in other organism during symbiotic interaction
GO:0052199
negative regulation of catalytic activity in other organism involved in symbiotic interaction
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
GOC:tb
negative regulation of enzyme activity in other organism during symbiotic interaction
GOC:tb
The process in which an organism effects a change in enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
modulation of enzyme activity within other organism during symbiotic interaction
biological_process
GO:0052203
modulation of catalytic activity in other organism involved in symbiotic interaction
The process in which an organism effects a change in enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
GOC:tb
modulation of enzyme activity within other organism during symbiotic interaction
GOC:tb
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of proteins in a second organism, where the two organisms are in a symbiotic interaction.
down regulation of protein function in other organism during symbiotic interaction
down-regulation of protein function in other organism during symbiotic interaction
downregulation of protein function in other organism during symbiotic interaction
inhibition of protein function in other organism
negative regulation of protein function in other organism during symbiotic interaction
inhibition of protein function in other organism during symbiotic interaction
biological_process
GO:0052204
negative regulation of molecular function in other organism involved in symbiotic interaction
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of proteins in a second organism, where the two organisms are in a symbiotic interaction.
GOC:dph
GOC:mtg_pamgo_17jul06
GOC:tb
negative regulation of protein function in other organism during symbiotic interaction
GOC:dph
GOC:tb
The process in which an organism effects a change in the function of proteins in a second organism, where the two organisms are in a symbiotic interaction.
modification of molecular function in other organism during symbiotic interaction
modification of protein function in other organism during symbiotic interaction
biological_process
modulation of molecular function in other organism during symbiotic interaction
GO:0052205
modulation of molecular function in other organism involved in symbiotic interaction
The process in which an organism effects a change in the function of proteins in a second organism, where the two organisms are in a symbiotic interaction.
GOC:dph
GOC:mtg_pamgo_17jul06
GOC:tb
modification of protein function in other organism during symbiotic interaction
GOC:dph
GOC:tb
modulation of molecular function in other organism during symbiotic interaction
GOC:dph
The chemical reactions and pathways performed by an organism in a second organism, where the two organisms are in a symbiotic interaction.
biological_process
metabolism of substance in other organism during symbiotic interaction
GO:0052214
metabolism of substance in other organism involved in symbiotic interaction
The chemical reactions and pathways performed by an organism in a second organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
metabolism of substance in other organism during symbiotic interaction
GOC:dph
OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism resulting in the formation of substances, where the two organisms are in a symbiotic interaction.
https://github.com/geneontology/go-ontology/issues/18787
biological_process
biosynthesis of substance in other organism during symbiotic interaction
GO:0052226
This term was obsoleted because there is no evidence that this process exists.
obsolete biosynthesis of substance in other organism involved in symbiotic interaction
true
OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism resulting in the formation of substances, where the two organisms are in a symbiotic interaction.
ISBN:0198547684
biosynthesis of substance in other organism during symbiotic interaction
GOC:dph
Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of a second organism, where the two organisms are in a symbiotic interaction.
modulation of intracellular trafficking in other organism
biological_process
modulation of intracellular transport in other organism during symbiotic interaction
GO:0052230
modulation of intracellular transport in other organism involved in symbiotic interaction
Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of a second organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
modulation of intracellular transport in other organism during symbiotic interaction
GOC:dph
Any process in which an organism modulates the frequency, rate or extent to which it enters into the host organism, where the two organisms are in a symbiotic interaction.
https://github.com/geneontology/go-ontology/issues/19027
GO:0052371
biological_process
modulation by organism of entry into other organism during symbiotic interaction
modulation by symbiont of entry into host
regulation by organism of entry into other organism during symbiotic interaction
regulation by organism of entry into other organism involved in symbiotic interaction
GO:0052372
modulation by symbiont of entry into host
Any process in which an organism modulates the frequency, rate or extent to which it enters into the host organism, where the two organisms are in a symbiotic interaction.
GOC:mtg_pamgo_17jul06
regulation by organism of entry into other organism during symbiotic interaction
GOC:tb
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
Wikipedia:Redox
oxidation reduction
oxidoreductase process
biological_process
GO:0055114
oxidation-reduction process
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
GOC:dhl
GOC:ecd
GOC:jh2
GOC:jid
GOC:mlg
GOC:rph
oxidoreductase process
A compound molecular function in which an effector function is controlled by one or more regulatory components.
molecular_function
GO:0060089
molecular transducer activity
A compound molecular function in which an effector function is controlled by one or more regulatory components.
GOC:dos
GOC:pdt
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biological_process
GO:0060255
regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
regulation of feeding behaviour
biological_process
GO:0060259
regulation of feeding behavior
Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
GOC:BHF
GOC:dph
GOC:tb
regulation of feeding behaviour
GOC:dph
GOC:tb
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
regulation of cellular localisation
biological_process
GO:0060341
regulation of cellular localization
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
GOC:dph
GOC:tb
regulation of cellular localisation
GOC:mah
Behavior by which an organism locates food.
dph
2009-06-22T02:46:25Z
biological_process
GO:0060756
foraging behavior
Behavior by which an organism locates food.
GOC:dph
GOC:tb
Any process that modulates the rate, frequency or extent of a small molecule metabolic process.
dph
2018-03-19T14:11:54Z
regulation of small molecule metabolism
biological_process
GO:0062012
regulation of small molecule metabolic process
Any process that modulates the rate, frequency or extent of a small molecule metabolic process.
GOC:vw
Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process.
dph
2018-03-19T14:25:10Z
positive regulation of small molecule metabolism
biological_process
GO:0062013
positive regulation of small molecule metabolic process
Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process.
GOC:vw
Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process.
dph
2018-03-19T14:27:23Z
negative regulation of small molecule metabolism
biological_process
GO:0062014
negative regulation of small molecule metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process.
GOC:vw
The cellular metabolic process in which organic chemical compounds are synthesized from carbon-containing molecules and nutrients using energy obtained from the oxidation of inorganic compounds or methane.
dph
2018-11-29T13:18:55Z
Wikipedia:Chemosynthesis
biological_process
GO:0062097
chemosynthesis
The cellular metabolic process in which organic chemical compounds are synthesized from carbon-containing molecules and nutrients using energy obtained from the oxidation of inorganic compounds or methane.
PMID:25050523
Any process that modulates a measurable attribute of any biological process, quality or function.
regulation
biological_process
GO:0065007
biological regulation
Any process that modulates a measurable attribute of any biological process, quality or function.
GOC:dph
GOC:isa_complete
GOC:mah
GOC:pr
GOC:vw
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
regulation of a molecular function
biological_process
GO:0065009
regulation of molecular function
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
GOC:isa_complete
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
mah
2009-08-20T02:44:53Z
regulation of glycogen metabolism
biological_process
GO:0070873
regulation of glycogen metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
GOC:mah
regulation of glycogen metabolism
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
mah
2009-08-20T02:50:41Z
negative regulation of glycogen metabolism
biological_process
GO:0070874
negative regulation of glycogen metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
GOC:mah
negative regulation of glycogen metabolism
GOC:mah
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
mah
2009-08-20T02:53:55Z
positive regulation of glycogen metabolism
biological_process
GO:0070875
positive regulation of glycogen metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen.
GOC:mah
positive regulation of glycogen metabolism
GOC:mah
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
mah
2010-03-08T03:32:18Z
organic molecular entity metabolic process
organic molecular entity metabolism
organic substance metabolism
biological_process
GO:0071704
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
GOC:mah
true
parasitism
true
Any process that activates or increases the frequency, rate or extent to which it enters into the host organism, where the two organisms are in a symbiotic interaction.
https://github.com/geneontology/go-ontology/issues/19027
GO:0075295
up regulation by symbiont of entry into host
up-regulation by symbiont of entry into host
upregulation by symbiont of entry into host
activation by organism of entry into other organism during symbiotic interaction
activation by symbiont of entry into host
biological_process
positive regulation by organism of entry into other organism during symbiotic interaction
positive regulation by organism of entry into other organism involved in symbiotic interaction
up regulation by organism of entry into other organism during symbiotic interaction
up-regulation by organism of entry into other organism during symbiotic interaction
upregulation by organism of entry into other organism during symbiotic interaction
GO:0075294
positive regulation by symbiont of entry into host
Any process that activates or increases the frequency, rate or extent to which it enters into the host organism, where the two organisms are in a symbiotic interaction.
GOC:pamgo_curators
positive regulation by organism of entry into other organism during symbiotic interaction
GOC:tb
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
dhl
2009-04-22T04:30:52Z
biological_process
GO:0080090
regulation of primary metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
PMID:19211694
true
A process carried out by symbiont gene products that enables a symbiotic interaction with a host organism, that is beneficial to the host organism.
jl
2010-07-27T01:25:21Z
biological_process
mutualism
GO:0085030
mutualism
symbiotic process benefiting host
A process carried out by symbiont gene products that enables a symbiotic interaction with a host organism, that is beneficial to the host organism.
GOC:pdt
true
commensalism
true
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
molecular_function
GO:0098772
molecular function regulator
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
GOC:dos
GOC:pt
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
kmv
2019-08-12T18:01:37Z
cellular_component
GO:0110165
cellular anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
GOC:kmv
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:53Z
regulation of receptor ligand
biological_process
GO:1900120
regulation of receptor binding
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
regulation of receptor ligand
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:57Z
down regulation of receptor binding
down-regulation of receptor binding
downregulation of receptor binding
inhibition of receptor binding
inhibition of receptor ligand
biological_process
down regulation of receptor-associated protein activity
GO:1900121
negative regulation of receptor binding
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
down regulation of receptor binding
GOC:TermGenie
down-regulation of receptor binding
GOC:TermGenie
downregulation of receptor binding
GOC:TermGenie
inhibition of receptor binding
GOC:TermGenie
inhibition of receptor ligand
GOC:TermGenie
down regulation of receptor-associated protein activity
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:41:00Z
up regulation of receptor binding
upregulation of receptor binding
activation of receptor binding
biological_process
GO:1900122
positive regulation of receptor binding
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
up regulation of receptor binding
GOC:TermGenie
upregulation of receptor binding
GOC:TermGenie
activation of receptor binding
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of fermentation.
al
2012-06-15T08:21:31Z
down regulation of fermentation
down-regulation of fermentation
downregulation of fermentation
inhibition of fermentation
biological_process
GO:1901003
negative regulation of fermentation
Any process that stops, prevents or reduces the frequency, rate or extent of fermentation.
GOC:TermGenie
down regulation of fermentation
GOC:TermGenie
down-regulation of fermentation
GOC:TermGenie
downregulation of fermentation
GOC:TermGenie
inhibition of fermentation
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
pr
2012-11-05T11:04:40Z
organic molecular entity anabolism
organic molecular entity biosynthesis
organic molecular entity biosynthetic process
organic molecular entity formation
organic molecular entity synthesis
organic substance anabolism
organic substance biosynthesis
organic substance formation
organic substance synthesis
biological_process
GO:1901576
organic substance biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
GOC:TermGenie
GOC:pr
organic molecular entity anabolism
GOC:TermGenie
organic molecular entity biosynthesis
GOC:TermGenie
organic molecular entity formation
GOC:TermGenie
organic molecular entity synthesis
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of cellular respiration.
yaf
2013-02-01T09:56:23Z
down regulation of respiration
down-regulation of respiration
downregulation of respiration
inhibition of respiration
negative regulation of respiration
down regulation of cellular respiration
down regulation of oxidative metabolic process
down regulation of oxidative metabolism
down-regulation of cellular respiration
down-regulation of oxidative metabolic process
down-regulation of oxidative metabolism
downregulation of cellular respiration
downregulation of oxidative metabolic process
downregulation of oxidative metabolism
inhibition of oxidative metabolic process
inhibition of oxidative metabolism
negative regulation of oxidative metabolic process
negative regulation of oxidative metabolism
inhibition of cellular respiration
biological_process
GO:1901856
negative regulation of cellular respiration
Any process that stops, prevents or reduces the frequency, rate or extent of cellular respiration.
GOC:TermGenie
GOC:yaf
PMID:23150719
down regulation of respiration
GOC:TermGenie
down-regulation of respiration
GOC:TermGenie
downregulation of respiration
GOC:TermGenie
inhibition of respiration
GOC:TermGenie
negative regulation of respiration
GOC:TermGenie
down regulation of cellular respiration
GOC:TermGenie
down regulation of oxidative metabolic process
GOC:TermGenie
down regulation of oxidative metabolism
GOC:TermGenie
down-regulation of cellular respiration
GOC:TermGenie
down-regulation of oxidative metabolic process
GOC:TermGenie
down-regulation of oxidative metabolism
GOC:TermGenie
downregulation of cellular respiration
GOC:TermGenie
downregulation of oxidative metabolic process
GOC:TermGenie
downregulation of oxidative metabolism
GOC:TermGenie
inhibition of oxidative metabolic process
GOC:TermGenie
inhibition of oxidative metabolism
GOC:TermGenie
negative regulation of oxidative metabolic process
GOC:TermGenie
negative regulation of oxidative metabolism
GOC:TermGenie
inhibition of cellular respiration
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of cellular respiration.
yaf
2013-02-01T09:56:28Z
activation of respiration
positive regulation of respiration
up regulation of respiration
up-regulation of respiration
upregulation of respiration
activation of oxidative metabolic process
activation of oxidative metabolism
positive regulation of oxidative metabolic process
positive regulation of oxidative metabolism
up regulation of cellular respiration
up regulation of oxidative metabolic process
up regulation of oxidative metabolism
up-regulation of cellular respiration
up-regulation of oxidative metabolic process
up-regulation of oxidative metabolism
upregulation of cellular respiration
upregulation of oxidative metabolic process
upregulation of oxidative metabolism
activation of cellular respiration
biological_process
GO:1901857
positive regulation of cellular respiration
Any process that activates or increases the frequency, rate or extent of cellular respiration.
GOC:TermGenie
GOC:yaf
PMID:23150719
activation of respiration
GOC:TermGenie
positive regulation of respiration
GOC:TermGenie
up regulation of respiration
GOC:TermGenie
up-regulation of respiration
GOC:TermGenie
upregulation of respiration
GOC:TermGenie
activation of oxidative metabolic process
GOC:TermGenie
activation of oxidative metabolism
GOC:TermGenie
positive regulation of oxidative metabolic process
GOC:TermGenie
positive regulation of oxidative metabolism
GOC:TermGenie
up regulation of cellular respiration
GOC:TermGenie
up regulation of oxidative metabolic process
GOC:TermGenie
up regulation of oxidative metabolism
GOC:TermGenie
up-regulation of cellular respiration
GOC:TermGenie
up-regulation of oxidative metabolic process
GOC:TermGenie
up-regulation of oxidative metabolism
GOC:TermGenie
upregulation of cellular respiration
GOC:TermGenie
upregulation of oxidative metabolic process
GOC:TermGenie
upregulation of oxidative metabolism
GOC:TermGenie
activation of cellular respiration
GOC:TermGenie
Any process that modulates the frequency, rate or extent of intracellular signal transduction.
bf
2013-12-02T11:32:52Z
GO:0010627
regulation of intracellular signaling cascade
regulation of intracellular signaling chain
regulation of intracellular protein kinase cascade
regulation of intracellular signal transduction pathway
regulation of signal transmission via intracellular cascade
biological_process
regulation of intracellular signaling pathway
regulation of signal transduction via intracellular signaling cascade
GO:1902531
regulation of intracellular signal transduction
Any process that modulates the frequency, rate or extent of intracellular signal transduction.
GOC:TermGenie
GOC:dph
GOC:signaling
GOC:tb
regulation of intracellular signaling cascade
GOC:TermGenie
regulation of intracellular signaling chain
GOC:TermGenie
regulation of intracellular signal transduction pathway
GOC:TermGenie
regulation of signal transmission via intracellular cascade
GOC:TermGenie
regulation of intracellular signaling pathway
GOC:TermGenie
regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.
bf
2013-12-02T11:33:01Z
GO:0010741
down regulation of intracellular signal transduction
down regulation of intracellular signaling chain
down-regulation of intracellular signal transduction
down-regulation of intracellular signaling chain
downregulation of intracellular signal transduction
downregulation of intracellular signaling chain
negative regulation of intracellular protein kinase cascade
negative regulation of intracellular signaling cascade
negative regulation of intracellular signaling chain
down regulation of intracellular signal transduction pathway
down regulation of intracellular signaling cascade
down regulation of signal transmission via intracellular cascade
down-regulation of intracellular signal transduction pathway
downregulation of intracellular signal transduction pathway
downregulation of intracellular signaling cascade
downregulation of signal transmission via intracellular cascade
inhibition of intracellular signal transduction
inhibition of intracellular signal transduction pathway
inhibition of intracellular signaling cascade
inhibition of intracellular signaling chain
inhibition of signal transmission via intracellular cascade
negative regulation of intracellular signal transduction pathway
negative regulation of signal transmission via intracellular cascade
biological_process
down regulation of intracellular signaling pathway
down regulation of signal transduction via intracellular signaling cascade
down-regulation of intracellular signaling cascade
down-regulation of intracellular signaling pathway
down-regulation of signal transduction via intracellular signaling cascade
down-regulation of signal transmission via intracellular cascade
downregulation of intracellular signaling pathway
downregulation of signal transduction via intracellular signaling cascade
inhibition of intracellular signaling pathway
inhibition of signal transduction via intracellular signaling cascade
negative regulation of intracellular signaling pathway
negative regulation of signal transduction via intracellular signaling cascade
GO:1902532
negative regulation of intracellular signal transduction
Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.
GOC:TermGenie
GOC:dph
GOC:signaling
GOC:tb
down regulation of intracellular signal transduction
GOC:TermGenie
down regulation of intracellular signaling chain
GOC:TermGenie
down-regulation of intracellular signal transduction
GOC:TermGenie
down-regulation of intracellular signaling chain
GOC:TermGenie
downregulation of intracellular signal transduction
GOC:TermGenie
downregulation of intracellular signaling chain
GOC:TermGenie
negative regulation of intracellular signaling cascade
GOC:TermGenie
negative regulation of intracellular signaling chain
GOC:TermGenie
down regulation of intracellular signal transduction pathway
GOC:TermGenie
down regulation of intracellular signaling cascade
GOC:TermGenie
down regulation of signal transmission via intracellular cascade
GOC:TermGenie
down-regulation of intracellular signal transduction pathway
GOC:TermGenie
downregulation of intracellular signal transduction pathway
GOC:TermGenie
downregulation of intracellular signaling cascade
GOC:TermGenie
downregulation of signal transmission via intracellular cascade
GOC:TermGenie
inhibition of intracellular signal transduction
GOC:TermGenie
inhibition of intracellular signal transduction pathway
GOC:TermGenie
inhibition of intracellular signaling cascade
GOC:TermGenie
inhibition of intracellular signaling chain
GOC:TermGenie
inhibition of signal transmission via intracellular cascade
GOC:TermGenie
negative regulation of intracellular signal transduction pathway
GOC:TermGenie
negative regulation of signal transmission via intracellular cascade
GOC:TermGenie
down regulation of intracellular signaling pathway
GOC:TermGenie
down regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
down-regulation of intracellular signaling cascade
GOC:TermGenie
down-regulation of intracellular signaling pathway
GOC:TermGenie
down-regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
down-regulation of signal transmission via intracellular cascade
GOC:TermGenie
downregulation of intracellular signaling pathway
GOC:TermGenie
downregulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
inhibition of intracellular signaling pathway
GOC:TermGenie
inhibition of signal transduction via intracellular signaling cascade
GOC:TermGenie
negative regulation of intracellular signaling pathway
GOC:TermGenie
negative regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
bf
2013-12-02T11:33:10Z
GO:0010740
positive regulation of intracellular signaling chain
up regulation of intracellular signal transduction
up regulation of intracellular signaling chain
up-regulation of intracellular signal transduction
up-regulation of intracellular signaling chain
upregulation of intracellular signal transduction
upregulation of intracellular signaling chain
activation of intracellular signal transduction
activation of intracellular signal transduction pathway
activation of intracellular signaling cascade
activation of intracellular signaling chain
activation of signal transmission via intracellular cascade
positive regulation of intracellular protein kinase cascade
positive regulation of intracellular signal transduction pathway
positive regulation of signal transmission via intracellular cascade
up regulation of intracellular signal transduction pathway
up regulation of signal transmission via intracellular cascade
up-regulation of intracellular signal transduction pathway
up-regulation of signal transmission via intracellular cascade
upregulation of intracellular signal transduction pathway
upregulation of signal transmission via intracellular cascade
biological_process
activation of intracellular signaling pathway
activation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signaling cascade
positive regulation of intracellular signaling pathway
positive regulation of signal transduction via intracellular signaling cascade
up regulation of intracellular signaling cascade
up regulation of intracellular signaling pathway
up regulation of signal transduction via intracellular signaling cascade
up-regulation of intracellular signaling cascade
up-regulation of intracellular signaling pathway
up-regulation of signal transduction via intracellular signaling cascade
upregulation of intracellular signaling cascade
upregulation of intracellular signaling pathway
upregulation of signal transduction via intracellular signaling cascade
GO:1902533
positive regulation of intracellular signal transduction
Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
GOC:BHF
GOC:TermGenie
GOC:dph
GOC:signaling
GOC:tb
positive regulation of intracellular signaling chain
GOC:TermGenie
up regulation of intracellular signal transduction
GOC:TermGenie
up regulation of intracellular signaling chain
GOC:TermGenie
up-regulation of intracellular signal transduction
GOC:TermGenie
up-regulation of intracellular signaling chain
GOC:TermGenie
upregulation of intracellular signal transduction
GOC:TermGenie
upregulation of intracellular signaling chain
GOC:TermGenie
activation of intracellular signal transduction
GOC:TermGenie
activation of intracellular signal transduction pathway
GOC:TermGenie
activation of intracellular signaling cascade
GOC:TermGenie
activation of intracellular signaling chain
GOC:TermGenie
activation of signal transmission via intracellular cascade
GOC:TermGenie
positive regulation of intracellular signal transduction pathway
GOC:TermGenie
positive regulation of signal transmission via intracellular cascade
GOC:TermGenie
up regulation of intracellular signal transduction pathway
GOC:TermGenie
up regulation of signal transmission via intracellular cascade
GOC:TermGenie
up-regulation of intracellular signal transduction pathway
GOC:TermGenie
up-regulation of signal transmission via intracellular cascade
GOC:TermGenie
upregulation of intracellular signal transduction pathway
GOC:TermGenie
upregulation of signal transmission via intracellular cascade
GOC:TermGenie
activation of intracellular signaling pathway
GOC:TermGenie
activation of signal transduction via intracellular signaling cascade
GOC:TermGenie
positive regulation of intracellular signaling cascade
GOC:TermGenie
positive regulation of intracellular signaling pathway
GOC:TermGenie
positive regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
up regulation of intracellular signaling cascade
GOC:TermGenie
up regulation of intracellular signaling pathway
GOC:TermGenie
up regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
up-regulation of intracellular signaling cascade
GOC:TermGenie
up-regulation of intracellular signaling pathway
GOC:TermGenie
up-regulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
upregulation of intracellular signaling cascade
GOC:TermGenie
upregulation of intracellular signaling pathway
GOC:TermGenie
upregulation of signal transduction via intracellular signaling cascade
GOC:TermGenie
A localization which involves another organism.
jl
2013-12-18T13:51:13Z
multi organism localization
biological_process
GO:1902579
multi-organism localization
A localization which involves another organism.
GOC:TermGenie
GOC:jl
GO_REF:0000089
multi organism localization
GOC:TermGenie
Any process that modulates the frequency, rate or extent of foraging behavior.
mr
2014-08-22T03:03:04Z
biological_process
GO:1903368
regulation of foraging behavior
Any process that modulates the frequency, rate or extent of foraging behavior.
GOC:TermGenie
GOC:mr
GO_REF:0000058
PMID:8677262
Any process that stops, prevents or reduces the frequency, rate or extent of foraging behavior.
mr
2014-08-22T03:03:12Z
down regulation of foraging behavior
down-regulation of foraging behavior
downregulation of foraging behavior
inhibition of foraging behavior
biological_process
GO:1903369
negative regulation of foraging behavior
Any process that stops, prevents or reduces the frequency, rate or extent of foraging behavior.
GOC:TermGenie
GOC:mr
GO_REF:0000058
PMID:8677262
down regulation of foraging behavior
GOC:TermGenie
down-regulation of foraging behavior
GOC:TermGenie
downregulation of foraging behavior
GOC:TermGenie
inhibition of foraging behavior
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of foraging behavior.
mr
2014-08-22T03:03:20Z
up regulation of foraging behavior
up-regulation of foraging behavior
upregulation of foraging behavior
activation of foraging behavior
biological_process
GO:1903370
positive regulation of foraging behavior
Any process that activates or increases the frequency, rate or extent of foraging behavior.
GOC:TermGenie
GOC:mr
GO_REF:0000058
PMID:8677262
up regulation of foraging behavior
GOC:TermGenie
up-regulation of foraging behavior
GOC:TermGenie
upregulation of foraging behavior
GOC:TermGenie
activation of foraging behavior
GOC:TermGenie
Any process that modulates the frequency, rate or extent of aerobic respiration.
al
2014-12-08T00:40:37Z
biological_process
GO:1903715
regulation of aerobic respiration
Any process that modulates the frequency, rate or extent of aerobic respiration.
GOC:TermGenie
GO_REF:0000058
PMID:19266076
Any signal transduction that is involved in regulation of aerobic respiration.
al
2014-12-18T16:37:50Z
signaling cascade involved in regulation of aerobic respiration
signalling cascade involved in regulation of aerobic respiration
biological_process
signaling pathway involved in regulation of aerobic respiration
signalling pathway involved in regulation of aerobic respiration
GO:1903759
signal transduction involved in regulation of aerobic respiration
Any signal transduction that is involved in regulation of aerobic respiration.
GOC:TermGenie
GO_REF:0000060
PMID:19266076
signaling cascade involved in regulation of aerobic respiration
GOC:TermGenie
signalling cascade involved in regulation of aerobic respiration
GOC:TermGenie
signaling pathway involved in regulation of aerobic respiration
GOC:TermGenie
signalling pathway involved in regulation of aerobic respiration
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis.
tb
2016-04-19T16:12:29Z
down regulation of photosynthesis
down-regulation of photosynthesis
downregulation of photosynthesis
inhibition of photosynthesis
biological_process
GO:1905156
negative regulation of photosynthesis
Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis.
GOC:TermGenie
GO_REF:0000058
PMID:7592491
down regulation of photosynthesis
GOC:TermGenie
down-regulation of photosynthesis
GOC:TermGenie
downregulation of photosynthesis
GOC:TermGenie
inhibition of photosynthesis
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of photosynthesis.
tb
2016-04-19T16:12:39Z
up regulation of photosynthesis
up-regulation of photosynthesis
upregulation of photosynthesis
activation of photosynthesis
biological_process
GO:1905157
positive regulation of photosynthesis
Any process that activates or increases the frequency, rate or extent of photosynthesis.
GOC:TermGenie
GO_REF:0000058
PMID:7592491
up regulation of photosynthesis
GOC:TermGenie
up-regulation of photosynthesis
GOC:TermGenie
upregulation of photosynthesis
GOC:TermGenie
activation of photosynthesis
GOC:TermGenie
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of intracellular transport in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
ml
2013-10-10T15:42:22Z
biological_process
GO:1990215
negative regulation by symbiont of host intracellular transport
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of intracellular transport in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
PMID:22319451
Any process that modulates the frequency, rate or extent of multicellular organismal development.
tb
2010-08-05T11:25:59Z
biological_process
GO:2000026
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of multicellular organismal development.
GOC:obol
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
tb
2010-09-15T08:55:45Z
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
biological_process
GO:2000112
regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
GOC:obol
regulation of cellular biopolymer biosynthetic process
GOC:obol
regulation of cellular macromolecule anabolism
GOC:obol
regulation of cellular macromolecule biosynthesis
GOC:obol
regulation of cellular macromolecule formation
GOC:obol
regulation of cellular macromolecule synthesis
GOC:obol
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
tb
2010-09-15T08:55:48Z
negative regulation of cellular biopolymer biosynthetic process
negative regulation of cellular macromolecule anabolism
negative regulation of cellular macromolecule biosynthesis
negative regulation of cellular macromolecule formation
negative regulation of cellular macromolecule synthesis
biological_process
GO:2000113
negative regulation of cellular macromolecule biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
GOC:obol
negative regulation of cellular biopolymer biosynthetic process
GOC:obol
negative regulation of cellular macromolecule anabolism
GOC:obol
negative regulation of cellular macromolecule biosynthesis
GOC:obol
negative regulation of cellular macromolecule formation
GOC:obol
negative regulation of cellular macromolecule synthesis
GOC:obol
Any process that modulates the frequency, rate or extent of reproductive process.
mah
midori
2010-11-10T02:44:02Z
biological_process
GO:2000241
regulation of reproductive process
Any process that modulates the frequency, rate or extent of reproductive process.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
mah
midori
2010-11-10T02:44:05Z
biological_process
GO:2000242
negative regulation of reproductive process
Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.
GOC:mah
Any process that activates or increases the frequency, rate or extent of reproductive process.
mah
midori
2010-11-10T02:44:08Z
biological_process
GO:2000243
positive regulation of reproductive process
Any process that activates or increases the frequency, rate or extent of reproductive process.
GOC:mah
Any process that stops, prevents or reduces the frequency, rate or extent of feeding behavior.
yaf
2010-11-18T11:24:14Z
negative regulation of behavioral response to food
negative regulation of behavioural response to food
negative regulation of feeding behaviour
biological_process
negative regulation of drinking
negative regulation of eating
GO:2000252
negative regulation of feeding behavior
Any process that stops, prevents or reduces the frequency, rate or extent of feeding behavior.
GOC:obol
negative regulation of behavioral response to food
GOC:obol
negative regulation of behavioural response to food
GOC:obol
negative regulation of feeding behaviour
GOC:obol
negative regulation of drinking
GOC:obol
negative regulation of eating
GOC:obol
Any process that activates or increases the frequency, rate or extent of feeding behavior.
yaf
2010-11-18T11:24:18Z
positive regulation of behavioral response to food
positive regulation of behavioural response to food
positive regulation of feeding behaviour
biological_process
positive regulation of drinking
positive regulation of eating
GO:2000253
positive regulation of feeding behavior
Any process that activates or increases the frequency, rate or extent of feeding behavior.
GOC:obol
positive regulation of behavioral response to food
GOC:obol
positive regulation of behavioural response to food
GOC:obol
positive regulation of feeding behaviour
GOC:obol
positive regulation of drinking
GOC:obol
positive regulation of eating
GOC:obol
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
bf
rfoulger
2010-12-02T09:28:47Z
negative regulation of receptor activity
biological_process
GO:2000272
negative regulation of signaling receptor activity
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
GOC:obol
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
bf
rfoulger
2010-12-02T09:28:50Z
biological_process
GO:2000273
positive regulation of signaling receptor activity
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
GOC:obol
Any process that modulates the frequency, rate or extent of starch metabolic process.
tb
2011-07-28T11:33:13Z
regulation of starch metabolism
biological_process
GO:2000904
regulation of starch metabolic process
Any process that modulates the frequency, rate or extent of starch metabolic process.
GOC:obol
regulation of starch metabolism
GOC:obol
Any process that stops, prevents or reduces the frequency, rate or extent of starch metabolic process.
tb
2011-07-28T11:33:17Z
negative regulation of starch metabolism
biological_process
GO:2000905
negative regulation of starch metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of starch metabolic process.
GOC:obol
negative regulation of starch metabolism
GOC:obol
Any process that activates or increases the frequency, rate or extent of starch metabolic process.
tb
2011-07-28T11:33:19Z
positive regulation of starch metabolism
biological_process
GO:2000906
positive regulation of starch metabolic process
Any process that activates or increases the frequency, rate or extent of starch metabolic process.
GOC:obol
positive regulation of starch metabolism
GOC:obol
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
"Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences." [wikipedia:Emotions]
2011-04-14T01:03:39Z
George Gkoutos
affective behaviour
mood
behavior_ontology
emotional behavior
Behavior directly related to the production of offspring [NBO:AC]
2011-04-14T01:03:39Z
George Gkoutos
reproduction
reproductive behaviour
behavior_ontology
GO:0019098
reproductive behavior
"A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior]
2011-04-14T01:03:39Z
George Gkoutos
social behaviour
behavior_ontology
GO:0035176
social behavior
"Behavior related to the interactions between organisms for the purpose of mating." [NBO:GVG]
2011-04-14T01:03:39Z
George Gkoutos
mating behaviour
behavior_ontology
GO:0007617
mating behavior
"A behavioral interaction between organisms in which one organism has the intention of inflicting damage on another individual using physical or verbal means." [wikipedia:Aggression]
2011-04-14T01:03:39Z
George Gkoutos
aggression
aggressive behaviour
agonism
behavior_ontology
GO:0002118
aggressive behavior
"Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG]
2011-04-14T01:03:39Z
George Gkoutos
behavior_ontology
sexual actions
sexual activity
Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC]
2011-04-14T01:03:39Z
George Gkoutos
copulate
behavior_ontology
copulation
"The behavioral interactions between organisms for the purpose of attracting sexual partners." [GOC:dph]
2011-04-14T01:20:02Z
George Gkoutos
courtship
courtship behaviour
behavior_ontology
GO:0007619
courtship behavior
"Behavior related to the specific actions or reactions of an organism following mating." [GOC:bf]
2011-04-14T01:20:02Z
George Gkoutos
NBO:0000325
post mating behaviour
post-copulatory behavior
post-mating behaviour
behavior_ontology
GO:0045297
post-mating behavior
"Exhibiting a domineering, assault posture and/or hostile physical action towards animals." [NBO:GVG]
2011-03-31T10:51:12Z
George Gkoutos
aggressive behavior towards animals
behavior_ontology
aggressive behavior towards animals
2011-03-31T11:42:15Z
George Gkoutos
agonism
behavior_ontology
agonistic behavior
2011-03-31T02:17:36Z
George Gkoutos
behavior_ontology
mating receptivity
2011-03-31T02:21:53Z
George Gkoutos
mate attraction behavior
behavior_ontology
sexual display behavior
"A helping behavior (without expectation of extrinsic rewards and sometimes involving personal risk or sacrifice) that benefits individuals or society." [NBO:GVG]
2011-04-04T09:19:33Z
George Gkoutos
behavior_ontology
altruism behavior
"Prosocial behavior is caring about the welfare and rights of others, feeling concern and empathy for them, and acting in ways that benefit others." [wikipedia:Prosocial_behavior]
2011-04-04T09:22:04Z
George Gkoutos
behavior_ontology
prosocial behavior
"Helping behavior refers to voluntary actions intended to help the others, with reward regarded or disregarded." [wikipedia:Helping_behavior]
2011-04-04T09:23:26Z
George Gkoutos
behavior_ontology
helping behavior
"Reciprocal altruism is the idea that the incentive for an individual to help in the present is based on the expectation of the potential receipt in the future." [wikipedia:Helping_behavior]
2011-04-04T09:25:04Z
George Gkoutos
behavior_ontology
reciprocal altruism
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
2011-04-05T09:53:10Z
George Gkoutos
NBO:0000000
behavior
behaviour
behavior_ontology
GO:0007610
behavior process
"Behaviour related to the male activity which primary purpose is the sexual reproduction." [NBO:GVG]
2011-04-10T10:41:10Z
George Gkoutos
behavior_ontology
male sexual activity
"Behaviour related to the female activity which primary purpose is the sexual reproduction." [NBO:GVG]
2011-04-10T10:41:10Z
George Gkoutos
behavior_ontology
female sexual activity
"A social behavior related to the activity of conveying information." [wikipedia:Communication]
2011-04-14T04:39:42Z
George Gkoutos
communicating
signal exchange
behavior_ontology
communication behavior
"Communication behavior related to the process of conveying meaning in the form of non-word messages through for example gesture, body language or posture; facial expression and eye contact etc." [wikipedia:.wikipedia.org/wiki/Nonverbal_communication]
2011-04-14T04:40:59Z
George Gkoutos
non-verbal communication behaviour
nonverbal communication behaviour
behavior_ontology
nonverbal communication behavior
"Aggressive behavior related to the defence of a fixed area against intruders, typically conspecifics." [GOC:hjd]
2011-04-19T02:02:11Z
George Gkoutos
territorial aggression
territorial aggressive behaviour
behavior_ontology
GO:0002124
territorial aggressive behavior
"The actions or reactions of a male, for the purpose of attracting a sexual partner." [GOC:bf]
2011-04-21T08:40:33Z
George Gkoutos
male courtship behaviour
behavior_ontology
GO:0008049
male courtship behavior
"The actions or reactions of a female, for the purpose of attracting a sexual partner." [GOC:bf]
2011-04-21T08:42:23Z
George Gkoutos
female courtship behaviour
behavior_ontology
GO:0008050
female courtship behavior
2012-02-16T01:16:13Z
gkoutos
behavior_ontology
aggressive behavior by intent
"An aggressive behavior towards other members of the society." [NBO:RH]
2012-02-16T02:27:08Z
gkoutos
behavior_ontology
social aggression behavior
"Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795]
George Gkoutos
GO:0050795
regulation of behavior
"Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG]
George Gkoutos
regulation of sexual activity
Deposition of eggs either into the medium, or onto a substrate.
Luke Slater
facilitating oviposition
Facilitating release or transfer of gametes.
Luke Slater
gamete release function
Active search for possible mates.
Luke Slater
mate finding behavior
Behavior by one animals soliciting food provision by a potential mate.
Luke Slater
courtship begging
Consumption of one member of a mating pair, usually the male, usually after the mating.
Luke Slater
sexual cannibalism
Behavior that serves to demonstrate non-aggressive intent by one member of a courting or potentially mating pair to the other.
Luke Slater
mating appeasement
Any of several behaviors directed towards one animal unwilling to mate by another eager to do so.
Luke Slater
sexual harassment
Provision of food to a potential mate
Luke Slater
courtship feeding
Actions resulting in establishment or use of one locale for reproductive activity.
Luke Slater
breeding site selection
Usually interference by members of one sex in the completion of courtship or mating activities by one or more members of the same sex.
Luke Slater
sexual interference
Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor.
Luke Slater
mate rejection
GC_ID:1
ncbi_taxonomy
all
NCBITaxon:1
root
all
GC_ID:1
ncbi_taxonomy
Vira
Viridae
viruses
Viruses
Vira
Viridae
viruses
GC_ID:1
ncbi_taxonomy
Teleostomi
NCBITaxon:40673
GC_ID:1
bony vertebrates
ncbi_taxonomy
Euteleostomi
bony vertebrates
Lophotrochozoa
GC_ID:1
ncbi_taxonomy
biota
NCBITaxon:131567
cellular organisms
biota
biota
GC_ID:1
ncbi_taxonomy
Dipnotetrapodomorpha
GC_ID:1
PMID:11743200
PMID:11791233
ncbi_taxonomy
Boreotheria
Boreoeutheria
Boreotheria
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11542017
PMID:11542087
PMID:11760965
PMID:12054223
PMID:2112744
PMID:270744
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
eubacteria
ncbi_taxonomy
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
Bacteria
eubacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
prokaryote
prokaryotes
GC_ID:1
ncbi_taxonomy
Homo/Pan/Gorilla group
Homininae
Homo/Pan/Gorilla group
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11541975
PMID:11542064
PMID:11542149
PMID:11760965
PMID:12054223
PMID:2112744
PMID:25527841
PMID:270744
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
ncbi_taxonomy
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
Archaea
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
NCBITaxon:2759
Eukaryota
eucaryotes
eucaryotes
eukaryotes
eukaryotes
Eucarya
Eucarya
Eucaryotae
Eucaryotae
Eukarya
Eukarya
Eukaryotae
Eukaryotae
eukaryotes
eukaryotes
GC_ID:1
PMID:11214319
PMID:12082125
PMID:12878460
PMID:15522813
ncbi_taxonomy
Euarchontoglires
GC_ID:1
ncbi_taxonomy
Anthropoidea
Simiiformes
Anthropoidea
GC_ID:1
ape
apes
ncbi_taxonomy
Hominoidea
ape
apes
GC_ID:1
tetrapods
ncbi_taxonomy
Tetrapoda
tetrapods
GC_ID:1
amniotes
ncbi_taxonomy
Amniota
amniotes
GC_ID:1
Theria
ncbi_taxonomy
Theria <Mammalia>
Theria
GC_ID:1
green plants
ncbi_taxonomy
Chlorobionta
Chlorophyta/Embryophyta group
chlorophyte/embryophyte group
green plants
Viridiplantae
green plants
green plants
Chlorobionta
Chlorobionta
Chlorophyta/Embryophyta group
Chlorophyta/Embryophyta group
chlorophyte/embryophyte group
chlorophyte/embryophyte group
green plants
green plants
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
NCBITaxon:33154
Opisthokonta
Fungi/Metazoa group
Fungi/Metazoa group
opisthokonts
opisthokonts
GC_ID:1
metazoans
multicellular animals
ncbi_taxonomy
Animalia
animals
Metazoa
metazoans
multicellular animals
Animalia
animals
GC_ID:1
ncbi_taxonomy
Bilateria
Protostomia
GC_ID:1
deuterostomes
ncbi_taxonomy
Deuterostomia
deuterostomes
GC_ID:1
ncbi_taxonomy
Haplorrhini
GC_ID:1
mammals
ncbi_taxonomy
mammals
Mammalia
mammals
mammals
GC_ID:1
PMID:11062127
PMID:12684019
fungi
ncbi_taxonomy
fungi
NCBITaxon:4751
Fungi
fungi
fungi
GC_ID:1
ncbi_taxonomy
Eumetazoa
molluscs
mollusks
molluscs
Mollusca
bivalves
Lamellibranchiata
Pelecypoda
bivalves
Bivalvia
GC_ID:1
chordates
ncbi_taxonomy
chordates
Chordata
chordates
chordates
GC_ID:1
Vertebrata
vertebrates
ncbi_taxonomy
vertebrates
Vertebrata <Metazoa>
Vertebrata
vertebrates
vertebrates
GC_ID:1
Gnathostomata
jawed vertebrates
ncbi_taxonomy
Gnathostomata <vertebrate>
Gnathostomata
jawed vertebrates
GC_ID:1
ncbi_taxonomy
Sarcopterygii
GC_ID:1
Craniata
ncbi_taxonomy
Craniata <chordata>
Craniata
GC_ID:1
eutherian mammals
placental mammals
placentals
ncbi_taxonomy
Placentalia
placentals
Eutheria
eutherian mammals
placental mammals
placentals
Placentalia
placentals
GC_ID:1
primate
ncbi_taxonomy
Primata
primates
Primates
primate
Primata
primates
GC_ID:1
ncbi_taxonomy
Catarrhini
GC_ID:1
great apes
ncbi_taxonomy
Pongidae
Hominidae
great apes
Pongidae
GC_ID:1
humans
ncbi_taxonomy
Homo
humans
GC_ID:1
human
man
ncbi_taxonomy
Home sapiens
Homo sampiens
Homo sapeins
Homo sapian
Homo sapians
Homo sapien
Homo sapience
Homo sapiense
Homo sapients
Homo sapines
Homo spaiens
Homo spiens
Humo sapiens
Homo sapiens
human
man
Home sapiens
Homo sampiens
Homo sapeins
Homo sapian
Homo sapians
Homo sapien
Homo sapience
Homo sapiense
Homo sapients
Homo sapines
Homo spaiens
Homo spiens
Humo sapiens
planned process
A processual entity that realizes a plan which is the concretization of a plan specification.
planned process
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.
organism
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
quality (PATO)
PATO:0000072
trait
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
PATO:0002015
composed of
compositionality
content
structure, composition
quality
PATO:0000025
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
composition
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
PATOC:GVG
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
concentration
quality
PATO:0000033
concentration of
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
Wikipedia:http://en.wikipedia.org/wiki/concentration
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
quality
impenetrability
toughness
PATO:0000048
hardness
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
merriam-webster:merriam-webster
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
quality
PATO:0000051
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATOC:GVG
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATO:0001647
relational shape quality
quality
PATO:0000052
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
shape
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATOC:GVG
quality
PATO:0000068
TODO: define this or obsolete it and move children somewhere else.
qualitative
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
quality
PATO:0000069
deviation (from_normal)
deviation(from_normal)
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATOC:GVG
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
quality
PATO:0000117
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
WordNet:WordNet
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
quality
PATO:0000125
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
PATOC:GVG
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATO:0001032
PATO:0001631
location
placement
relational spatial quality
quality
PATO:0000140
position
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
PATOC:GVG
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATO:0001452
conformation
relational structural quality
quality
PATO:0000141
structure
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATOC:GVG
conformation
VT:1000738
A physical quality of the thermal energy of a system.
quality
PATO:0000146
temperature
A physical quality of the thermal energy of a system.
PATOC:GVG
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
quality
PATO:0000169
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
PATOC:GVG
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
quality
PATO:0000274
fertility
A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction.
PATOC:GVG
A hardness quality of being rigid and resistant to pressure.
quality
firm
impenetrable
tough
PATO:0000386
hard
A hardness quality of being rigid and resistant to pressure.
PATOC:GVG
A hardness quality of giving little resistance to pressure.
quality
PATO:0000387
soft
A hardness quality of giving little resistance to pressure.
PATOC:GVG
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
ramified
ramiform
quality
PATO:0000402
branched
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
WordNet:WordNet
A branchiness quality inhering in a bearer by virtue of the bearer's lacking branches.
quality
PATO:0000414
unbranched
A branchiness quality inhering in a bearer by virtue of the bearer's lacking branches.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
quality
aberrant
atypia
atypical
defective
PATO:0000460
abnormal
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
quality
average
PATO:0000461
normal
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
PATOC:GVG
A size quality which is relatively high.
PATO:0001202
quality
big
enlarged
expanded
great
large
PATO:0000586
increased size
A size quality which is relatively high.
PATOC:GVG
A size quality which is relatively low.
hypoplasia
underdeveloped
quality
reduced
small
tiny
PATO:0000587
decreased size
A size quality which is relatively low.
PATOC:GVG
A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
quality
PATO:0000719
viable
A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
PATOC:GVG
A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
quality
PATO:0000955
fertile
A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
quality
PATO:0000956
sterile
A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction.
PATOC:GVG
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
quality
PATO:0000957
opacity
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
PATOC:GVG
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
non-transparent
quality
clouding
cloudy
PATO:0000963
opaque
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
PATOC:GVG
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
clear
hyaline
quality
PATO:0000964
transparent
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
PATOC:GVG
A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
quality
PATO:0000970
permeability
A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
Biology-online:Biology-online
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
quality
PATO:0000973
porosity
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
PATOC:GVG
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
quality
PATO:0000984
porous
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
PATOC:GVG
A porosity quality inhering in a bearer by virtue of the bearer's being incapable of admitting the passage of gas or liquid through pores or interstices.
quality
PATO:0000985
non-porous
A porosity quality inhering in a bearer by virtue of the bearer's being incapable of admitting the passage of gas or liquid through pores or interstices.
PATOC:GVG
A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
quality
PATO:0000992
viscosity
A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
PATOC:GVG
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
quality
PATO:0000998
viscous
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
PATOC:GVG
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0002079
Wikipedia:Physical_property
relational physical quality
quality
PATO:0001018
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
quality
PATO:0001154
elongated
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
WordNet:WordNet
true
physical object quality
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
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.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
quality
PATO:0001291
electromagnetic (EM) radiation quality
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
quality
PATO:0001300
optical quality
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
PATOC:GVG
A temperature which is relatively high.
PATO:0000678
high temperature
hot
quality
PATO:0001305
increased temperature
A temperature which is relatively high.
PATOC:GVG
A temperature which is relatively low.
PATO:0000677
cold
low temperature
quality
PATO:0001306
decreased temperature
A temperature which is relatively low.
PATOC:GVG
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
quality
PATO:0001332
amorphous
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
PATOC:GVG
A monadic quality of continuant that exists at the cellular level of organisation.
quality
PATO:0001396
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATOC:GVG
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
quality
PATO:0001404
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
quality
PATO:0001405
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
quality
PATO:0001406
binucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
quality
PATO:0001407
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
Biology-online:Biology-online
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
quality
PATO:0001421
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
PATOC:GVG
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
quality
PATO:0001422
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's decomposition into component parts.
quality
PATO:0001432
decayed
A quality inhering in a bearer by virtue of the bearer's decomposition into component parts.
Medical-dictionary:Medical-dictionary
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
quality
PATO:0001434
reproductive quality
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
WordNet:WordNet
A position which is relatively high.
quality
high position
PATO:0001475
increased position
A position which is relatively high.
PATOC:GVG
A positional which is relatively low.
quality
low position
PATO:0001476
decreased position
A positional which is relatively low.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
quality
PATO:0001481
sloped
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
WordNet:WordNet
A reproductive quality inhering in the young of an animal by virtue of the bearer's disposition to survive and develop normally.
quality
PATO:0001497
brood viability
A reproductive quality inhering in the young of an animal by virtue of the bearer's disposition to survive and develop normally.
PATOC:GVG
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
solidity
quality
PATO:0001546
quality of a solid
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
gaseous
quality
PATO:0001547
quality of a gas
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm
PATOC:GVG
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
liquidity
quality
PATO:0001548
quality of a liquid
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
url:http://www.chemistry-dictionary.com/definition/liquid.php
A mass which is lower than normal or average.
PATO:0000579
low mass
small mass
quality
PATO:0001562
decreased mass
A mass which is lower than normal or average.
PATO:GVG
A mass which is higher than normal or average.
PATO:0000578
high mass
large mass
quality
PATO:0001563
increased mass
A mass which is higher than normal or average.
PATO:GVG
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
quality
PATO:0001655
osmolarity
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
Wikipedia:http://en.wikipedia.org/wiki/Osmolarity
A osmolarity which is relatively low.
low osmolarity
quality
PATO:0001656
decreased osmolarity
A osmolarity which is relatively low.
PATOC:GVG
A osmolarity which is relatively high.
high osmolarity
quality
PATO:0001657
increased osmolarity
A osmolarity which is relatively high.
PATOC:GVG
A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface.
quality
PATO:0001687
elevation
A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface.
Trailillustrated:Trailillustrated
An elevation which is relatively high.
high elevation
quality
elevated
PATO:0001688
increased elevation
An elevation which is relatively high.
PATOC:GVG
An elevation which is relatively low.
low elevation
quality
PATO:0001689
decreased elevation
An elevation which is relatively low.
PATOC:GVG
A viscosity which relatively high.
high viscosity
quality
PATO:0001693
increased viscosity
A viscosity which relatively high.
PATOC:GVG
A viscosity which relatively low.
low viscosity
quality
PATO:0001694
decreased viscosity
A viscosity which relatively low.
PATOC:GVG
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
quality
PATO:0001739
radiation quality
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
PATOC:GVG
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
quality
PATO:0001759
granular
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
thefreedictionary.com:thefreedictionary.com
A viability quality inhering in a population by virtue of some of it's members' ability to survive.
quality
PATO:0001770
semi-viable
A viability quality inhering in a population by virtue of some of it's members' ability to survive.
PATOC:CVC
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
quality
PATO:0001822
wetness
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
wordreference.com:wordreference.com
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
quality
PATO:0001823
wet
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
PATOC:GVG
A wetness quality that is relatively high.
quality
PATO:0001825
increased wetness
A wetness quality that is relatively high.
PATOC:GVG
A wetness quality that is relatively low.
low wetness
quality
PATO:0001826
decreased wetness
A wetness quality that is relatively low.
PATOC:GVG
A fertility which is relatively low.
low fertility
quality
PATO:0001834
decreased fertility
A fertility which is relatively low.
PATOC:GVG
A fertility which is relatively high.
high fertility
quality
PATO:0001835
increased fertility
A fertility which is relatively high.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
quality
PATO:0001908
multinucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
quality
PATO:0001985
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
OBI:OBI
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
quality
PATO:0001992
cellularity
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
PATOC:GVG
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
quality
PATO:0001993
multicellular
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
PATOC:GVG
A quality that inheres in an entire organism or part of an organism.
quality
PATO:0001995
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATOC:CJM
A quality that inheres in an entire population or part of a population.
quality
PATO:0002003
population quality
A quality that inheres in an entire population or part of a population.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
quality
PATO:0002009
branchiness
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
PATOC:MAH
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
george
2009-10-06T04:37:14Z
quality
PATO:0002124
laminar
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
PATOC:GVG
george
2009-10-30T02:18:39Z
quality
PATO:0002143
sloped downward
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
George Gkoutos
2010-03-01T02:56:33Z
quality
PATO:0002181
displaced
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
PATOC:GVG
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
George Gkoutos
2010-03-10T03:18:15Z
PATO:0002061
relational molecular quality
quality
PATO:0002182
molecular quality
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
PATOC:GVG
A quality inhering in a bearer by virtue of its constitution.
George Gkoutos
2010-03-15T04:35:27Z
quality
PATO:0002198
quality of a substance
A quality inhering in a bearer by virtue of its constitution.
PATOC:GVG
A quality that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:39:43Z
quality
PATO:0002300
increased quality
A quality that has a value that is increased compared to normal or average.
PATOC:GVG
A quality that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:40:15Z
quality
PATO:0002301
decreased quality
A quality that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:51:54Z
quality
PATO:0002303
decreased object quality
A quality of an object that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:54:01Z
quality
PATO:0002305
increased object quality
A quality of an object that has a value that is increased compared to normal or average.
PATOC:GVG
A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width.
gkoutos
2012-04-18T06:31:29Z
quality
PATO:0002364
shortened
A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
gkoutos
2013-10-21T05:44:34Z
quality
PATO:0002505
nucleated
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
PATOC:GVG
The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids.
quality
PATO:0015021
combustibility
The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids.
https://en.wikipedia.org/wiki/Combustibility
https://github.com/EnvironmentOntology/envo/issues/384
An increase in combustibility.
combustible
quality
PATO:0015022
increased combustibility
An decrease in combustibility.
quality
noncombustible
PATO:0015023
decreased combustibility
An increase in porosity.
quality
PATO:0015024
increased porosity
An increase in porosity.
https://github.com/pato-ontology/pato/issues/110
An decrease in porosity.
quality
PATO:0015025
decreased porosity
An decrease in porosity.
https://github.com/pato-ontology/pato/issues/110
2
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organism
organism collection
May be of the same or different species.
collection of organisms
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
ISBN:0878932739
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms.
Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
2
A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.
multispecies community
ISBN:0865423504
envoPolar
Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.
ecological community
A quality that inheres in a biological population.
See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term.
quality of a population
A quality that inheres in a community.
These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.
quality of an ecological community
A process that has as primary participant a population.
Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes.
population process
The number of different species represented in an ecological community.
This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019).
adapted from http://en.wikipedia.org/wiki/Species_richness
community species richness
A process that leads to a change in the number of individuals (positive or negative) in a population.
population growth
A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat.
logistic population growth
A population growth process that leads to an exponential increase in the number of individuals in a population.
exponential population growth
A collection of organisms that has as parts every organism of given species and no organisms of any other species.
At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible.
This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.
species as a collection of organisms
1
2
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.
If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity.
adapted from http://en.wikipedia.org/wiki/Species_diversity
The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
community species diversity
A population process that ultimately leads to the death of all individuals in a population.
population extinction
A process that ultimately leads to the death of all individuals in a population.
species extinction
If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even.
A quality of a community that reflects how close in abundance all species in a community are.
adapted from http://en.wikipedia.org/wiki/Species_evenness
community species evenness
2
A collection of organisms of the same species that has as members only humans.
human community
human population
collection of humans
A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete.
These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community).
community
true
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
2
A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.
pair of interacting organisms
1
pair of interacting organisms of the same species
A plant structure (PO:0005679) which is a whole organism.
genet (broad)
ramet (broad)
PO_GIT:538
PO_GIT:69
planta entera (Spanish, exact)
植物体全体 (Japanese, exact)
bush (narrow)
frutex (narrow)
frutices (narrow)
gametophyte (narrow)
herb (narrow)
liana (narrow)
prothalli (narrow)
prothallium (narrow)
prothallus (narrow)
seedling (narrow)
shrub (narrow)
sporophyte (narrow)
suffrutex (narrow)
suffrutices (narrow)
tree (narrow)
vine (narrow)
woody clump (narrow)
plant_anatomy
clonal colony (related)
colony (related)
PO:0000003
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
whole plant
A plant structure (PO:0005679) which is a whole organism.
POC:curators
planta entera (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物体全体 (Japanese, exact)
NIG:Yukiko_Yamazaki
frutex (narrow)
FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba
frutices (narrow)
FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b
prothalli (narrow)
FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0
prothallus (narrow)
FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8
suffrutex (narrow)
FNA:99508f62-7116-4e2b-90c0-19ff55ebd967
suffrutices (narrow)
FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2
woody clump (narrow)
FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0
A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003).
PO_GIT:465
portion of ovule primordium tissue (exact)
primordio de óvulo (Spanish, exact)
胚珠原基(可視的) (Japanese, exact)
plant_anatomy
PO:0000018
The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210).
ovule primordium
A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003).
ISBN:0471245208
POC:curators
primordio de óvulo (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
胚珠原基(可視的) (Japanese, exact)
NIG:Yukiko_Yamazaki
A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
PO_GIT:465
pistil primordium (exact)
portion of gynoecium primordium tissue (exact)
primordio de gineceo (Spanish, exact)
雌蕊原基(可視的) (Japanese, exact)
plant_anatomy
PO:0000019
Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).
gynoecium primordium
A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
POC:curators
primordio de gineceo (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
雌蕊原基(可視的) (Japanese, exact)
NIG:Yukiko_Yamazaki
A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
PO_GIT:234
ápice del epiblasto (epiblastema) (Spanish, exact)
シュート頂、茎頂 (Japanese, exact)
plant_anatomy
PO:0000037
shoot axis apex
A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
POC:curators
ápice del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
シュート頂、茎頂 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
zona periférica (Spanish, exact)
周辺帯 (Japanese, exact)
plant_anatomy
peripheral meristem (related)
PO:0000225
peripheral zone
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
ISBN:0521288959
TAIR_curator:Leonore_Reiser
zona periférica (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
周辺帯 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
PO:0006329
PO:0006373
PO:0006374
PO:0025091
floral meristem (exact)
mersitema floral (Spanish, exact)
花芽分裂組織 (Japanese, exact)
Poaceae floret meristem (narrow)
ear floret meristem (narrow)
floret meristem (narrow)
tassel floret meristem (narrow)
plant_anatomy
floral apical meristem (related)
PO:0000229
In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
flower meristem
A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
Gramene:Pankaj_Jaiswal
POC:curators
mersitema floral (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
花芽分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
CL:0000034
PO_GIT:272
célula meristemática (Spanish, exact)
stem cell (exact)
分裂組織細胞 (Japanese, exact)
plant_anatomy
PO:0004010
meristematic cell
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
ISBN:0471245208
POC:Laurel_Cooper
célula meristemática (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
分裂組織細胞 (Japanese, exact)
NIG:Yukiko_Yamazaki
A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
PO_GIT:467
portion of root primordium tissue (exact)
primordio de raíz (Spanish, exact)
root primordia (exact, plural)
根原基(可視的) (Japanese, exact)
plant_anatomy
PO:0005029
A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
root primordium
A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
ISBN:0521288959
POC:curators
primordio de raíz (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
根原基(可視的) (Japanese, exact)
NIG:Yukiko_Yamazaki
A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
filoma (Spanish, exact)
フィロム、葉(的)器官 (Japanese, exact)
plant_anatomy
PO:0006001
phyllome
A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
POC:curators
filoma (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
フィロム、葉(的)器官 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
PO_GIT:472
PO_GIT:583
meristema del epiblasto (epiblastema) (Spanish, exact)
シュート分裂組織 (Japanese, exact)
plant_anatomy
PO:0006079
shoot system meristem
A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
Gramene:Pankaj_Jaiswal
POC:Laurel_Cooper
meristema del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
シュート分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
PO_GIT:125
portion of protoderm tissue (exact)
protodermis (Spanish, exact)
前表皮、原表皮 (Japanese, exact)
plant_anatomy
dermatogen cell (related)
PO:0006210
A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state.
protoderm
A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
ISBN:0471245208
POC:Laurel_Cooper
protodermis (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
前表皮、原表皮 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
PO_GIT:390
plant_structure_development_stage
Solanaceae whole plant growth stages (SGN:0000001) (related)
cereal plant growth stage ontology (GRO:0007199) (related)
maize growth stage (GRO:0007002) (related)
plant growth stages in Arabidopsis (TAIR:0000021) (related)
rice growth stage (GRO:0007040) (related)
sorghum growth stage (GRO:0007124) (related)
wheat, barley and oat growth stage (GRO:0007156) (related)
PO:0007033
whole plant development stage
A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
POC:curators
A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
PO_GIT:36
meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
生殖シュート頂端 分裂組織 (Japanese, exact)
plant_anatomy
PO:0008028
reproductive shoot apical meristem
A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
Gramene:Chih-Wei_Tung
meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
生殖シュート頂端 分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
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).
PO:0020067
PO:0020068
PO:0020069
PO:0020070
PO:0020071
PO:0020072
PO:0020073
PO:0020074
PO:0020076
PO:0020077
PO:0020078
PO:0020079
PO:0020080
PO:0020082
PO:0020083
PO:0020087
PO:0020107
aggregate fruit (broad)
compound fruit (broad)
dehiscent fruit (broad)
diaspore (broad)
indehiscent fruit (broad)
multiple fruit (broad)
propagule (broad)
PO_GIT:76
frucht (exact, German)
fruto (exact, Spanish)
果実 (exact, Japanese)
coenocarp (narrow)
syncarp (narrow)
plant_anatomy
PO:0009001
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.
fruit
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).
NYBG:Brandon_Sinn
NYBG:Dario_Cavaliere
POC:Laurel_Cooper
POC:curators
frucht (exact, German)
NYBG:Brandon_Sinn
NYBG:Dario_Cavaliere
fruto (exact, Spanish)
POC:Maria_Alejandra_Gandolfo
果実 (exact, Japanese)
NIG:Yukiko_Yamazaki
coenocarp (narrow)
FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da
syncarp (narrow)
FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a
A cell which is a plant structure (PO:0009011).
cell (broad)
GO:0005623
PO_GIT:56
célula vegetal (Spanish, exact)
植物細胞 (Japanese, exact)
plant_anatomy
PO:0009002
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
plant cell
A cell which is a plant structure (PO:0009011).
GO:0005623
POC:curators
célula vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物細胞 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
PO:0003006
PO_GIT:578
raíz (Spanish, exact)
radices (exact, plural)
radix (exact)
根 (Japanese, exact)
aerial root (narrow)
climbing root (narrow)
plant_anatomy
PO:0009005
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).
root
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
ISBN:978-0879015329
ISBN:9780964022157
NYBG:Brandon_Sinn
NYBG:Dario_Cavaliere
POC:Laurel_Cooper
POC:curators
raíz (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
radices (exact, plural)
FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d
radix (exact)
FNA:e6315684-fc99-4976-b39d-b356c4b7e7fd
根 (Japanese, exact)
NIG:Yukiko_Yamazaki
climbing root (narrow)
FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f
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.
PO_GIT:135
sistema de epiblasto (epiblastema) (Spanish, exact)
シュート系、苗条系 (Japanese, exact)
tree crown (narrow)
plant_anatomy
Poaceae crown (related)
shoot (related)
thalli (related)
thallus (related)
PO:0009006
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.
shoot system
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.
POC:Laurel_Cooper
POC:curators
sistema de epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
シュート系、苗条系 (Japanese, exact)
NIG:Yukiko_Yamazaki
thalli (related)
FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85
thallus (related)
FNA:02756ad4-a09c-48d7-8754-903254e557a9
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
portion of tissue (broad)
tissue (broad)
PO_GIT:59
porción de un tejido vegetal (Spanish, exact)
植物組織の一部 (Japanese, exact)
plant_anatomy
plant tissue (related)
PO:0009007
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.
portion of plant tissue
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
POC:curators
TAIR_curator:Leonore_Reiser
porción de un tejido vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物組織の一部 (Japanese, exact)
NIG:Yukiko_Yamazaki
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.
organ (broad)
PO_GIT:55
órgano vegetal (Spanish, exact)
植物 器官 (Japanese, exact)
plant_anatomy
compound plant organ (related)
simple plant organ (related)
PO:0009008
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).
plant organ
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.
POC:curators
órgano vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物 器官 (Japanese, exact)
NIG:Yukiko_Yamazaki
simple plant organ (related)
PATO:01503
A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
embryo (broad)
PO_GIT:92
embrión (Spanish, exact)
植物胚 (Japanese, exact)
plant_anatomy
germ (related)
PO:0009009
A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
plant embryo
A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631).
POC:curators
embrión (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物胚 (Japanese, exact)
NIG:Yukiko_Yamazaki
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).
diaspore (broad)
PO_GIT:405
semilla (Spanish, exact)
種子 (Japanese, exact)
pyrene (narrow)
plant_anatomy
PO:0009010
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).
seed
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).
POC:curators
semilla (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
種子 (Japanese, exact)
NIG:Yukiko_Yamazaki
pyrene (narrow)
FNA:f5c50e73-61e3-48ec-b918-6f85b3f40738
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
PO_GIT:57
estructura vegetal (Spanish, exact)
植物 構造 (Japanese, exact)
plant_anatomy
PO:0009011
'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
plant structure
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
CARO:0000003
POC:curators
estructura vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物 構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
PO:cooperl
A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
PO:0007021
PO_GIT:185
etapa de desarrollo de estructura vegetal (Spanish, exact)
plant growth and development stage (exact)
plant_structure_development_stage
Arabidopsis growth (related)
PO:0009012
Refers to GO:0032502 'developmental process', which includies growth, differentiation, and senescence, and BFO:0000003 'ocurrent'.
plant structure development stage
A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
BFO:0000003
GO:0032502
POC:curators
etapa de desarrollo de estructura vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
Arabidopsis growth (related)
TAIR:0000205
A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
PO_GIT:472
meristem (exact)
meristema (Spanish, exact)
meristematic tissue (exact)
分裂組織 (Japanese, exact)
plant_anatomy
PO:0009013
portion of meristem tissue
A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
APweb:Glossary
Gramene:Pankaj_Jaiswal
meristema (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
PO:0004541
PO_GIT:160
PO_GIT:259
flor (Spanish, exact)
花 (Japanese, exact)
Asteraceae floret (narrow)
basal flower (narrow)
double flower (narrow)
hermaphrodite flower (narrow)
monoclinous flower (narrow)
perfect flower (narrow)
plant_anatomy
floret (related)
PO:0009046
The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form.
flower
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
POC:curators
flor (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
花 (Japanese, exact)
NIG:Yukiko_Yamazaki
basal flower (narrow)
CO_125:0000019
hermaphrodite flower (narrow)
CO_125:0000028
A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
PO:0006317
PO:0006357
PO:0006365
PO:0006384
PO:0006391
PO:0006394
PO:0006403
PO:0006404
PO:0006423
PO:0006424
PO:0006425
PO:0006426
PO:0025089
pistil (broad)
PO_GIT:470
PO_GIT:71
PO_GIT:98
ginoecio (Spanish, exact)
gynaecium (exact)
gynoecia (exact, plural)
雌蕊群 (Japanese, exact)
Poaceae gynoecium (narrow)
Zea gynoecium (narrow)
apocarpous gynoecium (narrow)
gynoecium of ear floret (narrow)
gynoecium of lower floret of pedicellate spikelet of ear (narrow)
gynoecium of lower floret of pedicellate spikelet of tassel (narrow)
gynoecium of lower floret of sessile spikelet of ear (narrow)
gynoecium of lower floret of sessile spikelet of tassel (narrow)
gynoecium of tassel floret (narrow)
gynoecium of upper floret of pedicellate spikelet of ear (narrow)
gynoecium of upper floret of pedicellate spikelet of tassel (narrow)
gynoecium of upper floret of sessile spikelet of ear (narrow)
gynoecium of upper floret of sessile spikelet of tassel (narrow)
syncarpous gynoecium (narrow)
plant_anatomy
PO:0009062
If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
gynoecium
A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
POC:curators
ginoecio (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
gynaecium (exact)
FNA:03f034c5-6bd6-4846-8ef7-c5190d09008c
gynoecia (exact, plural)
FNA:226a743c-7988-4b66-b163-2ce80d7c8a70
雌蕊群 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
PO:0006457
PO:0006491
PO_GIT:464
PO_GIT:70
óvulo vegetal (Spanish, exact)
胚珠 (Japanese, exact)
Poaceae ovule (narrow)
Zea ovule (narrow)
plant_anatomy
PO:0020003
A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
plant ovule
A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
POC:curators
óvulo vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
胚珠 (Japanese, exact)
NIG:Yukiko_Yamazaki
A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
promeristem (broad)
PO_GIT:579
AM (exact)
meristema apical (Spanish, exact)
頂端分裂組織 (Japanese, exact)
plant_anatomy
primary meristem (related)
PO:0020144
apical meristem
A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
Gramene:Pankaj_Jaiswal
POC:Laurel_Cooper
POC:curators
meristema apical (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
頂端分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
promeristem (broad)
PO_GIT:472
SAM (exact)
meristema apical del epiblasto (epiblastema) (Spanish, exact)
茎頂分裂組織 (Japanese, exact)
plant_anatomy
primary shoot meristem (related)
PO:0020148
shoot apical meristem
A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
POC:Laurel_Cooper
UMSL_curator:fz
meristema apical del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
茎頂分裂組織 (Japanese, exact)
NIG:Yukiko_Yamazaki
An axial plant organ (PO:0009008).
rwalls
2010-07-01T03:44:41Z
eje de la planta (Spanish, exact)
plant axes (exact, plural)
植物軸(軸柱) (Japanese, exact)
plant_anatomy
PO:0025004
Includes roots and shoots.
plant axis
An axial plant organ (PO:0009008).
POC:curators
eje de la planta (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
plant axes (exact, plural)
FNA:2355281f-ab10-4ae2-a3d8-672cace068a8
植物軸(軸柱) (Japanese, exact)
NIG:Yukiko_Yamazaki
A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
rwalls
2010-02-09T04:12:11Z
PO_GIT:63
estructura vegetal colectiva de órgano (Spanish, exact)
集合植物器官構造 (Japanese, exact)
plant_anatomy
PO:0025007
Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure.
collective plant organ structure
A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
POC:curators
estructura vegetal colectiva de órgano (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
集合植物器官構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
Laurel_Cooper
2010-04-28T11:04:34Z
PO:0008033
cycle (broad)
verticil (broad)
PO_GIT:90
PO_GIT:99
estructura colectiva del filoma (Spanish, exact)
葉的器官が集まった構造 (Japanese, exact)
floral whorl (narrow)
whorl (narrow)
plant_anatomy
phyllome whorl (related)
PO:0025023
collective phyllome structure
A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
POC:curators
cycle (broad)
FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe
verticil (broad)
FNA:12607624-3d2a-4113-bd86-0e2557f2f473
estructura colectiva del filoma (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
葉的器官が集まった構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
floral whorl (narrow)
GO:0048438
GO:0048457
GO:0048458
GO:0048459
A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
rwalls
2010-07-01T02:11:26Z
root (broad)
PO_GIT:136
sistema de raíz (Spanish, exact)
根系 (Japanese, exact)
plant_anatomy
PO:0025025
Generally the below ground portion of a vascular plant.
root system
A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
POC:Laurel_Cooper
POC:curators
root (broad)
FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9
sistema de raíz (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
根系 (Japanese, exact)
NIG:Yukiko_Yamazaki
A native plant cell (PO:0025606) that is part of a plant embryo (PO:0009009).
rwalls
2010-05-07T02:41:17Z
embryo cell (broad)
embryonic cell (broad)
PO_GIT:281
célula embriónica vegetal (Spanish, exact)
embryonic plant cell (exact)
胚性植物細胞 (Japanese, exact)
plant_anatomy
PO:0025028
embryo plant cell
A native plant cell (PO:0025606) that is part of a plant embryo (PO:0009009).
POC:Laurel_Cooper
POC:curators
célula embriónica vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
胚性植物細胞 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
rwalls
2010-07-01T03:46:35Z
caullome (exact)
eje del epiblasto (epiblastema) (Spanish, exact)
シュート軸 (Japanese, exact)
plant_anatomy
shoot (related)
PO:0025029
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
shoot axis
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
POC:curators
eje del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
シュート軸 (Japanese, exact)
NIG:Yukiko_Yamazaki
A phyllome (PO:0006001) that is not associated with a reproductive structure.
rwalls
2010-07-12T01:31:44Z
PO_GIT:274
PO_GIT:301
hoja (Spanish, exact)
葉 (Japanese, exact)
plant_anatomy
PO:0025034
leaf
A phyllome (PO:0006001) that is not associated with a reproductive structure.
POC:curators
hoja (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
葉 (Japanese, exact)
NIG:Yukiko_Yamazaki
A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
rwalls
2010-09-17T09:49:10Z
sistema de brote reproductivo (Spanish, exact)
生殖シュート 系、苗条系 (Japanese, exact)
plant_anatomy
PO:0025082
reproductive shoot system
A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
POC:curators
sistema de brote reproductivo (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
生殖シュート 系、苗条系 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009).
rwalls
2010-11-05T01:36:24Z
PO_GIT:245
PO_GIT:339
embryonic plant structure (exact)
estructura vegetal embriónica (Spanish, exact)
胚性植物構造 (Japanese, exact)
plant_anatomy
PO:0025099
Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).
embryo plant structure
A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009).
POC:curators
estructura vegetal embriónica (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
胚性植物構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
rwalls
2010-11-15T09:10:22Z
PO_GIT:186
portion of primordial tissue (exact)
portion of primordium tissue (exact)
primordia (exact, plural)
primordio (Spanish, exact)
原基(可視的) (Japanese, exact)
plant_anatomy
PO:0025127
A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.
primordium
A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
POC:curators
primordio (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
原基(可視的) (Japanese, exact)
NIG:Yukiko_Yamazaki
A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
rwalls
2010-11-15T09:27:11Z
PO_GIT:466
phyllome primordia (exact, plural)
portion of phyllome primordium tissue (exact)
primordio del filoma (Spanish, exact)
フィロム原基(可視的) (Japanese, exact)
plant_anatomy
PO:0025128
The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.
phyllome primordium
A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
PMID:11572953
POC:curators
primordio del filoma (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
フィロム原基(可視的) (Japanese, exact)
NIG:Yukiko_Yamazaki
An anatomical entity that is or was part of a plant.
rwalls
2010-11-15T11:41:38Z
PO_GIT:224
entidad anatómica vegetal (Spanish, exact)
植物 解剖学(形態)的実体 (Japanese, exact)
plant_anatomy
PO:0025131
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
plant anatomical entity
cjm
An anatomical entity that is or was part of a plant.
BFO:0000004
CARO:0000000
POC:curators
entidad anatómica vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物 解剖学(形態)的実体 (Japanese, exact)
NIG:Yukiko_Yamazaki
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
CAROC:Brownsville2014
A shoot apex that has as part a reproductive shoot apical meristem.
rwalls
2010-12-20T08:47:03Z
ápice reproductivo del epiblasto (epiblastema) (Spanish, exact)
生殖シュート頂、茎頂 (Japanese, exact)
plant_anatomy
PO:0025222
reproductive shoot apex
A shoot apex that has as part a reproductive shoot apical meristem.
POC:Ramona_Walls
ápice reproductivo del epiblasto (epiblastema) (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
生殖シュート頂、茎頂 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009).
rwalls
2010-12-20T12:27:10Z
portion of embryo tissue (broad)
PO_GIT:338
portion of embryonic plant tissue (exact)
tejido embriónico vegetal (Spanish, exact)
植物胚性組織 の一部 (Japanese, exact)
plant_anatomy
PO:0025233
This class is for tissues that only occur as part of an embryo.
portion of embryo plant tissue
A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009).
POC:curators
tejido embriónico vegetal (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物胚性組織 の一部 (Japanese, exact)
NIG:Yukiko_Yamazaki
A maximal whole plant development stage.
rwalls
2011-10-19T10:54:37Z
PO_GIT:230
vida de la planta entera (Spanish, exact)
植物体の一生 (Japanese, exact)
plant_structure_development_stage
PO:0025337
There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
life of whole plant stage
A maximal whole plant development stage.
POC:curators
vida de la planta entera (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
植物体の一生 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
rwalls
2011-10-19T11:12:49Z
PO_GIT:391
etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
集合的植物構造の発生過程 (Japanese, exact)
plant_structure_development_stage
PO:0025338
Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083).
collective plant organ structure development stage
A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
POC:curators
etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
集合的植物構造の発生過程 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant organ (PO:0009008) that is part of a flower (PO:0009046).
rwalls
2012-01-19T11:44:36Z
PO_GIT:423
órgano floral (Spanish, exact)
flower organ (exact)
花器官 (Japanese, exact)
plant_anatomy
PO:0025395
Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.
floral organ
A plant organ (PO:0009008) that is part of a flower (PO:0009046).
POC:curators
órgano floral (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
花器官 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
Laurel_Cooper
2012-02-07T08:20:10Z
phyllome meristem (broad)
PO_GIT:427
フィロム原基 (Japanese, exact)
plant_anatomy
PO:0025430
The phyllome anlagen is only detectable by gene expression, not morphology.
phyllome anlagen
A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
POC:Laurel_Cooper
POC:curators
フィロム原基 (Japanese, exact)
NIG:Yukiko_Yamazaki
A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
Laurel_Cooper
2012-02-08T01:00:56Z
PO_GIT:427
precursor de raí (Spanish, exact)
根原基 (Japanese, exact)
plant_anatomy
PO:0025433
Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).
root anlagen
A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
POC:curators
precursor de raí (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
根原基 (Japanese, exact)
NIG:Yukiko_Yamazaki
A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
rwalls
2012-04-26T03:57:09Z
PO_GIT:465
floral structure primordia (exact, plural)
portion of floral structure primordium tissue (exact)
primordio de organo floral (Spanish, exact)
花器官原基 (Japanese, exact)
plant_anatomy
PO:0025477
If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).
floral organ primordium
A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
POC:curators
primordio de organo floral (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
花器官原基 (Japanese, exact)
NIG:Yukiko_Yamazaki
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.
Laurel_Cooper
2012-06-11T14:57:00Z
PO_GIT:480
estructura vegetal con múltiples tejidos (Spanish, exact)
複数の組織からなる植物構造 (Japanese, exact)
plant_anatomy
PO:0025496
Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types.
multi-tissue plant structure
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.
CARO:0000055
POC:curators
estructura vegetal con múltiples tejidos (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
複数の組織からなる植物構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
Laurel_Cooper
2012-06-11T15:09:20Z
PO_GIT:479
estructura vegetal colectiva (Spanish, exact)
集合的植物構造 (Japanese, exact)
plant_anatomy
PO:0025497
This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006).
collective plant structure
A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
POC:curators
estructura vegetal colectiva (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
集合的植物構造 (Japanese, exact)
NIG:Yukiko_Yamazaki
A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
Laurel_Cooper
2012-12-13T18:21:19Z
PO_GIT:517
plant_structure_development_stage
PO:0025527
The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003).
shoot system development stage
A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
POC:Laurel_Cooper
A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
Laurel_Cooper
2012-12-13T19:01:14Z
PO_GIT:517
plant_structure_development_stage
PO:0025530
reproductive shoot system development stage
A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
POC:Laurel_Cooper
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
Laurel_Cooper
2014-05-13T16:51:47Z
PO_GIT:586
plant_anatomy
PO:0025606
A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
native plant cell
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
POC:Laurel_Cooper
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
rwalls
2010-07-15T02:56:11Z
PO_GIT:139
PO_GIT:68
fase esporofítica (Spanish, exact)
sporophytic development stage (exact)
sporophytic phase (exact)
sporphyte phase (exact)
胞子体発生過程 (Japanese, exact)
plant_structure_development_stage
PO:0028002
A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis.
sporophyte development stage
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
POC:curators
fase esporofítica (Spanish, exact)
POC:Maria_Alejandra_Gandolfo
胞子体発生過程 (Japanese, exact)
NIG:Yukiko_Yamazaki
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Chris Mungall
http://www.jbiomedsem.com/content/4/1/43
system
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
uberon
UBERON:0000000
processual entity
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
span:ProcessualEntity
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
submucosal
BTO:0002107
FMA:85391
FMA:85392
NCIT:C13167
UMLS:C0225344
organ submucosa
region of submucosa
submucosa of organ
submucosa of region of organ
uberon
submucous layer
tela submucosa
tunica submucosa
UBERON:0000009
submucosa
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
UMLS:C0225344
ncithesaurus:Submucosa
organ submucosa
FMA:85391
region of submucosa
FMA:85392
submucosa of organ
FMA:85391
submucosa of region of organ
FMA:85392
submucous layer
BTO:0002107
tela submucosa
BTO:0002107
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
PNS
AAO:0000429
BAMS:PNS
BILA:0000081
BIRNLEX:1111
BTO:0001028
CALOHA:TS-0808
EFO:0000891
EHDAA2:0001445
EHDAA:2893
EMAPA:16665
EV:0100335
FBbt:00005098
FMA:9903
GAID:715
MA:0000218
MAT:0000338
MESH:D017933
MIAA:0000338
NCIT:C12465
TAO:0000142
UMLS:C0206417
UMLS:C1305921
VHOG:0000399
XAO:0000178
ZFA:0000142
pars peripherica
systema nervosum periphericum
uberon
UBERON:0000010
peripheral nervous system
cjm
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.
GO:0007422
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000142
TAO
ZFIN:curator
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
2012-06-20
AAO:0000429
AAO
AAO:BJB
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
2012-09-17
VHOG:0000399
VHOG
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
PNS
UMLS:C0206417
BIRNLEX:1111
UMLS:C0206417
ncithesaurus:Peripheral_Nervous_System
UMLS:C1305921
BIRNLEX:1111
pars peripherica
FMA:9903
FMA:TA
systema nervosum periphericum
FMA:9903
FMA:TA
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
EHDAA2:0001844
EHDAA:6530
EMAPA:17525
EV:0100152
FMA:86166
GAID:933
MA:0000151
MAT:0000284
MESH:D012867
MIAA:0000284
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
VHOG:0000860
portion of skin
region of skin
skin
skin region
skin zone
uberon
UBERON:0000014
zone of skin
FMA
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
(...) 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]
2012-09-17
VHOG:0000860
VHOG
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
skin
MA:0000151
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
AEO:0000192
CARO:0000010
FMA:50705
anatomical boundary
uberon
UBERON:0000015
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.
non-material anatomical boundary
CARO
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
CARO:0000010
anatomical boundary
CARO:0000010
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
eye
AAO:0010340
BIRNLEX:1169
BTO:0004688
EHDAA2:0000484
EHDAA:936
EMAPA:16198
FMA:54448
MA:0000261
NCIT:C12401
OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA
TAO:0000107
UMLS:C0015392
UMLS:C1280202
VHOG:0000275
XAO:0000179
ZFA:0000107
regio orbitalis
vertebrate eye
uberon
camera-type eye plus associated structures
eyes
orbital part of face
orbital region
UBERON:0000019
camera-type eye
definitional
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
GO:0043010
A cavitated compound organ that transduces light waves into neural signals.[TAO]
2012-08-14
TAO:0000107
TAO
TAO:wd
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]
2012-09-17
VHOG:0000275
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
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
FMA
eye
FMA:54448
UMLS:C0015392
BIRNLEX:1169
UMLS:C0015392
ncithesaurus:Eye
UMLS:C1280202
BIRNLEX:1169
regio orbitalis
FMA:54448
FMA:TA
eyes
TAO:0000107
orbital part of face
FMA:54448
orbital region
FMA:54448
An organ that is capable of transducing sensory stimulus to the nervous system.
AEO:0000094
BSA:0000121
BTO:0000202
CALOHA:TS-2043
EHDAA2:0001824
EHDAA:500
EMAPA:35955
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:D012679
NCIT:C33224
UMLS:C0935626
VHOG:0001407
WBbt:0006929
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensory organ
sensory organ system organ
sensory system organ
sensillum
uberon
Sinnesorgan
sensor
UBERON:0000020
sense organ
An organ that is capable of transducing sensory stimulus to the nervous system.
UMLS:C0935626
ncithesaurus:Organ_of_the_Special_Sense
organ of sense organ system
OBOL:accepted
organ of sensory organ system
OBOL:accepted
organ of sensory system
OBOL:accepted
sense organ system organ
OBOL:automatic
sensory organ system organ
OBOL:automatic
sensory system organ
OBOL:accepted
sensillum
WBbt:0006929
Sinnesorgan
BTO:0000202
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)
tubular
galen:Tube
anatomical tube
duct
uberon
UBERON:0000025
tube
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
AAO:0010335
AEO:0000106
BILA:0000115
BIRNLEX:1230
BTO:0000282
CALOHA:TS-0436
EFO:0000964
EHDAA2:0003106
EMAPA:31858
FBbt:00000004
FMA:7154
GAID:61
HAO:0000397
MA:0000023
MAT:0000294
MESH:D006257
MIAA:0000294
NCIT:C12419
OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg
OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA
SPD:0000016
TAO:0001114
TGMA:0000002
UMLS:C0018670
VHOG:0001644
WBbt:0005739
XAO:0003024
ZFA:0001114
galen:Head
head (volume)
adult head
uberon
cephalic area
UBERON:0000033
head
The head is the anterior-most division of the body [GO].
GO:0060322
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
2012-06-20
AAO:0010335
AAO
AAO:BJB
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
2012-08-14
TAO:0001114
TAO
ZFIN:curator
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
2012-09-17
VHOG:0001644
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
UMLS:C0018670
BIRNLEX:1230
UMLS:C0018670
ncithesaurus:Head
head (volume)
FMA:7154
cephalic area
SPD:0000016
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
FMA:9581
GAID:19
MESH:D012704
NCIT:C13169
TAO:0005425
UMLS:C0036760
ZFA:0005425
tunica serosa
wall of serous sac
uberon
serosa
UBERON:0000042
serous membrane
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
2012-08-14
TAO:0005425
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.
FMA
UMLS:C0036760
ncithesaurus:Serosa
tunica serosa
FMA:9581
wall of serous sac
FMA:9581
serosa
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
TGMA:0000729
uberon
UBERON:0000047
simple eye
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.
uberon
UBERON:0000055
vessel
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
AAO:0011123
FBbt:00100314
FMA:30320
NCIT:C12948
TAO:0005171
UMLS:C0687028
XAO:0004000
ZFA:0005171
galen:Duct
anatomical duct
exocrine duct
exocrine gland duct
uberon
ducts
UBERON:0000058
duct
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
ZFA:0005171
UMLS:C0687028
ncithesaurus:Duct
ducts
XAO:0004000
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
in FMA, serosa is a wall
UBERON:0009915
wall
EMAPA:25036
FMA:82482
galen:Wall
wall of organ
uberon
organ wall
UBERON:0000060
anatomical wall
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
FMA:82482
in FMA, serosa is a wall
FMA
wall of organ
FMA:82482
organ wall
FMA:82482
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
BIRNLEX:4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GO:0048513
UMLS:C0178784
ncithesaurus:Organ
element
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.
FMA:86140
uberon
organ region with fixed fiat boundary
organ segment
segment of organ
UBERON:0000063
organ subunit
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.
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.
FMA:86140
3
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.
FMA:86140
1
organ region with fixed fiat boundary
FMA:86140
organ segment
FMA:86140
segment of organ
FMA:86140
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
AAO:0011124
BIRNLEX:16
EFO:0000635
FMA:82472
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
A multicellular structure that is a part of an organ.
cardinal organ part
FMA:82472
regional part of organ
BIRNLEX:16
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
EHDAA2:0001606
EHDAA:1568
EHDAA:2219
EMAPA:16737
FMA:265130
OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA
VHOG:0000393
uberon
UBERON:0000065
respiratory tract
NCBIBook:NBK10107
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Uberon includes clade-specific subclasses, e.g. nematod larva
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
BTO:0000915
BTO:0000954
EFO:0001303
FBdv:00005336
MIAA:0000400
OGES:000008
ZFS:0000048
larva stage
ammocoete
ammocoete stage
bipinnaria
bipinnaria stage
caterpillar
caterpillar stage
glochidium
glochidium stage
grub
grub stage
leptocephalus
leptocephalus stage
maggot
maggot stage
metacestode
naiad, nymph
naiad, nymph stage
nauplius
nauplius stage
nymph
nymph stage
planula
planula stage
tornaria
trochophore
trochophore stage
veliger
veliger stage
wriggler
wriggler stage
zoea
zoea stage
uberon
larva
UBERON:0000069
larval stage
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
WP
ammocoete
ammocoete stage
bipinnaria
bipinnaria stage
caterpillar
caterpillar stage
glochidium
glochidium stage
grub
grub stage
leptocephalus
leptocephalus stage
maggot
maggot stage
metacestode
BTO:0000859
naiad, nymph
naiad, nymph stage
nauplius
nauplius stage
nymph
nymph stage
planula
planula stage
tornaria
NCBITaxon:10219
trochophore
trochophore stage
veliger
veliger stage
wriggler
wriggler stage
zoea
zoea stage
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
End of the life of an organism.
XAO:0000437
ncit:Death is an outcome
ncit
An section of a respiratory tract.
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
EMAPA:16737
FMA:45660
MA:0000434
uberon
respiratory tract
subdivision of respiratory tract
UBERON:0000072
proximo-distal subdivision of respiratory tract
An section of a respiratory tract.
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
MA
respiratory tract
MA:0000434
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Melissa Haendel
2009-06-18T09:00:04Z
BIRNLEX:1157
NCIT:C13040
UMLS:C1518256
part of nervous system
uberon
UBERON:0000073
regional part of nervous system
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
BIRNLEX:1157
UMLS:C1518256
ncithesaurus:Nervous_System_Part
part of nervous system
BIRNLEX:1157
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
UBERON:0010322
FMA:85544
NCIT:C34076
UMLS:C1519343
galen:ComplexSkeletalStructure
skeletal system subdivision
uberon
skeletal system part
UBERON:0000075
subdivision of skeletal system
cjm
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
UBERONREF:0000003
UMLS:C1519343
ncithesaurus:Skeletal_System_Part
skeletal system subdivision
FMA:85544
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
EHDAA2:0001968
EHDAA:1494
EHDAA:350
EHDAA:4784
EHDAA:4790
EHDAA:4796
EHDAA:7860
EMAPA:16096
FMA:87656
NCIT:C34309
UMLS:C1515087
surface (external) ectoderm
surface ectoderm
uberon
UBERON:0000076
external ectoderm
EHDAA2
EHDAA2
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
MGI:anna
MP:0012532
UMLS:C1515087
ncithesaurus:Surface_Ectoderm
surface ectoderm
MP:0012532
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
uberon
UBERON:0000077
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the endoderm and the mesoderm.
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
uberon
UBERON:0000078
mixed ectoderm/mesoderm/endoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
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]
cjm
2009-07-30T05:19:13Z
membrane
FMA:7145
membrane of organ
uberon
UBERON:0000094
membrane organ
FMA-def
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]
FMA:7145
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
FMA:73750
lung vascular network
pulmonary vasculature
vascular network of lung
vasculature of lung
uberon
UBERON:0000102
lung vasculature
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
GOC:GO
lung vascular network
OBOL:automatic
pulmonary vasculature
FMA:73750
vascular network of lung
OBOL:automatic
vasculature of lung
OBOL:automatic
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
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.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
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]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
NCIT:C12601
PdumDv:0000100
VHOG:0000745
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote 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]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
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.
BILS:0000107
BilaDO:0000006
EFO:0001290
FBdv:00000054
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
PdumDv:0000200
XAO:1000004
ZFS:0000046
uberon
UBERON:0000107
cleavage stage
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.
GO:0040016
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
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
WBls:0000005
XAO:1000003
ZFS:0000045
uberon
UBERON:0000108
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.
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.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
WBls:0000010
XAO:1000005
ZFS:0000047
uberon
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
UBERON:0000109
gastrula stage
BILS
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.
GO:0007369
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
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.
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000017
XAO:1000006
uberon
UBERON:0000110
neurula stage
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.
GO:0001841
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
uberon
segmentation stage
UBERON:0000111
organogenesis stage
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
BILS:0000112
BTO:0002168
EFO:0001300
EV:0300051
MmusDv:0000043
OGES:000009
XAO:1000010
XtroDO:0000083
ZFS:0000051
immature stage
juvenile stage
uberon
subadult stage
UBERON:0000112
sexually immature stage
The stage of being a sexually immature adult animal[XAO:1000010].
XAO:1000010
immature stage
VHOG:FB
juvenile stage
XAO:1000010
subadult stage
The stage of being a sexually mature adult animal.
adult stage
BILS:0000113
EV:0300064
EV:0300070
MIAA:0000403
MmusDv:0000110
OGES:000026
OGES:000027
XAO:1000093
ZFS:0000044
uberon
UBERON:0000113
post-juvenile adult stage
The stage of being a sexually mature adult animal.
the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
EMAPA:35521
FMA:27533
MA:0001782
connective tissue of lung
pulmonary interstitium
uberon
lung interstitial tissue
lung interstitium
pulmonary connective tissue
pulmonary interstitial tissue
UBERON:0000114
lung connective tissue
the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin
ISBN:0-683-40008-8
MGI:anna
MP:0002276
connective tissue of lung
OBOL:automatic
pulmonary interstitium
FMA:27533
lung interstitial tissue
MA:0001782
pulmonary connective tissue
EMAPA:35521
The epithelial layer of the lung.
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
BTO:0001653
EMAPA:32860
MA:0001783
epithelial tissue of lung
epithelium of lung
lung epithelial tissue
uberon
pulmonary epithelium
UBERON:0000115
lung epithelium
The epithelial layer of the lung.
MP:0006382
epithelial tissue of lung
OBOL:automatic
epithelium of lung
OBOL:automatic
lung epithelial tissue
OBOL:automatic
pulmonary epithelium
BTO:0001653
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
EMAPA:37946
FMA:12224
segment of tracheobronchial tree
respiratory conducting tube
segment of tracheobronchial tree
tracheobronchial tree segment
uberon
airway
UBERON:0000117
respiratory tube
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
GO:0030323
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
GO
EMAPA:37946
MA:th
segment of tracheobronchial tree
FMA:12224
respiratory conducting tube
MP:0004391
segment of tracheobronchial tree
FMA:12224
tracheobronchial tree segment
FMA:12224
Structure derived from foregut that becomes a lung[GO].
clarify successors - include bronchi?
BTO:0001643
EHDAA2:0004089
NCIT:C34260
NCIT:C34282
UMLS:C1514420
UMLS:C1514897
uberon
gemma pulmonalis
gemma respiratoria
lung bud
primary lung bud
respiratory diverticulum
UBERON:0000118
lung bud
GO:0060441
EHDAA2
Structure derived from foregut that becomes a lung[GO].
GO:0060431
UMLS:C1514420
ncithesaurus:Primary_Bronchial_Bud
UMLS:C1514897
ncithesaurus:Respiratory_Diverticulum
gemma pulmonalis
gemma respiratoria
lung bud
primary lung bud
GO:0060572
respiratory diverticulum
uberon
UBERON:0000153
anterior region of body
lexical
uberon
UBERON:0000154
posterior region of body
lexical
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
anatomical ostium
ostium
FMA:3724
anatomical orifice
hilum
uberon
UBERON:0000161
orifice
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
FMA:3724
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
FMA
anatomical ostium
FMA:3724
anatomical orifice
FMA:3724
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
oral
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
AAO:0010355
BTO:0001090
BTO:0004698
CALOHA:TS-1315
EFO:0000825
EHDAA2:0001326
EHDAA:542
EMAPA:16262
FBbt:00003126
FMA:49184
GAID:75
MA:0000341
MA:0002474
MAT:0000038
MESH:D009055
MIAA:0000038
OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
TADS:0000040
TAO:0000547
TAO:0000590
TGMA:0000131
VHOG:0000280
VHOG:0000812
XAO:0003029
ZFA:0000547
ZFA:0000590
galen:Mouth
regio oralis
adult mouth
uberon
cavital oralis
cavitas oris
cavum oris
mouth cavity
oral region
oral vestibule
rima oris
stoma
stomatodaeum
trophic apparatus
vestibule of mouth
vestibulum oris
UBERON:0000165
mouth
the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts
exceptions in some taxa
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
2012-06-20
AAO:0010355
AAO
AAO:BJB
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]
2012-09-17
VHOG:0000812
VHOG
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
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
FMA
regio oralis
BTO:0004698
regio oralis
FMA:49184
FMA:TA
cavital oralis
cavitas oris
BTO:0001090
cavum oris
BTO:0001090
mouth cavity
BTO:0001090
oral region
EHDAA2:0001326
oral vestibule
BTO:0001090
rima oris
BTO:0001090
stomatodaeum
VHOG:0000812
trophic apparatus
vestibule of mouth
BTO:0001090
vestibulum oris
BTO:0001090
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
FMA:59806
oral fissure
oral orifice
uberon
mouth
oral part of face
UBERON:0000166
oral opening
FMA
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
2012-09-17
VHOG:0000280
VHOG
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
oral fissure
FMA:59806
oral orifice
FMA:59806
mouth
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
AAO:0000053
AAO:0000960
BSA:0000107
CALOHA:TS-1315
EFO:0001975
EHDAA2:0001324
EHDAA:6970
EMAPA:17411
EMAPA:18399
EV:0100057
FMA:20292
HAO:0000669
NCIT:C12421
TAO:0001027
TGMA:0000102
UMLS:C0226896
VHOG:0000188
WBbt:0005255
XAO:0000126
ZFA:0001027
buccal cavity
cavity of mouth
uberon
bucca
UBERON:0000167
oral cavity
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
ISBN:0073040584
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
2012-06-20
AAO:0000960
AAO
AAO:EJS
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
2012-09-17
VHOG:0000188
VHOG
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
2012-09-17
VHOG:0000188
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
UMLS:C0226896
ncithesaurus:Oral_Cavity
buccal cavity
FMA:20292
ISBN:0073040584
1
1
1
1
The pair of anatomical structures comprised of a left lung and right lung.
FMA:68877
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
lungs
lungs pair
pulmones
set of lungs
uberon
UBERON:0000170
pair of lungs
FMA-abduced
The pair of anatomical structures comprised of a left lung and right lung.
pulmones
FMA:68877
FMA:TA
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
EMAPA:17607
SPD:0000428
TGMA:0001247
apparatus respiratorius organ
breathing organ
organ of apparatus respiratorius
organ of respiratory system
respiratory organ
respiratory system organ
uberon
gas exchange organ
UBERON:0000171
respiration organ
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
GO:0007585
apparatus respiratorius organ
OBOL:automatic
organ of apparatus respiratorius
OBOL:automatic
organ of respiratory system
OBOL:automatic
respiratory system organ
OBOL:automatic
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
AAO:0000046
BTO:0000089
CALOHA:TS-0079
EFO:0000296
EHDAA2:0000176
EHDAA:418
EMAPA:16332
ENVO:02000027
EV:0100047
FMA:9670
GAID:965
MA:0000059
MESH:D001769
MIAA:0000315
NCIT:C12434
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
TAO:0000007
UMLS:C0005767
VHOG:0000224
XAO:0000124
ZFA:0000007
galen:Blood
portion of blood
vertebrate blood
uberon
whole blood
UBERON:0000178
blood
Bgee:AN
A fluid that is composed of blood plasma and erythrocytes.
FMA:9670
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]
2012-08-14
TAO:0000007
TAO
ZFIN:curator
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
2012-06-20
AAO:0000046
AAO
AAO:LAP
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
2012-06-20
AAO:0000046
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]
2012-09-17
VHOG:0000224
VHOG
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
UMLS:C0005767
ncithesaurus:Blood
whole blood
BTO:0000089
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
cjm
2009-04-08T04:38:19Z
CARO:0000081
uberon
blood or blood analog
circulating fluid
UBERON:0000179
haemolymphatic fluid
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
UBERON:0007011
BILA:0000059
BTO:0000128
GAID:1294
MESH:A16.254.270.274
OGEM:000006
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
blastula embryo
uberon
blastosphere
UBERON:0000307
blastula
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.
blastula embryo
BILA:0000059
blastosphere
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.
BTO:0000547
FMA:45653
digestive tract wall
wall of digestive tract
wall of gut
uberon
wall of alimentary tract
UBERON:0000328
gut wall
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
wall of gut
FMA:45653
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]
mucosal
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
AEO:0000199
BTO:0000886
CALOHA:TS-2031
EHDAA2_RETIRED:0003234
EV:0100382
FMA:85355
FMA:85358
GAID:297
MESH:D009092
NCIT:C13166
OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA
UMLS:C0026724
galen:Mucosa
mucosa of organ
mucosa of organ part
mucosal region
mucous membrane
organ mucosa
uberon
region of mucosa
tunica mucosa
UBERON:0000344
mucosa
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
FMA
UMLS:C0026724
ncithesaurus:Mucosa
mucosa of organ
FMA:85355
mucosa of organ part
FMA:85358
mucosal region
FMA:85358
mucous membrane
FMA:85355
organ mucosa
FMA:85355
region of mucosa
FMA:85358
tunica mucosa
tunica mucosa
BTO:0000886
A mucosa that is part of a pharynx [Automatically generated definition].
UBERON:0003344
BTO:0001047
EMAPA:26957
FMA:55031
MA:0003143
mucosa of organ of pharynx
mucosa of pharynx
mucous membrane of pharynx
organ mucosa of pharynx
pharynx mucosa
pharynx mucosa of organ
pharynx mucous membrane
pharynx organ mucosa
tunica mucosa pharyngea
tunica mucosa pharyngis
uberon
mucous membrane of the pharynx
UBERON:0000355
pharyngeal mucosa
A mucosa that is part of a pharynx [Automatically generated definition].
OBOL:automatic
mucosa of organ of pharynx
OBOL:automatic
mucosa of pharynx
OBOL:automatic
mucous membrane of pharynx
FMA:55031
mucous membrane of pharynx
OBOL:automatic
organ mucosa of pharynx
OBOL:automatic
pharynx mucosa
OBOL:automatic
pharynx mucosa of organ
OBOL:automatic
pharynx mucous membrane
OBOL:automatic
pharynx organ mucosa
OBOL:automatic
tunica mucosa pharyngea
FMA:55031
FMA:TA
mucous membrane of the pharynx
BTO:0001047
A mucosa that is part of a respiratory airway.
BTO:0001390
FMA:7471
mucosa of organ of trachea
mucosa of organ of windpipe
mucosa of trachea
mucosa of windpipe
mucous membrane of trachea
mucous membrane of windpipe
organ mucosa of trachea
organ mucosa of windpipe
trachea mucosa
trachea mucosa of organ
trachea mucous membrane
trachea organ mucosa
tracheal mucous membrane
tunica mucosa (tracheae)
tunica mucosa tracheae
windpipe mucosa
windpipe mucosa of organ
windpipe mucous membrane
windpipe organ mucosa
uberon
UBERON:0000379
tracheal mucosa
A mucosa that is part of a respiratory airway.
OBOL:automatic
mucosa of organ of trachea
OBOL:automatic
mucosa of organ of windpipe
OBOL:automatic
mucosa of trachea
OBOL:automatic
mucosa of windpipe
OBOL:automatic
mucous membrane of trachea
FMA:7471
mucous membrane of trachea
OBOL:automatic
mucous membrane of windpipe
OBOL:automatic
organ mucosa of trachea
OBOL:automatic
organ mucosa of windpipe
OBOL:automatic
trachea mucosa
OBOL:automatic
trachea mucosa of organ
OBOL:automatic
trachea mucous membrane
OBOL:automatic
trachea organ mucosa
OBOL:automatic
tracheal mucous membrane
FMA:7471
tunica mucosa (tracheae)
FMA:7471
tunica mucosa tracheae
FMA:7471
FMA:TA
windpipe mucosa
OBOL:automatic
windpipe mucosa of organ
OBOL:automatic
windpipe mucous membrane
OBOL:automatic
windpipe organ mucosa
OBOL:automatic
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
AAO:0000307
BILA:0000088
BTO:0001369
BTO:0001485
EFO:0000801
EMAPA:35578
FBbt:00005069
FMA:72954
MA:0002888
MAT:0000025
MIAA:0000025
VSAO:0000033
XAO:0004042
muscle system
muscle system of body
muscular system
musculature system
set of all muscles
set of muscles of body
vertebrate muscular system
uberon
muskelsystem
UBERON:0000383
musculature of body
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
VSAO:0000033
Anatomical system that consists of the muscles of the body.[VSAO]
2012-08-14
VSAO:0000033
VSAO
VSAO:curator
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
MA
muscular system
FMA:72954
musculature system
BILA:0000088
set of all muscles
FMA:72954
set of muscles of body
FMA:72954
vertebrate muscular system
BTO:0001369
muskelsystem
BTO:0001485
Tissue that surrounds the lens nucleus
BTO:0001632
CALOHA:TS-0542
FMA:58970
MESH:A09.371.509.225
cortex of lens
uberon
UBERON:0000389
lens cortex
Tissue that surrounds the lens nucleus
cortex of lens
FMA:58970
The core of the crystalline lens, surrounded by the cortex.
BTO:0001633
FMA:58971
MESH:A09.371.509.670
nucleus of lens
uberon
UBERON:0000390
lens nucleus
The core of the crystalline lens, surrounded by the cortex.
BTO:0001633
nucleus of lens
FMA:58971
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
BTO:0001837
EMAPA:37950
FMA:62889
uberon
UBERON:0000409
serous gland
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
MP:0008052
EMAPA:37950
MA:th
An anatomical wall that is part of an artery [Automatically generated definition].
BTO:0002009
FMA:14155
galen:ArterialWall
arterial wall
wall of artery
uberon
UBERON:0000415
artery wall
An anatomical wall that is part of an artery [Automatically generated definition].
OBOL:automatic
arterial wall
FMA:14155
wall of artery
FMA:14155
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
UBERON:0006540
secretion
AEO:0001005
BTO:0002977
BTO:0002979
EMAPA:36535
FMA:9675
MA:0002504
MESH:D012634
NCIT:C34062
UMLS:C1516992
galen:Secretion
bodily secretion
exocrine gland fluid/secretion
secreted substance
uberon
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland secretion
external secretion
UBERON:0000456
secretion of exocrine gland
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
BTO
secretion
FMA:9675
UMLS:C1516992
ncithesaurus:Exocrine_Gland_Fluid_or_Secretion
bodily secretion
MESH:D012634
exocrine gland fluid/secretion
MA:0002504
external secretion
BTO:0002977
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.
AAO:0010839
AEO:0000004
BILA:0000004
CALOHA:TS-2101
CARO:0000004
EHDAA2:0003004
EMAPA:35178
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
NCIT:C13236
SPD:0000008
TAO:0001487
TGMA:0001824
VHOG:0001726
XAO:0004001
ZFA:0001487
galen:BodySubstance
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
uberon
UBERON:0000463
organism substance
this relationship may be too strong and may be weakened in future
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.
body fluid or substance
MA:0002450
body substance
FMA:9669
organism substance
CARO:0000004
portion of body substance
FMA:9669
portion of organism substance
ZFA:0001487
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.
lumen
space
AAO:0010110
AEO:0000005
BILA:0000005
CARO:0000005
EHDAA2:0003005
FBbt:00007017
FMA:5897
HAO:0000005
NCIT:C94478
TAO:0001668
TGMA:0001825
UMLS:C0524461
VHOG:0001728
XAO:0003190
ZFA:0001643
lumen space
uberon
anatomical spaces
UBERON:0000464
anatomical space
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.
UMLS:C0524461
ncithesaurus:Lumen_Space
anatomical spaces
ZFA:0001643
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
CARO:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
VHOG:0001727
immaterial physical anatomical entity
uberon
UBERON:0000466
immaterial anatomical entity
Anatomical entity that has no mass.
immaterial physical anatomical entity
FMA:67112
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
AAO:0000007
AEO:0000011
BILA:0000011
BIRNLEX:14
BSA:0000049
CALOHA:TS-2088
CARO:0000011
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NCIT:C12919
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
TAO:0001439
TGMA:0001831
UMLS:C0460002
VHOG:0001725
WBbt:0005746
WBbt:0005763
XAO:0003002
ZFA:0001439
galen:AnatomicalSystem
body system
connected anatomical system
organ system
uberon
anatomical systems
UBERON:0000467
anatomical system
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
CARO:0000011
system
GO:0048731
UMLS:C0460002
ncithesaurus:Organ_System
body system
BIRNLEX:14
connected anatomical system
CARO:0000011
anatomical systems
ZFA:0001439
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
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BIRNLEX:18
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
animal
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
Anatomical structure that is an individual member of a species and consists of more than one cell.
CARO:0000012
organism
FBbt:00000001
VHOG:0000671
WBbt:0007833
multi-cellular organism
CARO:0000012
animal
BTO:0000042
Koerper
BTO:0001489
body
AEO:0000103
BIRNLEX:18
FMA:256135
NCIT:C13041
whole body
BTO:0001489
whole organism
FBbt:00000001
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
AAO:0010053
AEO:0000032
BILA:0000032
BIRNLEX:7
CALOHA:TS-2084
CARO:0000032
EFO:0000808
EHDAA2:0003032
EMAPA:36031
FBbt:00007009
FMA:7153
HAO:0000032
MA:0002433
MAT:0000293
MESH:D001829
MIAA:0000293
NCIT:C32221
OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA
TAO:0001308
TGMA:0001840
UMLS:C0229962
VHOG:0001758
XAO:0003013
ZFA:0001308
galen:BodyPart
anatomic region
uberon
body part
body region
cardinal body part
UBERON:0000475
organism subdivision
CARO
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.
CARO:0000032
CARO:DOS
UMLS:C0229962
ncithesaurus:Body_Part
anatomic region
MA:0002433
body region
FMA:7153
cardinal body part
FMA:7153
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
uberon
acellular anatomical structures
UBERON:0000476
acellular anatomical structure
CARO
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
acellular anatomical structures
ZFA:0000382
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
AAO:0010009
AEO:0000041
BILA:0000041
CARO:0000041
EHDAA2:0003041
FBbt:00007277
FMA:49443
HAO:0000041
TADS:0000605
TAO:0001478
TGMA:0001842
VHOG:0001737
XAO:0003160
ZFA:0001478
uberon
UBERON:0000477
anatomical cluster
Anatomical group that has its parts adjacent to one another.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
AAO:0010020
AEO:0000042
BILA:0000042
CALOHA:TS-2119
CARO:0000042
EHDAA2:0003042
EHDAA:46
FBbt:00005835
FMA:85537
HAO:0000042
NCIT:C34055
TAO:0000020
TGMA:0001843
UMLS:C1282438
VHOG:0000292
XAO:0004005
ZFA:0000020
extra-embryonic structure
uberon
extraembryonic structures
extraembryonic tissue
UBERON:0000478
see also conceptus extraembryonic component in EHDAA2.
extraembryonic structure
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
CARO:DOS
UMLS:C1282438
ncithesaurus:Extraembryonic_Structure
extraembryonic structures
ZFA:0000020
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
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
BIRNLEX:19
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
tissue
CARO
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.
CARO:0000043
UMLS:C0040300
ncithesaurus:Tissue
portion of tissue
CARO:0000043
simple tissue
AEO:0000043
Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]
AAO:0010008
AEO:0000054
BILA:0000054
CARO:0000054
EHDAA2:0003054
FBbt:00007276
HAO:0000054
TAO:0001512
TGMA:0001846
VHOG:0001724
XAO:0003001
ZFA:0001512
uberon
UBERON:0000480
anatomical group
Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
CARO:0000054
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.
AAO:0010048
AEO:0000055
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
multi-tissue structures
UBERON:0000481
multi-tissue structure
CARO
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.
CARO:0000055
multi-tissue structures
ZFA:0001488
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]
epithelial
AAO:0000144
AAO:0010055
AEO:0000066
BILA:0000066
BTO:0000416
CALOHA:TS-0288
CARO:0000066
EHDAA2:0003066
EMAPA:32738
FBbt:00007005
FMA:9639
GAID:402
HAO:0000066
MA:0003060
MESH:D004848
NCIT:C12710
TAO:0001486
UMLS:C0014609
VHOG:0000387
XAO:0003045
ZFA:0001486
epithelial tissue
portion of epithelium
uberon
UBERON:0000483
epithelium
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]
2012-09-17
VHOG:0000387
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
UMLS:C0014609
ncithesaurus:Epithelium
portion of epithelium
FMA:9639
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
AAO:0010064
AEO:0000067
BILA:0000067
CARO:0000067
EHDAA2:0003067
FMA:45566
HAO:0000067
NCIT:C33553
TAO:0001497
UMLS:C0836134
XAO:0004009
ZFA:0001497
epithelium simplex cuboideum
uberon
simple cuboidal epithelia
UBERON:0000484
simple cuboidal epithelium
Unilaminar epithelium that consists of a single layer of cuboidal cells.
UMLS:C0836134
ncithesaurus:Simple_Cuboidal_Epithelium
simple cuboidal epithelia
ZFA:0001497
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
columnar epithelium
columnar epithlium
AAO:0010063
AEO:0000068
BILA:0000068
CARO:0000068
EHDAA2_RETIRED:0003068
FBbt:00007027
FMA:45567
HAO:0000068
NCIT:C33552
TAO:0001496
UMLS:C0836135
XAO:0004008
ZFA:0001496
epithelium simplex columnare
simple columnar epithelium
uberon
simple columnar epithelia
UBERON:0000485
simple columnar epithelium
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
FMA:FMA
columnar epithelium
EHDAA2:0003068
columnar epithlium
AEO:0000068
UMLS:C0836135
ncithesaurus:Simple_Columnar_Epithelium
simple columnar epithelia
ZFA:0001496
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
AAO:0010059
AEO:0000069
BILA:0000069
BTO:0002074
CARO:0000069
EHDAA2:0003069
FMA:45562
HAO:0000069
NCIT:C33622
TAO:0001494
UMLS:C0682575
XAO:0004006
ZFA:0001494
stratified epithelium
uberon
laminated epithelium
UBERON:0000486
multilaminar epithelium
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]
FMA:FMA
Epithelium that consists of more than one layer of epithelial cells.[CARO]
2012-06-20
CARO:0000069
CARO
FMA:45562
UMLS:C0682575
ncithesaurus:Stratified_Epithelium
laminated epithelium
BTO:0002074
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
AAO:0010066
AEO:0000070
BILA:0000070
BTO:0002073
CARO:0000070
EHDAA2:0003070
FMA:45565
HAO:0000070
NCIT:C13178
TAO:0001498
UMLS:C0836133
XAO:0004010
ZFA:0001498
epithelium simplex squamosum
uberon
simple squamous epithelia
UBERON:0000487
simple squamous epithelium
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
FMA:45565
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
2012-06-20
CARO:0000070
CARO
FMA:45565
UMLS:C0836133
ncithesaurus:Simple_Squamous_Epithelium
simple squamous epithelia
ZFA:0001498
Epithelium that consists of epithelial cells not arranged in one ore more layers.
AAO:0010057
AEO:0000071
BILA:0000071
CARO:0000071
EHDAA2:0003071
FMA:61741
HAO:0000071
TAO:0001493
XAO:0004004
ZFA:0001493
heterogenous epithelium
uberon
atypical epithelia
UBERON:0000488
atypical epithelium
Epithelium that consists of epithelial cells not arranged in one ore more layers.
atypical epithelia
ZFA:0001493
Compound organ that contains one or more macroscopic anatomical spaces.
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
AAO:0010016
AEO:0000072
BILA:0000072
CARO:0000072
EHDAA2:0003072
FMA:55671
HAO:0000072
TAO:0001490
TGMA:0001857
VHOG:0001730
XAO:0003165
ZFA:0001490
cavitated organ
uberon
cavitated compound organs
UBERON:0000489
cavitated compound organ
Compound organ that contains one or more macroscopic anatomical spaces.
cavitated organ
FMA:55671
cavitated compound organs
ZFA:0001490
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
AAO:0010062
AEO:0000073
BILA:0000073
BTO:0002073
CARO:0000073
EHDAA2:0003073
FMA:45561
HAO:0000073
NCIT:C33554
TAO:0001495
UMLS:C0682574
XAO:0004007
ZFA:0001495
simple epithelium
uberon
unilaminar epithelia
UBERON:0000490
unilaminar epithelium
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
FMA:45561
Epithelium that consists of a single layer of epithelial cells.[CARO]
2012-06-20
CARO:0000073
CARO
FMA:45561
UMLS:C0682574
ncithesaurus:Simple_Epithelium
simple epithelium
FMA:45561
unilaminar epithelia
ZFA:0001495
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
EMAPA:35862
FMA:259209
MA:0000022
thorax
uberon
anterior subdivision of trunk
upper body
upper trunk
UBERON:0000915
thoracic segment of trunk
FMA
Subdivision of trunk that lies between the head and the abdomen.
thorax
MA:0000022
upper trunk
FMA:259209
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.
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
AAO:0011035
AEO:0000169
BILA:0000056
BSA:0000039
BTO:0000379
CALOHA:TS-0229
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
MAT:0000226
MESH:D004622
MIAA:0000019
NCIT:C28147
OGEM:000001
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
UMLS:C0013935
VHOG:0001766
XAO:0000113
ZFA:0000103
embryonic organism
uberon
developing organism
developmental tissue
UBERON:0000922
embryo
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.
BTO:0000379
FB:FBrf0039741
FB:FBrf0041814
GO:0009790
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
ZFA
UMLS:C0013935
ncithesaurus:Embryo
embryonic organism
BILA:0000056
developing organism
BILA:0000056
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
embryonic tissue
AAO:0000480
BILA:0000035
BTO:0000556
EMAPA:36033
FBbt:00000110
FMA:69069
GAID:1303
MESH:A16.254.425
NCIT:C12950
NCIT:C54105
TAO:0001122
UMLS:C0920502
UMLS:C1708239
VHOG:0001223
XAO:0003011
ZFA:0001122
germinal layer
primary germ layer
uberon
embryonic germ layer
embryonic germ layers
UBERON:0000923
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]
germ layer
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0001223
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
embryonic tissue
FMA:69069
UMLS:C0920502
ncithesaurus:Embryonic_Tissue
UMLS:C1708239
ncithesaurus:Germinal_Layer
germinal layer
ncithesaurus:Germinal_Layer
primary germ layer
GO:0001704
ZFA:0001122
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]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
ectodermal
AAO:0000137
BILA:0000036
BTO:0000315
CALOHA:TS-0216
EFO:0000414
EHDAA2:0000428
EMAPA:16069
EV:0100003
FBbt:00000111
FMA:69070
GAID:1304
MAT:0000155
MAT:0000173
MESH:A16.254.425.273
MIAA:0000173
NCIT:C12703
TAO:0000016
UMLS:C0013574
VHOG:0000153
XAO:0000001
ZFA:0000016
embryonic ectoderm
uberon
UBERON:0000924
ectoderm
Bgee:AN
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]
2012-06-20
AAO:0000137
AAO
AAO:EJS
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000153
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
UMLS:C0013574
ncithesaurus:Ectoderm
embryonic ectoderm
VHOG:0000153
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
endodermal
AAO:0000139
BILA:0000038
BTO:0000800
CALOHA:TS-0273
EFO:0002545
EHDAA2:0000436
EMAPA:16062
EV:0100005
FBbt:00000125
FMA:69071
GAID:1305
MAT:0000175
MESH:A16.254.425.407
MIAA:0000175
NCIT:C12706
TAO:0000017
UMLS:C0014144
VHOG:0000154
XAO:0000090
ZFA:0000017
uberon
entoderm
UBERON:0000925
endoderm
Bgee:AN
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000154
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
UMLS:C0014144
ncithesaurus:Endoderm
entoderm
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
mesodermal
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
UBERON:0003263
AAO:0000304
BILA:0000037
BTO:0000839
CALOHA:TS-0623
EFO:0001981
EHDAA2:0001128
EHDAA:124
EHDAA:160
EHDAA:183
EMAPA:16083
EV:0100006
FBbt:00000126
FMA:69072
GAID:522
MAT:0000174
MESH:A16.254.425.660
MIAA:0000174
NCIT:C12750
TAO:0000041
UMLS:C0025485
VHOG:0000152
XAO:0000050
ZFA:0000041
uberon
embryonic mesoderm
entire mesoderm
mesodermal mantle
UBERON:0000926
mesoderm
sometimes not considered primary
Bgee:AN
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
2012-06-20
AAO:0000304
AAO
AAO:EJS
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000152
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
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
UMLS:C0025485
ncithesaurus:Mesoderm
embryonic mesoderm
VHOG:0000152
entire mesoderm
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
stomodeal
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.
stomodeal-hypophyseal primordium
BTO:0004224
EHDAA2:0001929
EMAPA:16263
FBbt:00000439
FMA:295846
NCIT:C34306
TAO:0001290
TGMA:0000135
UMLS:C1514977
XAO:0000269
ZFA:0001290
mouth primordium
primitive oral cavity
stomatodeum
stomodaeum
uberon
mouth pit
oral ectoderm
oral pit
UBERON:0000930
stomodeum
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.
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
2012-08-14
TAO:0001290
TAO
ZFIN:curator
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
MP:0012522
NCBITaxon:40674
stomodeal-hypophyseal primordium
XAO:0000269
UMLS:C1514977
ncithesaurus:Stomodeum
mouth primordium
XAO:0000269
primitive oral cavity
stomatodeum
mouth pit
EMAPA:16263
oral ectoderm
ZFA:0001290
ZFIN:ZDB-PUB-100726-23
oral pit
EMAPA:16263
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
cardiac
AAO:0010210
BILA:0000020
BTO:0000562
CALOHA:TS-0445
EFO:0000815
EHDAA2:0000738
EHDAA:420
EMAPA:16105
EV:0100018
FMA:7088
GAID:174
MA:0000072
MAT:0000036
MESH:D006321
MIAA:0000036
NCIT:C12727
OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA
TAO:0000114
UMLS:C0018787
VHOG:0000276
XAO:0000064
ZFA:0000114
galen:Heart
chambered heart
vertebrate heart
branchial heart
uberon
Herz@de
cardium
UBERON:0000948
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
heart
MA
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
2012-08-14
TAO:0000114
TAO
ZFIN:curator
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
2012-06-20
AAO:0010210
AAO
AAO:BJB
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
2012-06-20
AAO:0010210
AAO
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
2012-09-17
VHOG:0000276
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
UMLS:C0018787
ncithesaurus:Heart
chambered heart
branchial heart
Herz@de
BTO:0000562
cardium
EMAPA:16105
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
AAO:0010478
ABA:Brain
BAMS:Br
BAMS:Brain
BILA:0000135
BIRNLEX:796
BTO:0000142
CALOHA:TS-0095
DHBA:10155
EFO:0000302
EHDAA2:0000183
EHDAA:2641
EHDAA:6485
EMAPA:16894
EV:0100164
FBbt:00005095
FMA:50801
GAID:571
HBA:4005
MA:0000168
MAT:0000098
MBA:8
MBA:997
MESH:D001921
MIAA:0000098
NCIT:C12439
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
PBA:3999
TAO:0000008
UMLS:C0006104
UMLS:C1269537
VHOG:0000157
XAO:0000010
ZFA:0000008
galen:Brain
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
uberon
encephalon
suprasegmental levels of nervous system
suprasegmental structures
synganglion
the brain
UBERON:0000955
brain
GO
FMA
Bgee:AN
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].
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
2012-08-14
TAO:0000008
TAO
ZFIN:curator
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
2012-06-20
AAO:0010478
AAO
AAO:BJB
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000157
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
UMLS:C0006104
BIRNLEX:796
UMLS:C0006104
ncithesaurus:Brain
UMLS:C1269537
BIRNLEX:796
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
BIRNLEX:796
encephalon
BTO:0000142
suprasegmental levels of nervous system
NeuroNames:21
suprasegmental structures
NeuroNames:21
the brain
NeuroNames:21
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
corneal
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
AAO:0010344
BTO:0000286
CALOHA:TS-0171
EFO:0000377
EHDAA2:0000316
EHDAA:10199
EMAPA:17161
EV:0100341
FMA:58238
GAID:892
MA:0000266
MESH:D003315
NCIT:C12342
OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA
TAO:0000640
UMLS:C0010031
VHOG:0000164
XAO:0000180
ZFA:0000640
cornea of camera-type eye
uberon
corneas
tunica cornea
UBERON:0000964
cornea
XAO
MA
MA
FMA-isa
definitional
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
ISBN:0-683-40008-8
MESH:A09.371.060.217
MP:0001312
UMLS:C0010031
ncithesaurus:Cornea
cornea of camera-type eye
GO:0061303
corneas
ZFA:0000640
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
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]
This class excludes compound eye corneal lenses.
AAO:0010348
BTO:0000723
CALOHA:TS-0545
EHDAA:9057
EMAPA:17838
EV:0100343
FMA:58241
MA:0000275
MAT:0000141
MESH:A09.371.509
MIAA:0000141
NCIT:C12743
OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0000975
TAO:0000035
UMLS:C0023317
VHOG:0000169
XAO:0000008
ZFA:0000035
camera-type eye lens
eye lens
lens
lens crystallina
uberon
crystalline lens
lenses
ocular lens
UBERON:0000965
The lens is avascular and nourished by diffusion from the aqueous and vitreous
lens of camera-type eye
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
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]
2012-09-17
VHOG:0000169
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0023317
ncithesaurus:Crystalline_Lens
camera-type eye lens
GO:0002088
eye lens
lens
lens crystallina
crystalline lens
BTO:0000723
lenses
ZFA:0000035
ocular lens
BTO:0000723
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
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]
retinal
AAO:0010352
BAMS:R
BIRNLEX:1153
BTO:0001175
CALOHA:TS-0865
EFO:0000832
EHDAA2:0001627
EHDAA:4757
EMAPA:17168
EV:0100348
FMA:58301
GAID:755
MA:0000276
MAT:0000142
MBA:304325711
MESH:D012160
MIAA:0000142
NCIT:C12343
NIFSTD_RETIRED:birnlex_1156
OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA
TAO:0000152
UMLS:C0035298
UMLS:C1278894
VHOG:0000229
XAO:0000009
ZFA:0000152
inner layer of eyeball
retina of camera-type eye
tunica interna of eyeball
uberon
Netzhaut
retinas
UBERON:0000966
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
retina
EHDAA2
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.
ZFIN:curator
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]
2012-08-14
TAO:0000152
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000229
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0035298
BIRNLEX:1153
UMLS:C0035298
ncithesaurus:Retina
UMLS:C1278894
BIRNLEX:1153
retina of camera-type eye
GO:0060041
Netzhaut
BTO:0001175
retinas
ZFA:0000152
An organ that detects light.
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)
ocular
optic
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,
BILA:0000017
BTO:0000439
CALOHA:TS-0309
EFO:0000827
EV:0100336
FBbt:00005162
GAID:69
MAT:0000140
MESH:D005123
MIAA:0000140
OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
uberon
light-detecting organ
visual apparatus
UBERON:0000970
eye
An organ that detects light.
visual apparatus
EV:0100336
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
cervical
AEO:0000108
BTO:0000420
CALOHA:TS-2045
EFO:0000967
EHDAA2:0003108
EMAPA:35587
FMA:7155
GAID:86
MA:0000024
MAT:0000297
MESH:D009333
MIAA:0000297
NCIT:C13063
OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA
UMLS:C0027530
galen:Neck
uberon
collum
neck (volume)
UBERON:0000974
neck
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
ISBN:9780674021839
UMLS:C0027530
ncithesaurus:Neck
collum
neck (volume)
FMA:7155
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
articulation
joint
AEO:0000182
BTO:0001686
CALOHA:TS-2023
EFO:0000948
EMAPA:35456
FMA:7490
GAID:102
MA:0000319
MAT:0000188
MESH:D007596
MIAA:0000188
NCIT:C13044
OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0003182
TAO:0000367
UMLS:C0022417
VHOG:0001276
VSAO:0000101
XAO:0000171
ZFA:0001596
galen:Joint
uberon
articular joint
joints
UBERON:0000982
skeletal joint
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
GO_REF:0000034
VSAO:0000101
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
2012-08-14
VSAO:0000101
VSAO
PSPUB:0000170
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
2012-08-14
TAO:0000367
TAO
TAO:pem
articulation
VSAO:0000101
joint
FMA:7490
VSAO:0000101
UMLS:C0022417
ncithesaurus:Joint
articular joint
BTO:0001686
joints
ZFA:0001596
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
epidermal
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).
epidermis
skin
AAO:0000143
BTO:0000404
CALOHA:TS-0283
EFO:0000954
EMAPA:17528
EV:0100153
FMA:70596
GAID:932
MA:0000153
MAT:0000154
MESH:D004817
MIAA:0000154
NCIT:C12708
TAO:0000105
UMLS:C0014520
VHOG:0000077
XAO:0000028
ZFA:0000105
vertebrate epidermis
uberon
UBERON:0001003
skin epidermis
The outer epithelial layer of the skin that is superficial to the dermis.
ISBN:0073040584
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]
2012-08-14
TAO:0000105
TAO
ZFIN:curator
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
2012-06-20
AAO:0000143
AAO
AAO:BJB
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
2012-06-20
AAO:0000143
AAO
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
2012-09-17
VHOG:0000077
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
UMLS:C0014520
ncithesaurus:Epidermis
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]
AAO:0000541
BTO:0000203
CALOHA:TS-1319
EFO:0000804
EHDAA2:0001604
EHDAA:2203
EMAPA:16727
EV:0100036
FMA:7158
GAID:78
MA:0000327
MAT:0000030
MESH:D012137
MIAA:0000030
NCIT:C12779
OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
TAO:0000272
UMLS:C0035237
VHOG:0000202
XAO:0000117
ZFA:0000272
apparatus respiratorius
respiratory system
uberon
Atmungssystem
apparatus respiratorius
systema respiratorium
UBERON:0001004
respiratory system
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]
2012-06-20
AAO:0000541
AAO
AAO:BJB
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
2012-09-17
VHOG:0000202
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
UMLS:C0035237
ncithesaurus:Respiratory_System
Atmungssystem
BTO:0000203
apparatus respiratorius
BTO:0000203
systema respiratorium
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
airway
airways
FMA:265130
uberon
UBERON:0001005
respiratory airway
An airway through which respiratory air passes in organisms.
airway
airways
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
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
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:D004064
MIAA:0000018
TADS:0000170
TAO:0000339
WBbt:0005748
XAO:0000125
ZFA:0000339
galen:DigestiveSystem
ncithesaurus:Digestive_System
uberon
alimentary system
alimentary tract
gastrointestinal system
gut
UBERON:0001007
digestive system
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
FB:gg
NLM:alimentary+system
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
2012-06-20
AAO:0000129
AAO
AAO:BJB
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
MA
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
AAO:0000959
CALOHA:TS-2103
FBbt:00005057
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
VHOG:0001248
uberon
systema cardiovasculare
UBERON:0001009
circulatory system
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].
WBbt coelomocyte currently classified as circulating cell
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]
2012-06-20
AAO:0000959
AAO
AAO:BJB
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]
2012-09-17
VHOG:0001248
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
systema cardiovasculare
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
adipose
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
AAO:0000001
AEO:000020
BTO:0001487
CALOHA:TS-0013
EFO:0000790
EHDAA2:0003120
EMAPA:35112
EV:0100381
FMA:20110
GAID:920
MA:0000009
MAT:0000015
MESH:D000273
MIAA:0000015
NCIT:C12472
OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA
TAO:0002134
UMLS:C0001527
VHOG:0001284
XAO:0003049
ZFA:0005345
galen:FattyTissue
fat
fat tissue
fatty tissue
uberon
adipose
bodyfat
fatty depot
UBERON:0001013
adipose tissue
FMA
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
MESH:A10.165.114
MGI:cwg
MP:0000003
Connective tissue in which fat is stored.[TAO]
2012-08-14
TAO:0002134
TAO
ZFIN:curator
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
2012-06-20
AAO:0000001
AAO
AAO:LAP
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
2012-06-20
AAO:0000001
AAO
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
2012-09-17
VHOG:0001284
VHOG
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
in FMA this is dense irregular connective tissue
FMA
UMLS:C0001527
ncithesaurus:Adipose_Tissue
fat
MA:0000009
adipose
BTO:0001487
bodyfat
BTO:0001487
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.
AAO:0011066
BTO:0000887
EFO:0001949
EMAPA:32715
EMAPA:35577
FMA:32558
MA:0000165
NCIT:C13056
OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA
TAO:0000548
UMLS:C0026845
VSAO:0005038
WBbt:0005737
ZFA:0000548
muscle group
muscles set
musculature
musculi
set of muscles
set of skeletal muscles
uberon
muscle system
muscles
musculature system
UBERON:0001015
musculature
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.
FMA
UMLS:C0026845
ncithesaurus:Muscle
musculi
FMA:32558
FMA:TA
set of muscles
FMA:32558
set of skeletal muscles
MA:0000165
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
nervous
neural
AAO:0000324
BILA:0000079
BIRNLEX:844
BTO:0001484
CALOHA:TS-1313
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:D009420
MIAA:0000026
NCIT:C12755
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
TAO:0000396
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
neurological system
nerve net
uberon
systema nervosum
UBERON:0001016
nervous system
Bgee:AN
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].
BIRNLEX:844
ISBN:0-14-051288-8
ISBN:3110148986
NLM:nervous+system
WB:rynl
ZFIN:curator
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]
2012-08-14
TAO:0000396
TAO
ZFIN:curator
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
2012-06-20
AAO:0000324
AAO
AAO:BJB
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
2012-09-17
VHOG:0000402
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
UMLS:C0027763
ncithesaurus:Nervous_System
neurological system
GO:0050877
nerve net
systema nervosum
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
AAO:0000090
BAMS:CNS
BILA:0000080
BIRNLEX:1099
BTO:0000227
CALOHA:TS-0150
EFO:0000908
EHDAA2:0000225
EHDAA:828
EMAPA:16470
EMAPA:16754
EV:0100163
FBbt:00005094
FMA:55675
GAID:570
MA:0000167
MAT:0000457
MESH:D002490
NCIT:C12438
OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA
TAO:0000012
UMLS:C0927232
VHOG:0000293
XAO:0000215
ZFA:0000012
CNS
systema nervosum centrale
cerebrospinal axis
uberon
neuraxis
UBERON:0001017
central nervous system
FBbt
cjm
Bgee:AN
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.
GO:0021551
Part of the nervous system which includes the brain and spinal cord.[AAO]
2012-06-20
AAO:0000090
AAO
AAO:BJB
The brain and spinal cord. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000012
TAO
ZFIN:curator
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).
BIRNLEX:1099
(...) 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]
2012-09-17
VHOG:0000293
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
UMLS:C0927232
BIRNLEX:1099
UMLS:C0927232
ncithesaurus:Central_Nervous_System
CNS
systema nervosum centrale
FMA:55675
FMA:TA
cerebrospinal axis
FMA:55675
neuraxis
FMA:55675
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
AAO:0000555
BAMS:SEN
BILA:0000099
EFO:0000805
EHDAA2:0003094
EMAPA:16192
FBbt:00007692
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
NLXANAT:090816
TAO:0000282
VHOG:0001674
XAO:0003194
ZFA:0000282
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory subsystem
sensory systems
uberon
organa sensuum
sensory organ system
set of sense organs
UBERON:0001032
sensory system
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
2012-09-17
VHOG:0001674
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
organa sensuum
FMA:75259
FMA:TA
sense organs
FMA:75259
sense organs set
FMA:75259
sensory systems
TAO:0000282
organa sensuum
set of sense organs
FMA:75259
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]
AAO:0011042
BILA:0000085
BTO:0000507
EHDAA2:0000557
EHDAA:520
EMAPA:16548
FBbt:00005379
FMA:45616
MA:0001526
NCIT:C34180
TGMA:0001014
UMLS:C0231051
VHOG:0000285
XAO:0000232
uberon
praeenteron
proenteron
UBERON:0001041
foregut
Anterior subdivision of a digestive tract.
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.
MP:0000474
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]
2012-09-17
VHOG:0000285
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UMLS:C0231051
ncithesaurus:Foregut
praeenteron
proenteron
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
pharynx
AAO:0000967
BTO:0001049
CALOHA:TS-0785
EFO:0000836
EHDAA2:0001458
EHDAA:2947
EMAPA:16706
EV:0100065
FMA:46688
GAID:155
MA:0000432
MESH:A03.867
NCIT:C12425
OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA
TAO:0000056
UMLS:C0031354
VHOG:0000462
XAO:0003227
ZFA:0000056
galen:Pharynx
uberon
UBERON:0001042
Consider generalizing to deuterostome pharynx
chordate pharynx
EHDAA2
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
MESH:A03.867
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
2012-06-20
AAO:0000967
AAO
AAO:EJS
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000056
TAO
ZFIN:curator
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
ZFIN:ZDB-PUB-961014-576
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000462
VHOG
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
2012-06-20
AAO:0000967
AAO
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
2012-06-20
AAO:0000967
AAO
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
2012-09-17
VHOG:0000462
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
MA
pharynx
FMA:46688
UMLS:C0031354
ncithesaurus:Pharynx
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
AEO:0000171
BTO:0001886
EFO:0001652
EHDAA2:0003171
FBbt:00005495
FMA:86589
MAT:0000482
NCIT:C34275
UMLS:C0678727
XAO:0003043
uberon
bud
future organ
placode
primordia
rudiment
UBERON:0001048
primordium
EHDAA2
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
BTO:0001886
FB:DJS
FB:FBrf0089570
UMLS:C0678727
ncithesaurus:Primordium
placode
FBbt:00005495
primordia
XAO:0003043
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
AAO:0010617
BTO:0001057
CALOHA:TS-2371
DHBA:10154
EHDAA2:0001254
EHDAA:2869
EHDAA:908
EMAPA:16164
EMAPA:16757
FMA:293882
MAT:0000069
MIAA:0000069
NCIT:C34226
TAO:0001135
UMLS:C0231024
VHOG:0000307
XAO:0003204
ZFA:0001135
uberon
neural primordium
presumptive central nervous system
tubus neuralis
UBERON:0001049
neural tube
EHDAA2
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
2012-06-20
AAO:0010617
AAO
AAO:JOR
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
2012-09-17
VHOG:0000307
VHOG
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0000307
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
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
GO:0021915
UMLS:C0231024
ncithesaurus:Neural_Tube
tubus neuralis
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.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
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.
FMA:62955
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
A zone of skin that is part of a back [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
EMAPA:36392
FMA:10462
FMA:22985
MA:0000498
back skin
back zone of skin
skin, dorsal region
zone of skin of back
uberon
UBERON:0001068
skin of back
MA
MA
A zone of skin that is part of a back [Automatically generated definition].
OBOL:automatic
back zone of skin
OBOL:automatic
skin, dorsal region
zone of skin of back
OBOL:automatic
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
AAO:0010218
AAO:0010416
BTO:0004696
EFO:0001953
EHDAA2:0000461
EMAPA:18611
FMA:10635
GAID:480
MA:0001929
MESH:D002342
NCIT:C32551
OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA
UMLS:C0007275
VHOG:0000265
XAO:0000345
external carotid
uberon
arteria carotis externa
UBERON:0001070
external carotid artery
https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722
MA
FMA
EHDAA2
FMA
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]
MGI:anna
UMLS:C0007275
ncithesaurus:External_Carotid_Artery
external carotid
AAO:0010218
arteria carotis externa
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
EMAPA:37117
FMA:10665
MA:0002052
NCIT:C53005
UMLS:C0226271
superficial branch of transverse cervical artery
uberon
UBERON:0001071
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
superficial cervical artery
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
EMAPA:37117
MA:th
UMLS:C0226271
ncithesaurus:Superficial_Cervical_Artery
superficial branch of transverse cervical artery
A zone of skin that is part of a head [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
FMA:12166
FMA:24756
MA:0000582
NCIT:C52757
UMLS:C0205029
adult head zone of skin
head skin
head zone of skin
zone of skin of adult head
zone of skin of head
uberon
UBERON:0001084
skin of head
A zone of skin that is part of a head [Automatically generated definition].
OBOL:automatic
UMLS:C0205029
ncithesaurus:Head_Skin
adult head zone of skin
OBOL:automatic
head zone of skin
OBOL:automatic
zone of skin of adult head
OBOL:automatic
zone of skin of head
OBOL:automatic
A zone of skin that is part of a trunk [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
EMAPA:37278
FMA:12167
FMA:23093
MA:0000517
NCIT:C12295
UMLS:C0205031
torso zone of skin
trunk skin
trunk zone of skin
zone of skin of torso
zone of skin of trunk
uberon
UBERON:0001085
skin of trunk
A zone of skin that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37278
MA:th
UMLS:C0205031
ncithesaurus:Skin_of_the_Trunk
torso zone of skin
OBOL:automatic
trunk zone of skin
OBOL:automatic
zone of skin of torso
OBOL:automatic
zone of skin of trunk
OBOL:automatic
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
BTO:0001339
CALOHA:TS-0996
ENVO:02000039
FMA:12277
GAID:265
MA:0002544
MESH:D013582
NCIT:C33718
TAO:0005154
UMLS:C0039097
ZFA:0005154
galen:SynovialFluid
joint fluid
uberon
UBERON:0001090
synovial fluid
FMA
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
2012-08-14
TAO:0005154
TAO
ZFIN:curator
UMLS:C0039097
ncithesaurus:Synovial_Fluid
joint fluid
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
AAO:0010244
AEO:0000141
BTO:0001260
CALOHA:TS-0943
EFO:0000889
EHDAA2:0003141
EMAPA:32717
EV:0100378
FBbt:00003525
FMA:14070
GAID:167
MA:0000166
MAT:0000303
MESH:D009130
MIAA:0000303
NCIT:C12437
OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA
TAO:0005274
UMLS:C1267092
VHOG:0001246
WBbt:0005781
XAO:0000175
ZFA:0005274
galen:SmoothMuscle
galen:SmoothMuscleTissue
involuntary muscle
non-striated muscle
smooth muscle
textus muscularis nonstriatus
visceral muscle
visceral muscle tissue
uberon
textus muscularis levis; textus muscularis nonstriatus
UBERON:0001135
smooth muscle tissue
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].
GO:0006939
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
2012-08-14
TAO:0005274
TAO
ZFIN:curator
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
2012-06-20
AAO:0010244
AAO
AAO:CAM
(...) 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]
2012-09-17
VHOG:0001246
VHOG
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
UMLS:C1267092
ncithesaurus:Smooth_Muscle_Tissue
textus muscularis nonstriatus
FMA:14070
FMA:TA
visceral muscle
visceral muscle tissue
textus muscularis levis; textus muscularis nonstriatus
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
AEO:0000111
BTO:0002422
CALOHA:TS-1183
EHDAA2_RETIRED:0003111
EHDAA:2331
EHDAA:2349
EHDAA:295
EHDAA:6073
EHDAA:640
EHDAA:646
EMAPA:32856
FMA:14074
MA:0000565
NCIT:C33105
UMLS:C0086610
uberon
UBERON:0001136
mesothelium
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
FMA:14074
UMLS:C0086610
ncithesaurus:Mesothelium
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..
dorsal
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
BTO:0001713
CALOHA:TS-2223
EFO:0001405
FMA:14181
GAID:30
MESH:A01.176
NCIT:C13062
OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA
UMLS:C0004600
galen:Back
back
back of body proper
dorsal part of organism
uberon
UBERON:0001137
dorsum
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..
BSPO:0000063
UBERONREF:0000006
UMLS:C0004600
ncithesaurus:Back
back
FMA:14181
back of body proper
FMA:14181
A zone of skin that is part of a neck [Automatically generated definition].
EMAPA:37277
FMA:23021
FMA:23022
MA:0000590
NCIT:C52756
UMLS:C0205030
neck (volume) zone of skin
neck skin
neck zone of skin
zone of skin of neck
zone of skin of neck (volume)
uberon
UBERON:0001417
skin of neck
A zone of skin that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37277
MA:th
UMLS:C0205030
ncithesaurus:Neck_Skin
neck (volume) zone of skin
OBOL:automatic
neck zone of skin
OBOL:automatic
zone of skin of neck
OBOL:automatic
zone of skin of neck (volume)
OBOL:automatic
A zone of skin that is part of a thorax [Automatically generated definition].
EMAPA:37765
FMA:23028
FMA:23029
MA:0000564
thoracic skin
thorax skin
thorax zone of skin
zone of skin of thorax
uberon
upper body skin
UBERON:0001418
skin of thorax
A zone of skin that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37765
MA:th
thorax zone of skin
OBOL:automatic
zone of skin of thorax
OBOL:automatic
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
skeletal
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
AAO:0000566
BTO:0001486
CALOHA:TS-1320
EFO:0000806
EHDAA2:0003168
EMAPA:35773
FMA:23881
MA:0000018
NCIT:C12788
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
TAO:0000434
UMLS:C0037253
VHOG:0001254
VSAO:0000027
XAO:0003060
ZFA:0000434
skeleton system
set of all bones and joints
uberon
Skelettsystem
UBERON:0001434
skeletal system
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
GO_REF:0000034
VSAO:0000027
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
2012-08-14
TAO:0000434
TAO
TAO:wd
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
2012-08-14
VSAO:0000027
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
System that provides physical support to the organism.[AAO]
2012-06-20
AAO:0000566
AAO
AAO:LAP
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]
2012-09-17
VHOG:0001254
VHOG
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
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
GO
UMLS:C0037253
ncithesaurus:Skeletal_System
set of all bones and joints
Skelettsystem
BTO:0001486
FMA:24218
XAO:0000040
head subdivision
uberon
head region
region of head
UBERON:0001444
subdivision of head
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].
facial
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)
BTO:0003369
CALOHA:TS-2216
EMAPA:32763
FMA:24728
GAID:64
HAO:0000316
MA:0002473
MESH:D005145
NCIT:C13071
OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA
UMLS:C0015450
galen:Face
uberon
facia/facies
visage
UBERON:0001456
face
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.
FMA:24728
The area that extends from the median ocellus to the oral foramen[HAO].
HAO:0000316
NCBITaxon:7399
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)
vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf
UMLS:C0015450
ncithesaurus:Face
facia/facies
visage
BTO:0003369
A zone of skin that is part of a lip [Automatically generated definition].
EMAPA:37643
FMA:24764
MA:0001579
NCIT:C12291
UMLS:C0222101
lip skin
lip zone of skin
zone of skin of lip
uberon
skin of lips
UBERON:0001458
skin of lip
A zone of skin that is part of a lip [Automatically generated definition].
OBOL:automatic
EMAPA:37643
MA:th
UMLS:C0222101
ncithesaurus:Skin_of_the_Lip
lip zone of skin
OBOL:automatic
zone of skin of lip
OBOL:automatic
skin of lips
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
check ncita
EMAPA:37621
FMA:34836
GAID:263
MA:0001519
MESH:D017746
NCIT:C32259
NCIT:C84388
UMLS:C0206207
galen:JointCapsule
capsula articularis
fibrous capsule of joint
joint capsule
joint fibrous capsule
uberon
capsulae articulares
UBERON:0001484
articular capsule
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
check ncita
ncit
EMAPA:37621
MA:th
UMLS:C0206207
ncithesaurus:Joint_Capsule
capsula articularis
FMA:34836
FMA:TA
capsulae articulares
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
carotid artery
CALOHA:TS-0116
EHDAA2:0000217
EHDAA:7331
EMAPA:17855
FMA:3939
GAID:479
MA:0001926
MESH:D017536
NCIT:C32352
UMLS:C0162859
VHOG:0000272
carotid artery system
common carotid artery
trunk of common carotid tree
uberon
a. carotis communis
UBERON:0001530
common carotid artery plus branches
FMA
Wikipedia
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
carotid artery
FMA:3939
UMLS:C0162859
ncithesaurus:Common_Carotid_Artery
carotid artery system
EHDAA2:0000217
common carotid artery
FMA:3939
trunk of common carotid tree
FMA:3939
a. carotis communis
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
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]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
gut
AAO:0010023
BILA:0000083
BTO:0000511
BTO:0000545
EHDAA2:0000726
EHDAA:518
EMAPA:16247
FBbt:00003125
FMA:45615
MA:0000917
NCIT:C34082
OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA
TAO:0000112
TGMA:0001819
UMLS:C0017189
VHOG:0000309
WBbt:0005743
ZFA:0000112
galen:AlimentaryTract
digestive tube
enteric tract
alimentary canal
alimentary tract
uberon
digestive canal
gut tube
UBERON:0001555
digestive tract
NCBIBook:NBK10107
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
2012-08-14
TAO:0000112
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000309
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
FMA also has a term 'gastrointestinal tract', but this includes the liver.
FMA
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
MA
UMLS:C0017189
ncithesaurus:Gastrointestinal_Tract
enteric tract
ZFA:0000112
digestive canal
BTO:0000058
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
EHDAA2:0001036
EMAPA:16738
FMA:45662
MA:0000435
OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g
VHOG:0000382
lower respiratory system
uberon
UBERON:0001558
lower respiratory tract
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
AAO:0010236
EHDAA2:0000877
EHDAA:5407
EMAPA:17620
FMA:4724
MA:0002157
NCIT:C32849
OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0000878
UMLS:C0226550
XAO:0000382
galen:InternalJugularVein
internal jugular
internal jugular venous tree
uberon
vena jugularis interna
UBERON:0001586
internal jugular vein
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
2012-06-20
AAO:0010236
AAO
AAO:BJB
UMLS:C0226550
ncithesaurus:Internal_Jugular_Vein
internal jugular
EHDAA2:0000877
vena jugularis interna
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].
BTO:0000654
EMAPA:35240
FMA:49151
MA:0001269
NCIT:C32315
UMLS:C0559230
musculus ciliarus
uberon
Bowman`s muscles
ciliaris
musculus ciliaris
UBERON:0001605
ciliary muscle
MA
FMA
FMA
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].
UMLS:C0559230
ncithesaurus:Ciliary_Muscle
musculus ciliarus
BTO:0000654
Bowman`s muscles
BTO:0000654
ciliaris
musculus ciliaris
.
revisit this, see issue #331
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
EMAPA:35448
FMA:49154
MA:0001287
iris muscle
iris muscle organ
muscle organ of iris
uberon
UBERON:0001606
muscle of iris
FMA
.
iris muscle organ
OBOL:automatic
muscle organ of iris
OBOL:automatic
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
EMAPA:19213
FMA:49549
MA:0001950
NCIT:C32578
OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA
UMLS:C0226109
uberon
arteria maxillaris externa
external maxillary artery
UBERON:0001612
facial artery
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
UMLS:C0226109
ncithesaurus:Facial_Artery
arteria maxillaris externa
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
EHDAA2:0001069
EHDAA:7357
EMAPA:17311
FMA:49675
GAID:498
MA:0001919
MESH:D008438
NCIT:C34205
OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA
UMLS:C0024949
uberon
arteria maxillaris
internal maxillary artery
UBERON:0001616
maxillary artery
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
UMLS:C0024949
ncithesaurus:Maxillary_Artery
arteria maxillaris
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
muscular
muscle
AAO:0011066
EMAPA:32715
EMAPA:37474
EV:0100146
FMA:5022
GAID:131
MA:0000015
OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA
TAO:0005145
VHOG:0001245
XAO:0000172
ZFA:0005145
galen:Muscle
uberon
UBERON:0001630
muscle organ
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].
GO:0007517
Portion of tissue composed of contractile fibers.[TAO]
2012-08-14
TAO:0005145
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0001245
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
muscle
ZFA:0005145
EMAPA:37474
MA:th
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]
arterial
AAO:0010211
AEO:0000208
BTO:0000573
CALOHA:TS-0054
EFO:0000814
EHDAA2:0000143
EHDAA2:0003253
EMAPA:35147
EV:0100026
FMA:50720
GAID:468
MA:0000064
MAT:0000034
MESH:D001158
MIAA:0000034
NCIT:C12372
OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA
TAO:0000005
UMLS:C0003842
VHOG:0001251
XAO:0000114
ZFA:0000005
galen:Artery
arterial subtree
arterial tree organ part
arteries
uberon
arterial system
arterial vessel
UBERON:0001637
artery
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
AEO:JB
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
2012-06-20
AAO:0010211
AAO
AAO:BJB
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]
2012-09-17
VHOG:0001251
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0003842
ncithesaurus:Artery
arteries
TAO:0000005
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
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]
venous
venous subtree
venous vessel
AAO:0010212
AEO:0000209
BTO:0000234
CALOHA:TS-1108
EFO:0000816
EHDAA2:0003254
EMAPA:35906
EV:0100031
FMA:50723
GAID:492
MA:0000067
MAT:0000037
MESH:D014680
MIAA:0000037
NCIT:C12814
OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA
TAO:0000082
UMLS:C0042449
VHOG:0001743
XAO:0000115
ZFA:0000082
galen:Vein
venous tree organ part
uberon
vascular element
vena
venae
UBERON:0001638
vein
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]
2012-06-20
AAO:0010212
AAO
AAO:BJB
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]
2012-09-17
VHOG:0001743
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0042449
ncithesaurus:Vein
vascular element
EMAPA:th
vena
venae
VHOG:0001743
The pulmonary artery that supplies the right lung.
TODO - add class 'pulmonary artery tree organ'
EMAPA:37378
FMA:50872
MA:0002500
NCIT:C33489
UMLS:C0923924
galen:RightPulmonaryArtery
right main pulmonary artery
right pulmonary arterial tree
uberon
arteria pulmonalis dextra
UBERON:0001651
right pulmonary artery
The pulmonary artery that supplies the right lung.
UBERON:cjm
EMAPA:37378
MA:th
UMLS:C0923924
ncithesaurus:Right_Pulmonary_Artery
arteria pulmonalis dextra
The pulmonary artery that supplies the left lung.
TODO - add class 'pulmonary artery tree organ'
EMAPA:37097
FMA:50873
MA:0002032
NCIT:C32971
UMLS:C0923925
galen:LeftPulmonaryArtery
left main pulmonary artery
left pulmonary arterial tree
uberon
arteria pulmonalis sinistra
UBERON:0001652
left pulmonary artery
The pulmonary artery that supplies the left lung.
UBERON:cjm
EMAPA:37097
MA:th
UMLS:C0923925
ncithesaurus:Left_Pulmonary_Artery
arteria pulmonalis sinistra
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
AAO:0010513
EMAPA:19220
FMA:50874
MA:0002115
NCIT:C32579
OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA
UMLS:C0226532
face vein
vein of face
uberon
anterior facial vein
vena facialis anterior
UBERON:0001653
facial vein
FMA
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
2012-06-20
AAO:0010513
AAO
AAO:BJB
MA and NCITA also has 'anterior facial vein'
MA
UMLS:C0226532
ncithesaurus:Facial_Vein
face vein
OBOL:automatic
vein of face
OBOL:automatic
anterior facial vein
vena facialis anterior
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
AAO:0000988
BTO:0001749
EMAPA:35455
FMA:54396
GAID:214
MA:0001905
MESH:D007568
NCIT:C48821
OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA
TAO:0001227
UMLS:C0022359
ZFA:0001227
galen:Jaw
jaw
jaw cartilage
mandibular arch skeleton
uberon
anterior splanchnocranium
jaws
mandibular arch
oral jaw skeleton
pharyngeal arch 1 skeleton
visceral arch 1
UBERON:0001708
jaw skeleton
cjm
Subdivision of skeleton which includes upper and lower jaw skeletons.
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
2012-08-14
TAO:0001227
TAO
ZFIN:curator
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
FMA
UMLS:C0022359
ncithesaurus:Jaw
jaw
MA:0001905
jaw cartilage
ZFA:0001227
mandibular arch skeleton
ZFA:0001227
mandibular arch
TAO:0001227
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
Note isa/partof difference MA/FMA
AAO:0000272
EFO:0003660
EHDAA2:0001018
EHDAA:7995
EMAPA:17906
FMA:59398
MESH:D008334
VHOG:0000453
ncithesaurus:Lower_Jaw
mandibular part of mouth
uberon
lower part of mouth
mandibular series
UBERON:0001710
See notes for jaw w.r.t skeletal element vs subdivision of head
lower jaw region
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
2012-06-20
AAO:0000272
AAO
AAO:LAP
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
2012-09-17
VHOG:0000453
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
Note isa/partof difference MA/FMA
MA
mandibular part of mouth
FMA:59398
A anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
TOODO check
AAO:0010435
BSA:0000113
BTO:0002097
EMAPA:18381
FMA:54935
XAO:0000105
lumen of pharynx
pharyngeal cavity
uberon
cavitas pharyngealis
cavitas pharyngis
UBERON:0001731
cavity of pharynx
XAO
A anatomical space that is enclosed by a pharynx.
OBOL:automatic
cavitas pharyngealis
cavitas pharyngis
BTO:0002097
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
BTO:0002084
EHDAA2:0000129
EHDAA:9033
EMAPA:18231
FMA:58078
GAID:889
MA:0000262
MESH:D000867
NCIT:C12667
UMLS:C0003151
VHOG:0001431
anterior chamber
anterior chamber of eye
camera anterior
eye anterior chamber
uberon
camera anterior bulbi
camera anterior bulbi oculi
camera oculi anterior
UBERON:0001766
anterior chamber of eyeball
FMA
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
MESH:A09.371.060.067
MP:0005205
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
2012-09-17
VHOG:0001431
VHOG
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
EHDAA2
UMLS:C0003151
ncithesaurus:Anterior_Chamber_of_the_Eye
anterior chamber
HP:0000593
MP:0010709
camera anterior bulbi
BTO:0002084
camera anterior bulbi oculi
camera oculi anterior
BTO:0002084
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
uveal
CALOHA:TS-2228
EMAPA:35901
FMA:58103
GAID:912
MA:0002480
MESH:D014602
NCIT:C12811
UMLS:C0042160
tunica vasculosa of eyeball
uvea
uveal tract
uberon
pars iridica retinae
tunica vasculatis oculi
tunica vasculosa bulbi
vascular layer of eyeball
UBERON:0001768
uvea
FMA
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
MP:0005197
UMLS:C0042160
ncithesaurus:Uvea
tunica vasculosa of eyeball
FMA:58103
uvea
FMA:58103
uveal tract
FMA:58103
pars iridica retinae
tunica vasculatis oculi
tunica vasculosa bulbi
vascular layer of eyeball
FMA:58103
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The 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]
iridial
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]
AAO:0010347
BTO:0000653
CALOHA:TS-0491
EFO:0004245
EMAPA:19154
EV:0100345
FMA:58235
GAID:917
MA:0000273
MESH:D007498
NCIT:C12737
OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA
TAO:0001238
UMLS:C0022077
VHOG:0000101
XAO:0000185
ZFA:0001238
uberon
anterior uvea
irides
irises
UBERON:0001769
iris
XAO
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
ISBN:0-683-40008-8
MP:0001322
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]
2012-09-17
VHOG:0000101
VHOG
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]
2012-09-17
VHOG:0000101
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0022077
ncithesaurus:Iris
irides
irises
VHOG:0000101
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
BTO:0000287
CALOHA:TS-0173
EFO:0001917
EHDAA2:0000319
EMAPA:17162
FMA:58263
GAID:895
MA:0001243
MESH:D019573
NCIT:C12928
TAO:0002187
UMLS:C0459875
ZFA:0001683
anterior corneal epithelium
cornea epithelial tissue
cornea epithelium
epithelial tissue of cornea
epithelium anterius (cornea)
epithelium anterius corneae
epithelium corneæ anterior layer
epithelium of cornea
external epithelium of cornea
uberon
anterior endothelium of cornea
e. anterius corneae
endothelium anterius corneae
endothelium camerae anterioris bulbi
endothelium corneale
epithelium posterius corneae
UBERON:0001772
corneal epithelium
ISBN:0781772214
the smooth stratified squamous epithelium that covers the outer surface of the cornea
MESH:A09.371.060.217.325
MGI:smb
MP:0006000
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]
2012-08-14
TAO:0002187
TAO
ZFIN:ZDB-PUB-061010-3
UMLS:C0459875
ncithesaurus:Corneal_Epithelium
cornea epithelial tissue
OBOL:automatic
cornea epithelium
OBOL:automatic
epithelial tissue of cornea
OBOL:automatic
epithelium anterius corneae
FMA:58263
FMA:TA
anterior endothelium of cornea
BTO:0000287
e. anterius corneae
endothelium anterius corneae
BTO:0000287
endothelium camerae anterioris bulbi
BTO:0000287
endothelium corneale
BTO:0000287
epithelium posterius corneae
BTO:0000287
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
scleral
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
AAO:0010354
BTO:0001606
EMAPA:19027
EV:0100342
FMA:58269
GAID:911
MA:0000280
MESH:D012590
NCIT:C12784
OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA
UMLS:C0036410
VHOG:0001274
XAO:0000183
ZFA:0005563
uberon
scleral capsule
UBERON:0001773
Disease notes: implicated in rheumatoid arthritis.
sclera
FMA
ISBN:0781772214
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
ZFIN:ZDB-PUB-050701-15
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]
2012-09-17
VHOG:0001274
VHOG
UMLS:C0036410
ncithesaurus:Sclera
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
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]
AAO:0010341
BTO:0000260
CALOHA:TS-0694
EMAPA:19065
EV:0100346
FMA:58295
GAID:916
MA:0000264
MESH:D002924
NCIT:C12345
UMLS:C0008779
VHOG:0000102
XAO:0000186
ocular ciliary body
uberon
anterior uvea
ciliary bodies
corpus ciliare
UBERON:0001775
ciliary body
ISBN:0781772214
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
ISBN:0-683-40008-8
MP:0005099
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]
2012-09-17
VHOG:0000102
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0008779
ncithesaurus:Ciliary_Body
ciliary bodies
VHOG:0000102
corpus ciliare
corpus ciliare
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
choroidal
MP treats posterior uvea and optic choroid as distinct
BTO:0001829
CALOHA:TS-2054
EMAPA:19077
EV:0100347
FMA:58298
GAID:913
MA:0000263
MESH:D002829
NCIT:C12344
TAO:0005229
UMLS:C0008520
VHOG:0001568
ZFA:0005229
choroid
choroid coat
choroidea
eye choroid
posterior uvea
uberon
chorioid
choroidea
optic choroid
UBERON:0001776
optic choroid
MA
Wikipedia
lexical
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].
MP treats posterior uvea and optic choroid as distinct
MP
UMLS:C0008520
ncithesaurus:Choroid
choroid
MA:0000263
choroid coat
choroidea
eye choroid
VHOG:0001568
posterior uvea
chorioid
BTO:0001829
choroidea
optic choroid
ZFA:0005229
A double layer covering the ciliary body that produces aqueous humor.
BTO:0001770
CALOHA:TS-0695
EMAPA:35239
FMA:58464
MA:0001238
NCIT:C32314
UMLS:C0459736
ciliary body epithelium
epithelium of ciliary body
ocular ciliary epithelium
uberon
UBERON:0001778
ciliary epithelium
FMA
MA
Wikipedia
A double layer covering the ciliary body that produces aqueous humor.
UMLS:C0459736
ncithesaurus:Ciliary_Epithelium
ciliary body epithelium
FMA:58464
epithelium of ciliary body
FMA:58464
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
AAO:0010353
EMAPA:35742
FMA:58617
MA:0001319
NCIT:C49328
UMLS:C0459649
XAO:0000266
retina layer
retina neuronal layer
retinal layer
retinal neuronal layer
uberon
UBERON:0001781
layer of retina
Any of the layers that make up the retina[MP].
MP:0003727
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
MA
UMLS:C0459649
ncithesaurus:Retina_Layer
retina neuronal layer
MP:0006069
retinal neuronal layer
MP:0006069
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
EHDAA2:0000139
EHDAA:10196
EMAPA:18232
ENVO:02000024
FMA:58819
GAID:890
MA:0001236
MESH:D001082
NCIT:C13190
OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA
UMLS:C0003662
VHOG:0000548
ZFA:0005564
aqueous humor
aqueous humour
humor aquosus
uberon
UBERON:0001796
aqueous humor of eyeball
FMA def states A and P
located_in in EHDAA2
VHOG
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
2012-09-17
VHOG:0000548
VHOG
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000548
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
FMA
UMLS:C0003662
ncithesaurus:Aqueous_Humor
aqueous humour
EHDAA2:0000139
humor aquosus
FMA:58819
FMA:TA
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
EMAPA:36594
FMA:58865
MA:0002484
MESH:D000869
NCIT:C12668
UMLS:C0003153
ZFA:0005566
anterior eye segment
anterior segment eye
anterior segment of eye
anterior segment of the eye
eye anterior segment
segmentum anterius (bulbus oculi)
uberon
segmentum anterius bulbi oculi
UBERON:0001801
anterior segment of eyeball
FMA
cjm
lexical
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
ISBN:0-683-40008-8
MESH:A09.371.060
MP:0005193
UMLS:C0003153
ncithesaurus:Anterior_Eye_Segment
anterior segment eye
ZFA:0005566
segmentum anterius bulbi oculi
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
EMAPA:36595
FMA:58868
MA:0002485
NCIT:C12906
UMLS:C0278450
ZFA:0005567
eye posterior segment
posterior eye segment
posterior segment eye
posterior segment of eye
posterior segment of the eye
segmentum posterius (bulbus oculi)
uberon
segmentum posterius bulbi oculi
UBERON:0001802
posterior segment of eyeball
FMA
cjm
lexical
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
ISBN:0-683-40008-8
MP:0005195
UMLS:C0278450
ncithesaurus:Posterior_Eye_Segment
posterior segment eye
ZFA:0005567
segmentum posterius bulbi oculi
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
BTO:0001873
CALOHA:TS-0543
EMAPA:32871
FMA:58871
MA:0001301
TAO:0001326
XAO:0004094
ZFA:0001326
epithelial tissue of eye lens
epithelial tissue of lens
epithelium lentis
epithelium of eye lens
eye lens epithelial tissue
eye lens epithelium
lens epithelial tissue
lens epithelium
uberon
UBERON:0001803
epithelium of lens
A layer of epithelial cells that is part of the eye.
epithelial tissue of eye lens
OBOL:automatic
epithelial tissue of lens
OBOL:automatic
epithelium lentis
FMA:58871
FMA:TA
epithelium of eye lens
OBOL:automatic
eye lens epithelial tissue
OBOL:automatic
eye lens epithelium
OBOL:automatic
lens epithelial tissue
OBOL:automatic
the elastic, clear, membrane-like structure, that is outer most layer of the lens
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
EHDAA2:0000977
EMAPA:18237
FMA:58881
MA:0001300
NCIT:C32975
UMLS:C0229232
VHOG:0000550
ZFA:0005574
capsula lentis
lens capsule
uberon
UBERON:0001804
capsule of lens
EHDAA2
the elastic, clear, membrane-like structure, that is outer most layer of the lens
MGI:smb
MP:0003236
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000550
VHOG
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000550
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
FMA
UMLS:C0229232
ncithesaurus:Lens_Capsule
capsula lentis
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
labial
BTO:0001647
CALOHA:TS-0558
EMAPA:32839
FMA:59816
GAID:76
MA:0000343
MESH:D008046
NCIT:C12220
OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA
TAO:0007006
UMLS:C0023759
VHOG:0000677
ZFA:0007006
galen:Lip
uberon
labia oris
lips
UBERON:0001833
lip
ZFA
BTO
FMA-implicit
VHOG
ZFA
cjm
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
2012-08-14
TAO:0007006
TAO
ZFIN:curator
UMLS:C0023759
ncithesaurus:Lip
labia oris
Lip that covers the lower portion of the mouth.[TAO].
Lip that covers the lower portion of the mouth.[TAO]
UBERON:0003392
EHDAA2:0001020
EMAPA:17909
FMA:59818
MA:0000921
NCIT:C94572
OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA
TAO:0002060
UMLS:C0458583
ZFA:0005225
lower jaw lip
uberon
labium inferius oris
UBERON:0001835
lower lip
Lip that covers the lower portion of the mouth.[TAO].
TAO:0002060
Lip that covers the lower portion of the mouth.[TAO]
2012-08-14
TAO:0002060
TAO
TAO:wd
UMLS:C0458583
ncithesaurus:Lower_Lip
lower jaw lip
labium inferius oris
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
mesencephalic
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
MB
AAO:0010149
BAMS:MES
BIRNLEX:1667
BM:MB
BTO:0000138
CALOHA:TS-0630
DHBA:10648
DMBA:16649
EFO:0000919
EHDAA2:0001162
EHDAA:3694
EMAPA:16974
EV:0100242
FMA:61993
HBA:9001
MA:0000207
MAT:0000106
MBA:313
MESH:D008636
MIAA:0000106
NCIT:C12510
OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0001104
TAO:0000128
UMLS:C0025462
VHOG:0000069
XAO:0000014
ZFA:0000128
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462
uberon
mesencephalon
UBERON:0001891
midbrain
definitional
Bgee:AN
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].
GO:0030901
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
2012-06-20
AAO:0010149
AAO
AAO:BJB
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]
2012-08-14
TAO:0000128
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000069
VHOG
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
ABA
MB
BIRNLEX:1667
NIFSTD:NeuroNames_abbrevSource
UMLS:C0025462
BIRNLEX:1667
UMLS:C0025462
ncithesaurus:Mesencephalon
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462
BIRNLEX:1667
mesencephalon
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
hindbrain segment
segment of hindbrain
DHBA:12664
EFO:0003617
EMAPA:16148
FMA:295666
MAT:0000272
MIAA:0000272
RETIRED_EHDAA2:0000669
TAO:0001064
VHOG:0000672
XAO:0004079
ZFA:0001064
hindbrain neuromere
hindbrain neuromeres
rhombomere
uberon
future rhombencephalon
rhombomeres
UBERON:0001892
rhombomere
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
ZFIN:curator
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0001064
TAO
ZFIN:curator
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
2012-09-17
VHOG:0000672
VHOG
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
hindbrain segment
ZFA:0001064
segment of hindbrain
ZFA:0001064
hindbrain neuromeres
DHBA:HNM
future rhombencephalon
MIAA:0000272
rhombomeres
VHOG:0000672
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
bulb
medulla
AAO:0010486
BAMS:MY
BAMS:Md
BIRNLEX:957
BM:Me
BTO:0000041
CALOHA:TS-0607
DMBA:17352
EFO:0000924
EHDAA2:0001088
EHDAA:7588
EMAPA:17550
EV:0100275
FMA:62004
GAID:590
MA:0000206
MAT:0000111
MAT:0000367
MBA:354
MESH:D008526
MIAA:0000111
NCIT:C12442
OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA
OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA
TAO:0000545
UMLS:C0025148
UMLS:C1269575
VHOG:0000181
XAO:0003100
ZFA:0000545
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698
bulbus
uberon
medulla oblonzata
metepencephalon
UBERON:0001896
medulla oblongata
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].
FMA:62004
GO:0021550
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
2012-06-20
AAO:0010486
AAO
AAO:BJB
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]
2012-09-17
VHOG:0000181
VHOG
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
2012-09-17
VHOG:0000181
VHOG
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
medulla
ABA:MY
UMLS:C0025148
BIRNLEX:957
UMLS:C0025148
ncithesaurus:Medulla_Oblongata
UMLS:C1269575
BIRNLEX:957
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698
BIRNLEX:957
bulbus
FMA:62004
FMA:TA
medulla oblonzata
metepencephalon
FMA:62004
An endothelium that is part of a capillary [Automatically generated definition].
BTO:0004954
CALOHA:TS-0112
EMAPA:36292
FMA:62114
MA:0000711
NCIT:C49215
UMLS:C0006904
blood capillary endothelium
capillary endothelium
capillary vessel endothelium
endothelium of blood capillary
endothelium of capillary vessel
uberon
UBERON:0001915
endothelium of capillary
An endothelium that is part of a capillary [Automatically generated definition].
OBOL:automatic
UMLS:C0006904
ncithesaurus:Capillary_Endothelium
blood capillary endothelium
OBOL:automatic
capillary vessel endothelium
OBOL:automatic
endothelium of blood capillary
OBOL:automatic
endothelium of capillary vessel
OBOL:automatic
An endothelium that is part of an arteriole [Automatically generated definition].
EMAPA:36286
FMA:62115
MA:0000705
NCIT:C49192
UMLS:C1179024
arteriole endothelium
uberon
UBERON:0001916
endothelium of arteriole
An endothelium that is part of an arteriole [Automatically generated definition].
OBOL:automatic
UMLS:C1179024
ncithesaurus:Arteriole_Endothelium
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
AAO:0011013
BTO:0004757
EMAPA:35148
FMA:62116
MA:0000707
NCIT:C49194
UMLS:C1179025
VHOG:0001215
XAO:0000357
arterial endothelium
artery endothelium
uberon
UBERON:0001917
endothelium of artery
An endothelium that is part of an artery [Automatically generated definition].
OBOL:automatic
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
2012-06-20
AAO:0011013
AAO
XAO:curator
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001215
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C1179025
ncithesaurus:Artery_Endothelium
An endothelium that is part of a venule [Automatically generated definition].
EMAPA:36290
FMA:62117
MA:0000716
NCIT:C49319
UMLS:C1179026
venule endothelium
uberon
UBERON:0001918
endothelium of venule
An endothelium that is part of a venule [Automatically generated definition].
OBOL:automatic
UMLS:C1179026
ncithesaurus:Venule_Endothelium
An endothelium that is part of a vein [Automatically generated definition].
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
AAO:0011110
BTO:0004756
EMAPA:36288
FMA:62118
MA:0000712
NCIT:C49317
UMLS:C1179027
VHOG:0001216
XAO:0000358
vein endothelium
venous endothelium
uberon
veinous endothelium
UBERON:0001919
endothelium of vein
An endothelium that is part of a vein [Automatically generated definition].
OBOL:automatic
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001216
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C1179027
ncithesaurus:Vein_Endothelium
veinous endothelium
VHOG:0001216
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
MTg
tegmentum
BAMS:MTg
BIRNLEX:1200
BTO:0003388
DHBA:12195
EFO:0000921
EHDAA2:0004475
EMAPA:18215
FMA:62393
HBA:9002
MA:0000212
MAT:0000452
TAO:0000160
UMLS:C0039441
VHOG:0001367
XAO:0004271
ZFA:0000160
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491
tegmentum mesencephali
tegmentum of midbrain
uberon
mesencephalic tegmentum
tegmentum mesencephalicum
UBERON:0001943
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
midbrain tegmentum
ZFA
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
FMA:FMA
ISBN:0471888893
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]
2012-09-17
VHOG:0001367
VHOG
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
MTg
BIRNLEX:1200
NIFSTD:NeuroNames_abbrevSource
tegmentum
ISBN:0471888893
UMLS:C0039441
BIRNLEX:1200
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491
BIRNLEX:1200
tegmentum mesencephali
mesencephalic tegmentum
VHOG:0001367
tegmentum mesencephalicum
NeuroNames:491
A multi-tissue structure that is part of a spinal cord.
BIRNLEX:1496
NCIT:C33969
UMLS:C1268166
uberon
spinal cord part
UBERON:0001948
regional part of spinal cord
A multi-tissue structure that is part of a spinal cord.
OBOL:automatic
UMLS:C1268166
ncithesaurus:Spinal_Cord_Part
The liquid component of blood, in which erythrocytes are suspended.
plasma
portion of plasma
BTO:0000131
CALOHA:TS-0800
EFO:0001905
EMAPA:35690
FMA:62970
GAID:1178
MA:0002501
MAT:0000052
MESH:D010949
MIAA:0000052
NCIT:C13356
OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
UMLS:C0032105
blood plasm
portion of blood plasma
uberon
UBERON:0001969
blood plasma
The liquid component of blood, in which erythrocytes are suspended.
plasma
MA:0002501
portion of plasma
FMA:62970
UMLS:C0032105
ncithesaurus:Plasma
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
BTO:0002626
EMAPA:35917
FMA:63130
MA:0000071
MESH:A07.231.432.952
NCIT:C12818
TAO:0005315
UMLS:C0042520
VHOG:0001765
ZFA:0005315
uberon
venula
UBERON:0001979
venule
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
MESH:A07.231.432.952
MP:0004125
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
2012-08-14
TAO:0005315
TAO
ZFIN:curator
UMLS:C0042520
ncithesaurus:Venule
venula
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
AAO:0010253
BTO:0001997
EMAPA:35146
FMA:63182
MA:0000063
MESH:D001160
NCIT:C12672
TAO:0002138
UMLS:C0003847
VHOG:0001763
ZFA:0005255
uberon
arteriola
UBERON:0001980
arteriole
MA
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
GO:0014830
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
2012-08-14
TAO:0002138
TAO
ZFIN:curator
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
2012-06-20
AAO:0010253
AAO
AAO:BJB
UMLS:C0003847
ncithesaurus:Arteriole
arteriola
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
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]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
vascular element
AAO:0011004
AEO:0000207
BTO:0001102
CALOHA:TS-0080
EFO:0000817
EHDAA2:0003252
EHDAA:240
EMAPA:32743
EMAPA:35993
FMA:50722
FMA:63183
GAID:169
MA:0000060
MAT:0000393
MESH:D001808
NCIT:C12679
NLXANAT:090901
OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA
TAO:0002137
UMLS:C0005847
VHOG:0001250
XAO:0001011
ZFA:0005314
region of vascular tree organ
vascular tree organ region
uberon
vas sanguineum
UBERON:0001981
blood vessel
EHDAA2
GO:0072360
A vessel through which blood circulates in the body.
BTO:0001102
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
2012-09-17
VHOG:0001250
VHOG
Any of the vessels through which blood circulates in the body.[AAO]
2012-06-20
AAO:0011004
AAO
AAO:EJS
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]
2012-09-17
VHOG:0001250
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
FMA
vascular element
EMAPA:35993
UMLS:C0005847
ncithesaurus:Blood_Vessel
region of vascular tree organ
FMA:50722
vascular tree organ region
FMA:50722
vas sanguineum
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
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]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
AAO:0010252
BTO:0002045
CALOHA:TS-2006
EFO:0001906
EMAPA:35198
EV:0100035
FMA:63194
MA:0000065
MESH:A07.231.432.410
NCIT:C12685
NLXANAT:090902
OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA
TAO:0005250
UMLS:C0935624
VHOG:0001253
XAO:0000116
ZFA:0005250
blood capillary
capillary vessel
uberon
UBERON:0001982
capillary
FMA
MA
XAO
ZFA
Any of the smallest blood vessels connecting arterioles with venules.
ISBN:0073040584
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
2012-06-20
AAO:0010252
AAO
AAO:BJB
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]
2012-09-17
VHOG:0001253
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0935624
ncithesaurus:Capillary
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
CALOHA:TS-0172
EMAPA:35935
FMA:63882
GAID:891
MA:0001242
MESH:D004728
NCIT:C12707
TAO:0002186
UMLS:C0014259
ZFA:0001687
cornea endothelium
endothelium of cornea
uberon
epithelium posterius corneae
UBERON:0001985
corneal endothelium
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
UMLS:C0014259
ncithesaurus:Corneal_Endothelium
cornea endothelium
OBOL:automatic
endothelium of cornea
OBOL:automatic
epithelium posterius corneae
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
endothelial
BTO:0000393
CALOHA:TS-0278
EFO:0002548
FMA:63916
GAID:520
MESH:D004727
NCIT:C12481
UMLS:C0014257
galen:Endothelium
uberon
UBERON:0001986
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
endothelium
FMA-text-def
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
FMA:63916
MESH:A10.272.491
UMLS:C0014257
ncithesaurus:Endothelium
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
AAO:0010221
BTO:0000778
CALOHA:TS-0839
EFO:0001399
EHDAA2:0001575
EHDAA:4351
EMAPA:17008
FMA:66326
GAID:505
MA:0002031
MESH:D011651
NCIT:C12774
OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA
UMLS:C0034052
VHOG:0000982
XAO:0004162
galen:PulmonaryArtery
pulmonary arterial tree
pulmonary arterial tree organ part
uberon
arteria pulmonalis
pulmonary arterial subtree
truncus pulmonalis
UBERON:0002012
pulmonary artery
Wikipedia
EHDAA2
XAO
EHDAA2
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
2012-06-20
AAO:0010221
AAO
AAO:BJB
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
2012-09-17
VHOG:0000982
VHOG
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
2012-09-17
VHOG:0000982
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
UMLS:C0034052
ncithesaurus:Pulmonary_Artery
pulmonary arterial tree
FMA:66326
pulmonary arterial tree organ part
FMA:66326
arteria pulmonalis
pulmonary arterial subtree
FMA:66326
truncus pulmonalis
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
AAO:0010521
BTO:0001799
CALOHA:TS-0840
EHDAA2:0001579
EHDAA:2629
EMAPA:18645
FMA:66643
GAID:543
MA:0002206
MESH:D011667
NCIT:C12776
UMLS:C0034090
VHOG:0001133
XAO:0000394
galen:PulmonaryVein
pulmonary venous tree organ part
uberon
venae pulmonales
UBERON:0002016
pulmonary vein
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
GO:0060577
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
2012-06-20
AAO:0010521
AAO
AAO:BJB
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
2012-09-17
VHOG:0001133
VHOG
the veins that return oxygenated blood from the lungs to the left atrium of the heart
MP:0002726,MGI:cwg
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
2012-09-17
VHOG:0001133
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
UMLS:C0034090
ncithesaurus:Pulmonary_Vein
venae pulmonales
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]
AEO:0001012
EHDAA2:0003136
EHDAA2_RETIRED:0004658
EMAPA:37596
FMA:67242
HBA:4006
MA:0001112
NCIT:C32695
OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA
TAO:0002197
UMLS:C0018220
VHOG:0001768
ZFA:0001681
gray matter
gray matter of neuraxis
grey matter
grey matter of neuraxis
grey substance
neuronal grey matter
substantia grisea
uberon
gray mater
grisea
UBERON:0002020
gray matter
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]
2012-08-14
TAO:0002197
TAO
ZFIN:curator
EMAPA:37596
MA:th
UMLS:C0018220
ncithesaurus:Gray_Matter
gray matter of neuraxis
FMA:67242
neuronal grey matter
AEO:0001012
substantia grisea
FMA:67242
FMA:TA
gray mater
ZFA:0001681
grisea
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
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]
rhombencephalic
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
AAO:0010150
BAMS:HB
BIRNLEX:942
BTO:0000672
CALOHA:TS-0457
DHBA:10653
DMBA:16808
EFO:0000923
EHDAA2:0000746
EHDAA:3514
EHDAA:6487
EMAPA:16916
FMA:67687
MA:0000195
MAT:0000107
MBA:1065
MESH:D012249
MIAA:0000107
NCIT:C40336
TAO:0000029
UMLS:C0035507
UMLS:C1522180
VHOG:0000070
XAO:0000015
ZFA:0000029
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540
uberon
rhombencephalon
UBERON:0002028
hindbrain
modified-source-relation
ABA
Bgee:AN
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].
ZFA:0000029
ZFIN:curator
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
2012-06-20
AAO:0010150
AAO
AAO:BJB
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]
2012-08-14
TAO:0000029
TAO
ZFIN:curator
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
2012-08-14
TAO:0000029
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]
2012-09-17
VHOG:0000070
VHOG
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
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
MA
UMLS:C0035507
BIRNLEX:942
UMLS:C0035507
ncithesaurus:Hind-Brain
UMLS:C1522180
BIRNLEX:942
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540
BIRNLEX:942
A systemic artery that supplies the lung with with oxygenated blood.
EMAPA:18608
FMA:68109
GAID:477
MA:0001923
MESH:D001981
NCIT:C32230
OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg
UMLS:C0006257
bronchial arterial tree
uberon
arteriae bronchiales
rami bronchiales partis thoracicae aortae
UBERON:0002040
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
bronchial artery
A systemic artery that supplies the lung with with oxygenated blood.
UBERON:cjm
UMLS:C0006257
ncithesaurus:Bronchial_Artery
arteriae bronchiales
rami bronchiales partis thoracicae aortae
Respiration organ that develops as an oupocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
pulmonary
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
AAO:0000275
AAO:0010567
BTO:0000763
CALOHA:TS-0568
EFO:0000934
EHDAA2:0001042
EHDAA:1554
EHDAA:2205
EMAPA:16728
EV:0100042
FMA:7195
GAID:345
MA:0000415
MAT:0000135
MESH:D008168
MIAA:0000135
NCIT:C12468
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0024109
VHOG:0000310
XAO:0000119
galen:Lung
pulmo
uberon
UBERON:0002048
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
lung
some species only have a single lung
Respiration organ that develops as an oupocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
2012-06-20
AAO:0010567
AAO
AAO:SBH
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000310
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
UMLS:C0024109
ncithesaurus:Lung
pulmo
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?
vascular
BTO:0003718
FMA:69050
TAO:0005249
ZFA:0005249
vascular network
uberon
UBERON:0002049
vasculature
FMA
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
ZFA:0005249
vascular network
FMA:69050
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
in FMA embryo is_a embryonic structure
AAO:0000138
BILA:0000034
BTO:0000174
CALOHA:TS-2110
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:D004628
NCIT:C13229
RETIRED_EHDAA2:0003169
TAO:0001105
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
embryonic anatomical structure
uberon
developing structure
embryonale Struktur
embryonic structures
UBERON:0002050
embryonic structure
Anatomical structure that is part of an embryo.
BTO:0000174
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
2012-06-20
AAO:0000138
AAO
AAO:BJB
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
2012-08-14
TAO:0001105
TAO
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
2012-08-14
VSAO:0000178
VSAO
ZFIN:curator
in FMA embryo is_a embryonic structure
FMA
UMLS:C0013948
ncithesaurus:Embryonic_Structure
developing embryonic structure
FBbt:00004208
embryonic anatomical structure
RETIRED_EHDAA2:0003169
embryonale Struktur
BTO:0000174
embryonic structures
ZFA:0001105
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
assume spelling error for ncit
EHDAA2:0004143
EMAPA:35887
FMA:70301
GAID:554
MA:0000103
MESH:D014338
NCIT:C34317
OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw
UMLS:C1519589
uberon
UBERON:0002061
truncus arteriosus
EHDAA2
FMA
MA
EHDAA2
EHDAA2
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
assume spelling error for ncit
ncit
UMLS:C1519589
ncithesaurus:Trancus_Arteriosus
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
dermal
AAO:0000128
BTO:0000294
CALOHA:TS-2076
EFO:0000953
EMAPA:17527
EV:0100154
FMA:70323
GAID:1321
MA:0000152
MAT:0000153
MESH:D020405
MIAA:0000153
NCIT:C12701
TAO:0001119
UMLS:C0011646
VHOG:0000108
XAO:0000217
ZFA:0001119
vertebrate dermis
uberon
corium
cutis
UBERON:0002067
dermis
FMA
definitional
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].
ZFIN:curator
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]
2012-08-14
TAO:0001119
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000108
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
UMLS:C0011646
ncithesaurus:Dermis
corium
corium
BTO:0000294
cutis
BTO:0000294
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
hypodermal
subcutaneous
subcutaneus
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.
BTO:0001314
CALOHA:TS-2366
EMAPA:37505
FMA:70544
NCIT:C33645
TAO:0001136
UMLS:C0278403
ZFA:0001136
hypoderm
vertebrate hypodermis
uberon
sub-tegumental tissue
subcutaneous tissue
subcutis
subtegumental tissue
superficial fascia
tela subcutanea
UBERON:0002072
hypodermis
ZFA
FMA-modified
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0001136
TAO
ZFIN:curator
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].
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.
BTO
EMAPA:37505
MA:th
UMLS:C0278403
ncithesaurus:Subcutis
sub-tegumental tissue
BTO:0004525
subcutaneous tissue
subtegumental tissue
BTO:0004525
superficial fascia
tela subcutanea
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
AAO:0010386
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:D014781
NCIT:C28287
RETIRED_EHDAA2:0002201
UMLS:C0042779
XAO:0003034
visceral organ
visceral organ system
uberon
Organsystem@de
splanchnic tissue
viscera
visceral tissue
UBERON:0002075
viscus
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.
BTO:0001491
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
2012-06-20
AAO:0010386
AAO
BTO:0001491
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
FMA
UMLS:C0042779
ncithesaurus:Viscera
visceral organ
RETIRED_EHDAA2:0002201
visceral organ system
MA:0000019
Organsystem@de
BTO:0001491
splanchnic tissue
BTO:0001491
visceral tissue
BTO:0001491
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
axial skeleton
AAO:0000034
EFO:0000942
EHDAA2:0000161
EHDAA:5049
EMAPA:17214
EMAPA:37721
FMA:71221
MA:0002986
MAT:0000148
MIAA:0000148
TAO:0000317
VHOG:0000317
VSAO:0000093
XAO:0003073
ZFA:0000317
post-cranial axial skeleton
uberon
UBERON:0002090
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
postcranial axial skeleton
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
ZFA:0000317
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
2012-08-14
VSAO:0000093
VSAO
PSPUB:0000170
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]
2012-06-20
AAO:0000034
AAO
AAO:LAP
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]
2012-08-14
TAO:0000317
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000317
VHOG
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
axial skeleton
FMA:71221
EMAPA:37721
MA:th
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
BTO:0001253
CALOHA:TS-0934
EFO:0000962
EHDAA2:0001844
EMAPA:17525
FMA:7163
MESH:D012867
MFMO:0000099
NCIT:C12470
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
UMLS:C1123023
XAO:0000023
galen:Skin
entire skin
skin organ
uberon
entire integument
integument
integumental organ
pelt
skin
UBERON:0002097
skin of body
Wikipathways:WP2062
The organ covering the body that consists of the dermis and epidermis.
UBERON:cjm
MA uses the term skin to refer to what is called here: zone of skin
FMA
UMLS:C1123023
ncithesaurus:Skin
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
EMAPA:35400
FMA:7180
GAID:562
MA:0000083
MESH:D006346
NCIT:C49485
UMLS:C0018819
XAO:0004141
cardiac septa
heart septa
heart septum
septum of heart
uberon
spiral septa
UBERON:0002099
cardiac septum
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
MESH:A07.541.459
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
GO
UMLS:C0018819
ncithesaurus:Heart_Septum
cardiac septa
heart septa
spiral septa
XAO:0004141
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
AAO:0010339
BILA:0000116
BTO:0001493
CALOHA:TS-1071
EFO:0000966
EMAPA:31857
FMA:7181
MA:0000004
MAT:0000296
MIAA:0000296
NCIT:C33816
OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA
TAO:0001115
UMLS:C0460005
XAO:0000054
XAO:0003025
ZFA:0001115
galen:Trunk
thoracolumbar region
torso
trunk region
uberon
Rumpf
UBERON:0002100
trunk
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.
TAO:0001115
UBERONREF:0000006
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
2012-06-20
AAO:0010339
AAO
AAO:BJB
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
2012-08-14
TAO:0001115
TAO
ZFIN:curator
UMLS:C0460005
ncithesaurus:Trunk
trunk region
XAO:0000054
Rumpf
BTO:0001493
The sensory system subserving the sense of vision.
The sensory system used for sight.[AAO]
UBERON:0007036
AAO:0000632
BILA:0000140
EMAPA:36003
FMA:7191
MA:0002444
NCIT:C12888
OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA
TAO:0001127
UMLS:C0587900
XAO:0003198
ZFA:0001127
photosensory system
visual organ system
uberon
UBERON:0002104
visual system
The sensory system subserving the sense of vision.
NIFSTD:FMAID_7191
The sensory system used for sight.[AAO]
2012-06-20
AAO:0000632
AAO
AAO:EJS
UMLS:C0587900
ncithesaurus:Visual_System
photosensory system
BILA:0000140
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
BTO:0000087
CALOHA:TS-1198
EMAPA:36285
FMA:72024
MA:0000708
NCIT:C49195
UMLS:C1706851
arterial smooth muscle
artery smooth muscle
artery smooth muscle tissue
smooth muscle of artery
uberon
arterial smooth muscle cell
UBERON:0002111
artery smooth muscle tissue
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
OBOL:automatic
UMLS:C1706851
ncithesaurus:Artery_Smooth_Muscle_Tissue
arterial smooth muscle
BTO:0000087
smooth muscle of artery
FMA:72024
arterial smooth muscle cell
BTO:0000087
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
UBERON:0006225
AAO:0010408
BTO:0000387
CALOHA:TS-2075
EFO:0000821
EHDAA2:0004153
EMAPA:17868
EMAPA:32686
EV:0100021
FMA:7280
GAID:550
MA:0000076
MAT:0000455
MESH:D004699
NCIT:C13004
OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw
TAO:0001320
UMLS:C0014124
VHOG:0000084
XAO:0000066
ZFA:0001320
galen:Endocardium
endocardial lining
endocardial tissue
heart endocardium
uberon
heart endocardial tissue
UBERON:0002165
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
endocardium
Bgee:AN
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
GO:0003157
Layer that lines the lumen of the heart.[TAO]
2012-08-14
TAO:0001320
TAO
ZFIN:curator
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
2012-06-20
AAO:0010408
AAO
AAO:BJB
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
FMA:7280
UMLS:C0014124
ncithesaurus:Endocardium
endocardial lining
EMAPA:32686
endocardial tissue
EMAPA:17868
heart endocardial tissue
VHOG:0000084
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0001730
EHDAA:4969
EMAPA:17661
FMA:7309
MA:0000426
NCIT:C33483
OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225706
VHOG:0000301
uberon
UBERON:0002167
right lung
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
FMA:FMA
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
2012-09-17
VHOG:0000301
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
UMLS:C0225706
ncithesaurus:Right_Lung
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0000943
EHDAA:4947
EMAPA:17653
FMA:7310
MA:0000425
NCIT:C32967
OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225730
VHOG:0000618
uberon
UBERON:0002168
left lung
Lung which consists of the left upper lobe and left lower lobe.[FMA]
FMA:FMA
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
2012-09-17
VHOG:0000618
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
UMLS:C0225730
ncithesaurus:Left_Lung
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
UBERON:0008875
panniculus adiposus
BTO:0004042
EMAPA:35829
FMA:74315
MA:0000473
fatty layer of subcutaneous tissue
hypodermis fat layer
panniculus adiposus (tela subcutanea)
panniculus adiposus telae subcutaneae
subcutaneous fat layer
uberon
fatty layer of superficial fascia
subcutaneous fat
UBERON:0002190
subcutaneous adipose tissue
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
MP:0011156
panniculus adiposus
MP:0011156
fatty layer of subcutaneous tissue
FMA:74315
hypodermis fat layer
MP:0011156
panniculus adiposus (tela subcutanea)
FMA:74315
FMA:TA
panniculus adiposus telae subcutaneae
FMA:74315
FMA:TA
subcutaneous fat layer
MP:0011156
fatty layer of superficial fascia
FMA:74315
subcutaneous fat
BTO:0004042
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
CALOHA:TS-2018
EHDAA2:0004615
EMAPA:18765
FMA:74562
MA:0000013
hematolymphoid system
lymphomyeloid complex
uberon
haemolymphoid system
UBERON:0002193
hemolymphoid system
MA
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
The dermis, epidermis and hypodermis.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
integumental
integumentary
AAO:0000239
BTO:0000634
EMAPA:37504
FMA:74657
TAO:0000368
VSAO:0000029
ZFA:0000368
galen:Integument
dermis plus epidermis plus hypodermis
integumentum commune
skin and subcutaneous tissue
skin plus hypodermis
the integument
uberon
Hautsystem@de
dermal system
dermoid system
skin
tegument
vertebrate integument
UBERON:0002199
integument
FMA
FMA
The dermis, epidermis and hypodermis.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
2012-06-20
AAO:0000239
AAO
AAO:EJS
Surface structure that is the outer protective covering of the body.[VSAO]
2012-08-14
VSAO:0000029
VSAO
PSPUB:0000170
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0000368
TAO
ZFIN:curator
EMAPA:37504
MA:th
integumentum commune
FMA:74657
FMA:TA
the integument
FMA:74657
Hautsystem@de
BTO:0000634
dermal system
BTO:0000634
dermoid system
BTO:0000634
tegument
BTO:0000634
Vasculature that is part of a head [Automatically generated definition].
EFO:0003656
FMA:74710
TAO:0001267
XAO:0004152
ZFA:0001267
adult head vascular network
adult head vasculature
cranial vasculature
head vascular network
vascular network of adult head
vascular network of head
vasculature of adult head
uberon
head vasculature
UBERON:0002200
vasculature of head
Vasculature that is part of a head [Automatically generated definition].
OBOL:automatic
adult head vascular network
OBOL:automatic
adult head vasculature
OBOL:automatic
head vascular network
OBOL:automatic
vascular network of adult head
OBOL:automatic
vascular network of head
OBOL:automatic
vasculature of adult head
OBOL:automatic
A vasculature that is part of a trunk [Automatically generated definition].
FMA:74712
TAO:0005024
ZFA:0005024
torso vascular network
torso vasculature
trunk vascular network
trunk vasculature
vascular network of torso
vascular network of trunk
vasculature of torso
uberon
UBERON:0002201
vasculature of trunk
A vasculature that is part of a trunk [Automatically generated definition].
OBOL:automatic
torso vascular network
OBOL:automatic
torso vasculature
OBOL:automatic
trunk vascular network
OBOL:automatic
vascular network of torso
OBOL:automatic
vascular network of trunk
OBOL:automatic
vasculature of torso
OBOL:automatic
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
FMA:74743
TAO:0007057
ZFA:0007057
eye vascular network
ocular blood vessel
ocular vasculature
vascular network of eye
uberon
eye vasculature
optic vasculature
UBERON:0002203
vasculature of eye
ISBN:0781772214
Vasculature that is part of the eye region.
OBOL:automatic
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
ZFA
eye vascular network
OBOL:automatic
ocular blood vessel
ZFA:0007057
vascular network of eye
OBOL:automatic
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]
musculoskeletal
AAO:0010546
CALOHA:TS-1311
EMAPA:32714
EV:0100139
FMA:7482
GAID:98
MA:0002418
MESH:D009141
NCIT:C12754
OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
UMLS:C0026860
VHOG:0001275
VSAO:0000031
XAO:0000168
musculo-skeletal system
uberon
UBERON:0002204
musculoskeletal system
check ctenophore
Anatomical system that consists of the muscular and skeletal systems.
VSAO:0000031
VSAO:curator
Anatomical system that provides locomotion and physical support to the organism.[AAO]
2012-06-20
AAO:0010546
AAO
AAO:EJS
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]
2012-09-17
VHOG:0001275
VHOG
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
UMLS:C0026860
ncithesaurus:Musculoskeletal_System
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
AEO:0000183
CALOHA:TS-2138
EHDAA2:0003183
FMA:7501
MA:0000322
NCIT:C32461
OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA
TAO:0005153
ZFA:0005153
galen:SynovialJoint
articulatio synoviale
diarthroses
diarthrosis
diarthrosis joint
uberon
diarthrodial joints
UBERON:0002217
synovial joint
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]
FMA:7501
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]
2012-08-14
TAO:0005153
TAO
ZFIN:Curator
diarthroses
ZFA:0005153
diarthrodial joints
ZFA:0005153
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
EMAPA:36497
FMA:7565
GAID:93
MA:0000032
MESH:A01.911.800
NCIT:C12905
OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg
OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA
UMLS:C0230139
cavitas thoracis
cavity of chest
cavity of thorax
chest cavity
pectoral cavity
space of thoracic compartment
thoracic lumen
uberon
UBERON:0002224
thoracic cavity
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
UBERON:cjm
UMLS:C0230139
ncithesaurus:Thoracic_Cavity
cavitas thoracis
space of thoracic compartment
FMA:7565
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
(...) 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]
AAO:0010151
BAMS:SP
BAMS:Spinal
BIRNLEX:1709
BM:SpC
BTO:0001279
CALOHA:TS-0953
DHBA:12890
DMBA:17651
EFO:0000110
EHDAA2:0001255
EHDAA:2863
EMAPA:17577
EV:0100316
FMA:7647
GAID:695
MA:0000216
MAT:0000183
MESH:D013116
MIAA:0000183
NCIT:C12464
OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA
TAO:0000075
UMLS:C0037925
VHOG:0000601
XAO:0000020
ZFA:0000075
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22
uberon
SpC
cerebro-cerebellar fissure
cerebrocerebellar fissure
fissura cerebro-cerebellaris
fissura cerebrocerebellaris
medulla spinalis
spinal cord structure
spinal medulla
UBERON:0002240
spinal cord
definitional
definitional
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)
BIRNLEX:1709
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
2012-06-20
AAO:0010151
AAO
AAO:BJB
(...) 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]
2012-09-17
VHOG:0000601
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
UMLS:C0037925
BIRNLEX:1709
UMLS:C0037925
ncithesaurus:Spinal_Cord
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22
BIRNLEX:1709
SpC
cerebro-cerebellar fissure
NeuroNames:22
cerebrocerebellar fissure
NeuroNames:22
fissura cerebro-cerebellaris
NeuroNames:22
fissura cerebrocerebellaris
NeuroNames:22
medulla spinalis
medulla spinalis
BTO:0001279
spinal cord structure
ZFA:0000075
spinal medulla
BTO:0001279
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
BAMS:BS
BIRNLEX:1565
BTO:0000146
CALOHA:TS-0093
EFO:0001962
EMAPA:32678
EV:0100241
FMA:79876
MA:0000169
MBA:343
MESH:D001933
NCIT:C12441
TAO:0002156
UMLS:C0006121
VHOG:0001457
ZFA:0001707
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236
brain stem
truncus encephali
uberon
accessory medullary lamina of pallidum
lamella pallidi incompleta
lamina medullaris accessoria
lamina medullaris incompleta pallidi
lamina pallidi incompleta
truncus encephalicus
UBERON:0002298
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
brainstem
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].
ISBN:0471888893
MP:0005277
ZFA:0001707
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
2012-08-14
TAO:0002156
TAO
ISBN:3764351209
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
ZFA:0001707
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
MP:0005277
UMLS:C0006121
BIRNLEX:1565
UMLS:C0006121
ncithesaurus:Brain_Stem
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236
BIRNLEX:1565
brain stem
ABA:BS
truncus encephali
accessory medullary lamina of pallidum
NeuroNames:236
lamella pallidi incompleta
NeuroNames:236
lamina medullaris accessoria
NeuroNames:236
lamina medullaris incompleta pallidi
NeuroNames:236
lamina pallidi incompleta
NeuroNames:236
truncus encephalicus
BTO:0000146
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
BAMS:Scgrey
DHBA:146035048
EMAPA:35792
FMA:256580
MA:0000002
NCIT:C32696
NLXANAT:100204
UMLS:C0475853
gray matter of spinal cord
gray substance of spinal cord
grey matter of spinal cord
grey substance of spinal cord
spinal cord gray matter
spinal cord grey matter
spinal cord grey substance
substantia grisea medullae spinalis
uberon
UBERON:0002315
gray matter of spinal cord
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
MP:0008503
UMLS:C0475853
ncithesaurus:Gray_Matter_of_the_Spinal_Cord
gray matter of spinal cord
OBOL:automatic
gray substance of spinal cord
FMA:256580
spinal cord gray matter
OBOL:automatic
spinal cord grey substance
OBOL:automatic
substantia grisea medullae spinalis
FMA:256580
FMA:TA
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
UBERON:0000169
body cavity
AEO:0000186
BTO:0001707
EHDAA2:0000267
FBbt:00005060
FMA:85006
NCIT:C25444
RETIRED_EHDAA2:0003186
TAO:0001438
UMLS:C0333343
ZFA:0001438
galen:BodyCavity
coelomic cavity
coelomic cavity lumen
main body cavity
space of body compartment
ventral body cavity
uberon
celom
coelom
coelome
hemocoel
UBERON:0002323
coelemic cavity lumen
definitional
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:0001707
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
2012-09-12
ZFA:0001438
ZFA
ZFIN:curator
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].
2012-09-12
BTO:0001707
BTO
BTO
body cavity
BTO:0001707
UMLS:C0333343
ncithesaurus:Cavity
coelomic cavity
EHDAA2:0000267
coelomic cavity lumen
EHDAA2:0000267
space of body compartment
FMA:85006
ventral body cavity
NCBITaxon:7742
celom
BTO:0001707
coelome
BTO:0001707
hemocoel
FBbt:00005060
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
notochordal
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.
AAO:0000327
BTO:0001768
CALOHA:TS-0690
EHDAA2:0001277
EHDAA:1241
EHDAA:6021
EMAPA:16191
EV:0100002
FMA:85521
GAID:1311
MAT:0000281
MESH:A16.254.610
NCIT:C12463
TAO:0000135
UMLS:C0028439
VHOG:0000199
VSAO:0000032
XAO:0000055
ZFA:0000135
embryonic notocord
notocord
uberon
notochorda
UBERON:0002328
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]
notochord
VSAO
ZFA
EHDAA2
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.
ISBN:0815318960
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
2012-08-14
VSAO:0000032
VSAO
PSPUB:0000170
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]
2012-08-14
TAO:0000135
TAO
ZFIN:curator
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]
2012-06-20
AAO:0000327
AAO
AAO:LAP
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
2012-06-20
AAO:0000327
AAO
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
2012-09-17
VHOG:0000199
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
UMLS:C0028439
ncithesaurus:Notochord
notocord
ZFA:0000135
notochorda
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
somitic
mesodermal cluster
AAO:0010569
AEO:0001015
BTO:0001558
EHDAA2:0003436
EHDAA:366
EHDAA:699
EMAPA:31169
FMA:85522
GAID:1306
MAT:0000068
MESH:A16.254.425.660.750
MIAA:0000068
NCIT:C34302
TAO:0000155
UMLS:C0376449
VHOG:0000191
XAO:0000058
ZFA:0000155
uberon
epimere
epimere mesoderm
epithelial somite
somites
somitic mesoderm
somitus
UBERON:0002329
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]
somite
EHDAA2
ZFA
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.
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
2012-06-20
AAO:0010569
AAO
AAO:EJS
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]
2012-08-14
TAO:0000155
TAO
ZFIN:curator
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
2012-08-14
TAO:0000155
TAO
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
2012-08-14
TAO:0000155
TAO
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
2012-06-20
AAO:0010569
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]
2012-09-17
VHOG:0000191
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
mesodermal cluster
GO:0001756
UMLS:C0376449
ncithesaurus:Somite
epimere
ISBN:0073040584
epithelial somite
somites
somitus
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].
CALOHA:TS-2057
EHDAA2:0002225
EMAPA:35329
FMA:85539
MA:0002411
NCIT:C12957
UMLS:C1516995
WikipediaCategory:Exocrine_system
exocrine glandular system
uberon
UBERON:0002330
exocrine system
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].
UMLS:C1516995
ncithesaurus:Exocrine_System
exocrine glandular system
EHDAA2:0002225
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
EHDAA2:0001576
EHDAA:9831
EMAPA:17015
FMA:8612
MA:0002033
NCIT:C116918
OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA
VHOG:0001134
galen:PulmonaryTrunk
pulmonary artery (trunk)
trunk of pulmonary arterial tree
uberon
main pulmonary artery
UBERON:0002333
pulmonary trunk
MA
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
2012-09-17
VHOG:0001134
VHOG
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
2012-09-17
VHOG:0001134
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
main pulmonary artery
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
AAO:0010578
BTO:0001764
CALOHA:TS-0676
EHDAA2:0004419
EMAPA:32737
FMA:86666
GAID:1310
MAT:0000066
MESH:A16.254.600
MIAA:0000066
NCIT:C34222
TAO:0000045
UMLS:C0027789
VHOG:0000057
XAO:0000048
ZFA:0000045
NC
uberon
crista neuralis
neural crest material
UBERON:0002342
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.
neural crest
XAO
BTO
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].
MP:0009846
ISBN:0073040584
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]
2012-08-14
TAO:0000045
TAO
ZFIN:curator
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
2012-06-20
AAO:0010578
AAO
AAO:EJS
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
2012-09-17
VHOG:0000057
VHOG
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
UMLS:C0027789
ncithesaurus:Neural_Crest
NC
XAO:0000048
crista neuralis
neural crest material
VHOG:0000057
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
neurectodermal
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
AAO:0011074
BILA:0000039
CALOHA:TS-1212
EHDAA2:0001248
EHDAA:1498
EHDAA:255
EMAPA:16073
EV:0100004
FBbt:00001061
FMA:87657
MAT:0000176
MIAA:0000176
NCIT:C34228
TAO:0001120
UMLS:C1518271
VHOG:0000150
XAO:0000042
ZFA:0001120
neural ectoderm
neuroectoderm
uberon
epithelium tubi neuralis; neuroectoderma
neuaral ectoderm
presumptive central nervous system
ventral neurogenic region
UBERON:0002346
neurectoderm
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
2012-09-17
VHOG:0000150
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
UMLS:C1518271
ncithesaurus:Neuroectoderm
epithelium tubi neuralis; neuroectoderma
ventral neurogenic region
VHOG:0000150
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
AEO:0000097
BTO:0000765
CALOHA:TS-2012
EHDAA2:0003097
EMAPA:35327
FMA:9596
GAID:34
MA:0002564
MESH:D005088
NCIT:C12712
UMLS:C0015282
ducted gland
glandula exocrina
uberon
UBERON:0002365
exocrine gland
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
UMLS:C0015282
ncithesaurus:Exocrine_Gland
ducted gland
AEO:0000097
glandula exocrina
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
MA also has set of connective tissues
AAO:0000098
BTO:0000421
CALOHA:TS-2009
EFO:0000952
EMAPA:35251
FMA:9640
GAID:100
MA:0000011
MAT:0000301
MESH:D003238
MIAA:0000301
NCIT:C12374
OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA
TAO:0001641
UMLS:C0009780
VSAO:0000017
XAO:0001017
ZFA:0001632
galen:ConnectiveTissue
portion of connective tissue
textus connectivus
uberon
Bindegewebe
UBERON:0002384
connective tissue
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
GO_REF:0000034
PSPUB:0000170
VSAO:0000017
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]
2012-06-20
AAO:0000098
AAO
AAO:LAP
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]
2012-08-14
TAO:0001641
TAO
TAO:wd
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
2012-08-14
VSAO:0000017
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
MA also has set of connective tissues
MA
UMLS:C0009780
ncithesaurus:Connective_Tissue
portion of connective tissue
FMA:9640
Bindegewebe
BTO:0000421
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]
AAO:0000306
AEO:0000122
CALOHA:TS-0642
EHDAA2:0003122
EMAPA:32715
FMA:9641
MA:0002437
MESH:D009132
NCIT:C12435
UMLS:C2328219
galen:MuscleTissue
muscular tissue
portion of muscle tissue
textus muscularis
uberon
UBERON:0002385
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.
muscle tissue
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
GO:0060537
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]
2012-06-20
AAO:0000306
AAO
AAO:LAP
UMLS:C2328219
ncithesaurus:Muscle_Tissue
muscular tissue
portion of muscle tissue
FMA:9641
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
hematopoietic
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
AAO:0011002
BTO:0000570
CALOHA:TS-0449
EFO:0000798
EMAPA:35402
EV:0100045
FMA:9667
GAID:1008
MA:0002434
MAT:0000022
MESH:D006413
MIAA:0000022
NCIT:C12909
TAO:0005023
UMLS:C0018957
VHOG:0001624
XAO:0000122
ZFA:0005023
haematological system
haemopoietic system
organa haemopoietica
uberon
Blutbildungssystem
haematopoietic system
hematological system
hematolymphoid system
hemopoietic system
UBERON:0002390
hematopoietic system
FMA
definitional
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
2012-06-20
AAO:0011002
AAO
AAO:EJS
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
2012-09-17
VHOG:0001624
VHOG
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
WP
UMLS:C0018957
ncithesaurus:Hematopoietic_System
Blutbildungssystem
BTO:0000570
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
UBERON:0007029
AEO:0000154
BILA:0000118
CALOHA:TS-1299
CARO:0002001
EFO:0000807
EHDAA2:0000836
EHDAA2_RETIRED:0003154
EHDAA:6520
EMAPA:17524
EV:0100151
FBbt:00004969
FMA:72979
HAO:0000421
MA:0000014
MAT:0000033
MESH:D034582
MIAA:0000033
NCIT:C12907
TADS:0000108
UMLS:C0037267
VHOG:0000403
XAO:0000176
galen:Surface
integumentary system
uberon
body surface
dermal system
external covering of organism
integumentum commune
organism surface
surface
UBERON:0002416
integumental system
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.
CARO:0002001
(...) 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]
2012-09-17
VHOG:0000403
VHOG
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
UMLS:C0037267
ncithesaurus:Integumentary_System
integumentary system
FMA:72979
dermal system
MIAA:0000033
integumentum commune
organism surface
EHDAA2:0003154
surface
BILA:0000118
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
EMAPA:35774
FMA:71878
MA:0000146
glandulae cutis
uberon
set of skin glands
skin glands
skin glands set
UBERON:0002419
skin gland
A gland that is part of a skin of body [Automatically generated definition].
OBOL:automatic
glandulae cutis
FMA:71878
FMA:TA
set of skin glands
FMA:71878
skin glands
skin glands set
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
AAO:0010357
BTO:0001775
CALOHA:TS-0715
EHDAA2:0001325
EHDAA:2187
EMAPA:16839
EMAPA:26942
FMA:265152
MA:0000344
NCIT:C49595
TAO:0000816
UMLS:C1709332
VHOG:0000187
XAO:0003201
ZFA:0000816
epithelium of mucosa of mouth
epithelium of oral mucosa
uberon
UBERON:0002424
oral epithelium
AAO-modified
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
ZFA:0000816
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
UMLS:C1709332
ncithesaurus:Oral_Cavity_Epithelium
epithelium of mucosa of mouth
FMA:265152
epithelium of oral mucosa
FMA:265152
A blood vessel that is part of a choroid [Automatically generated definition].
EMAPA:17828
FMA:76550
MA:0001237
blood vessel of choroid
blood vessel of choroid coat
blood vessel of choroidea
blood vessel of posterior uvea
choroid blood vessel
choroid blood vessels
choroid blood vessels set
choroid coat blood vessel
choroidea blood vessel
posterior uvea blood vessel
vasa sanguinea choroideae
uberon
set of choroid blood vessels
UBERON:0002443
cannot find singular in FMA, using Set class
choroidal blood vessel
A blood vessel that is part of a choroid [Automatically generated definition].
OBOL:automatic
blood vessel of choroid
OBOL:automatic
blood vessel of choroid coat
OBOL:automatic
blood vessel of choroidea
OBOL:automatic
blood vessel of posterior uvea
OBOL:automatic
choroid blood vessel
OBOL:automatic
choroid coat blood vessel
OBOL:automatic
choroidea blood vessel
OBOL:automatic
posterior uvea blood vessel
OBOL:automatic
vasa sanguinea choroideae
FMA:76550
FMA:TA
set of choroid blood vessels
FMA:76550
Arteries that supply the spinal cord.
EHDAA2:0001890
EHDAA:4355
EMAPA:18241
MA:0002043
NCIT:C33587
TAO:0000682
UMLS:C0447043
ZFA:0000682
spinal arteries
uberon
UBERON:0002458
spinal artery
Arteries that supply the spinal cord.
UMLS:C0447043
ncithesaurus:Spinal_Artery
spinal arteries
ZFA:0000682
An epithelium that is part of a iris [Automatically generated definition].
EMAPA:35447
FMA:58517
MA:0002826
epithelial tissue of iris
epithelium of iris
epithelium pigmentosum (iris)
epithelium pigmentosum iridis
iris epithelial tissue
iris epithelium
pigmented epithelium of iris
uberon
iris pigmented epithelium
UBERON:0002506
iris epithelium
FMA
MA
An epithelium that is part of a iris [Automatically generated definition].
OBOL:automatic
epithelial tissue of iris
OBOL:automatic
epithelium of iris
OBOL:automatic
epithelium pigmentosum (iris)
FMA:58517
epithelium pigmentosum iridis
FMA:58517
FMA:TA
iris epithelial tissue
OBOL:automatic
iris epithelium
FMA:58517
pigmented epithelium of iris
FMA:58517
iris pigmented epithelium
MA:0002826
Connective tissue composed of elastic fibers.
FMA:20113
GAID:926
MA:0002853
MESH:D004547
NCIT:C32495
elastic connective tissue
textus connectivus elasticus
elastic fiber
uberon
UBERON:0002521
elastic tissue
Connective tissue composed of elastic fibers.
textus connectivus elasticus
The middle layer of an artery or vein. [WP,unvetted].
BTO:0002011
EMAPA:36298
FMA:55590
GAID:170
MA:0002855
MESH:D017540
NCIT:C33821
UMLS:C0162867
uberon
tunica media vasorum
UBERON:0002522
May be composed of smooth muscle and elastic tissue
tunica media
MA
cjm
cjm
The middle layer of an artery or vein. [WP,unvetted].
UMLS:C0162867
ncithesaurus:Tunica_Media
tunica media vasorum
tunica media vasorum
BTO:0002011
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
BTO:0002012
EMAPA:36297
FMA:55589
GAID:523
MA:0002861
MESH:D017539
NCIT:C33820
UMLS:C0162864
uberon
Bichat's tunic
intima
tunica intima vasorum
UBERON:0002523
tunica intima
FMA
check for exceptions, e.g. capillaries
ISBN:0073040584
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
ISBN:0073040584
NCIT:C33820
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
Wikipedia
UMLS:C0162864
ncithesaurus:Tunica_Intima
Bichat's tunic
BTO:0002012
intima
BTO:0002012
tunica intima vasorum
BTO:0002012
an organ that functions as a secretory or excretory organ
glandular
UBERON:MIAA_0000021
AAO:0000212
AEO:0000096
BTO:0000522
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:7146
FMA:86294
HAO:0000375
MA:0003038
MAT:0000021
MIAA:0000021
NCIT:C13319
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandular organ
uberon
Druese
glandula
UBERON:0002530
gland
an organ that functions as a secretory or excretory organ
MGI:csmith
MP:0002163
UMLS:C1285092
ncithesaurus:Gland
glandular organ
Druese
BTO:0000522
glandula
glandula
BTO:0000522
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
BTO:0004593
FMA:296704
MAT:0000067
MIAA:0000067
VHOG:0000243
epiblast
uberon
blastocyst
ectoblast
epiblastus
primitive ectoderm
UBERON:0002532
epiblast (generic)
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]
ZFIN:curator
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]
2012-09-17
VHOG:0000243
VHOG
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
epiblast
VHOG:0000243
ectoblast
MP:0003886
epiblastus
primitive ectoderm
VHOG:0000243
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
AAO:0010359
BTO:0001785
EFO:0000959
EHDAA:571
EMAPA:16117
FMA:293015
GAID:1292
MAT:0000242
MESH:A16.254.160
MIAA:0000242
NCIT:C34249
TAO:0001306
UMLS:C0080322
VHOG:0000155
XAO:0000096
ZFA:0001306
pharyngeal arches
branchial arch
uberon
arcus pharyngei
visceral arch
UBERON:0002539
pharyngeal arch
EHDAA2
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
ZFA:yb
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
2012-06-20
AAO:0010359
AAO
NLM:branchial+arch
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
2012-09-17
VHOG:0000155
VHOG
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
UMLS:C0080322
ncithesaurus:Pharyngeal_Arch
pharyngeal arches
branchial arch
BTO:0001785
MP:0002884
arcus pharyngei
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.
Do not merge with neurogenic placode
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
ectodermal placode
placode
AAO:0010466
EFO:0001650
FMA:293966
MAT:0000369
MIAA:0000369
XAO:0000305
ectodermal cranial placode
uberon
cranial placodes
UBERON:0002546
cranial placode
cjm
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
ectodermal placode
FMA:293966
placode
ectodermal cranial placode
UBERON:cjm
cranial placodes
XAO:0000305
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
TODO discriminate between stages and organisms
Whole organism that is premetamorphic or a very immature individual.[TAO]
larval
AEO:0000126
BTO:0000707
FBbt:00001727
HAO:0000459
OpenCyc:Mx4rwQCBvZwpEbGdrcN5Y29ycA
TAO:0002048
larval organism
ammocoete
bipinnaria
caterpillar
glochidium
grub
leptocephalus
maggot
naiad
nymph
planula
tadpole
trochophore
veliger
wriggler
zoea
uberon
UBERON:0002548
larva
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Whole organism that is premetamorphic or a very immature individual.[TAO]
2012-08-14
TAO:0002048
TAO
TAO:wd
larval organism
TAO:0002048
ammocoete
bipinnaria
caterpillar
glochidium
grub
leptocephalus
maggot
naiad
nymph
planula
tadpole
trochophore
veliger
wriggler
zoea
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.
cavity
BIRNLEX:1011
EMAPA:37442
FMA:67552
MA:0002447
NCIT:C34007
galen:Cavity
uberon
UBERON:0002553
anatomical cavity
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.
FMA:67552
EMAPA:37442
MA:th
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.
BIRNLEX:1167
FMA:55676
NCIT:C13031
UMLS:C0445620
anatomical structure of brain
biological structure of brain
brain anatomical structure
brain biological structure
brain part
neuraxis segment
neuroanatomical region
segment of brain
uberon
UBERON:0002616
regional part of brain
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.
BIRNLEX:1167
UMLS:C0445620
ncithesaurus:Brain_Part
anatomical structure of brain
OBOL:automatic
biological structure of brain
OBOL:automatic
brain anatomical structure
OBOL:automatic
brain biological structure
OBOL:automatic
neuraxis segment
FMA:55676
segment of brain
BIRNLEX:1167
A wall, dividing a cavity or structure into smaller ones[WP].
septal
AAO:0011127
FMA:86461
OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ
septa
uberon
UBERON:0003037
general anatomical term in FMA
septum
A wall, dividing a cavity or structure into smaller ones[WP].
septa
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
AAO:0011064
DMBA:16810
EHDAA2:0004395
EHDAA:5789
EMAPA:32857
NCIT:C93172
TAO:0000042
VHOG:0000649
XAO:0000016
ZFA:0000042
MHB
mid-hindbrain boundary
mid-hindbrain junction
midbrain hindbrain boundary
uberon
isthmic organizer territory
isthmo-cerebellar region
isthmus
isthmus/MHB
UBERON:0003052
midbrain-hindbrain boundary
ZFA
ZFA
ZFA
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.
GO:0021555
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
2012-09-17
VHOG:0000649
VHOG
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
isthmic organizer territory
XAO:0000016
isthmo-cerebellar region
VHOG:0000649
isthmus/MHB
Geisha:syn
NCBITaxon:8782
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
EHDAA2:0001846
EHDAA:6538
FMA:295662
NCIT:C34247
TAO:0001185
UMLS:C1518973
VHOG:0001680
XAO:0000029
ZFA:0001185
skin periderm
uberon
EVL
epidermis epithelial layer
epidermis outer layer
epitrichium
periderm
UBERON:0003055
periderm
EHDAA2
EHDAA2
ZFA
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.
ISBN:9780878932504
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]
2012-08-14
TAO:0001185
TAO
ZFIN:curator
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
2012-08-14
TAO:0001185
TAO
UMLS:C1518973
ncithesaurus:Periderm
skin periderm
EHDAA2:0001846
EVL
ZFA:0001185
epitrichium
MP:0013530
The portion of neural plate anterior to the mid-hindbrain junction.
(...) 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]
AAO:0011084
TAO:0007016
VHOG:0001200
XAO:0000045
ZFA:0007016
uberon
anterior neural plate
UBERON:0003056
pre-chordal neural plate
The portion of neural plate anterior to the mid-hindbrain junction.
XB:curator
(...) 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]
2012-09-17
VHOG:0001200
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The portion of neural plate posterior to the mid-hindbrain junction.
(...) 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]
TAO:0007017
VHOG:0001201
XAO:0000046
ZFA:0007017
uberon
posterior neural plate
UBERON:0003057
chordal neural plate
The portion of neural plate posterior to the mid-hindbrain junction.
XB:curator
(...) 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]
2012-09-17
VHOG:0001201
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
AAO:0011086
EFO:0001982
EMAPA:16189
EMAPA:16752
TAO:0000279
VHOG:0000559
XAO:0000057
ZFA:0000279
segmental plate
unsegmented paraxial mesoderm
uberon
PSM
presumptive somite mesoderm
somitogenic mesoderm
somitomeric mesoderm
unsegmented mesenchyme
UBERON:0003059
presomitic mesoderm
Bgee:AN
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
ZFIN:curator
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000279
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000559
VHOG
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
unsegmented paraxial mesoderm
somitomeric mesoderm
GO:0002075
unsegmented mesenchyme
VHOG:0000559
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ventral lateral plate mesoderm
AAO:0011006
EFO:0003489
EHDAA:207
NCIT:C34113
TAO:0000094
TE:E5.11.2.0.0.0.4
UMLS:C1511224
VHOG:0000085
XAO:0000067
ZFA:0000094
blood islands
uberon
VBI
caudal hematopoietic tissue
posterior ICM
posterior blood island
ventral blood island
UBERON:0003061
blood island
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000094
TAO
ZFIN:curator
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]
2012-06-20
AAO:0011006
AAO
AAO:EJS
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
2012-08-14
TAO:0000094
TAO
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000085
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
EHDAA2
UMLS:C1511224
ncithesaurus:Blood_Island
blood islands
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
UBERON:0004881
head mesenchyme
head mesoderm
AAO:0011085
EHDAA2:0001493
EHDAA:181
FMA:295532
TAO:0000060
VHOG:0000086
XAO:0000079
ZFA:0000060
uberon
UBERON:0003063
prechordal plate
ZFA
PMID:16313393
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
ISBN:0838580343
MP:0004387
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000060
TAO
ZFIN:curator
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
2012-09-17
VHOG:0000086
VHOG
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
2012-09-17
VHOG:0000086
VHOG
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
head mesenchyme
XAO:0000079
head mesoderm
XAO:0000079
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]
AAO:0011017
EFO:0003647
TAO:0001204
VHOG:0000107
XAO:0000205
ZFA:0001204
uberon
chordamesoderm
UBERON:0003068
axial mesoderm
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
GO:0048318
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]
2012-09-17
VHOG:0000107
VHOG
chordamesoderm
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.
UBERON:0005060
AAO:0011038
EFO:0003541
EHDAA2:0004431
TAO:0000570
XAO:0000227
XAO:0004090
ZFA:0000570
eye placode
occular primordium
ocular primordium
optic placode
optic placode of camera-type eye
optic primordium
uberon
eye anlage
eye field
optic field
optic placodes
UBERON:0003071
eye primordium
EHDAA2
XAO
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.
GO:0046619
ZFA:0000570
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.
GO
eye placode
OBOL:automatic
optic placode
GO:0046619
optic placode of camera-type eye
GO:0046619
eye anlage
XAO:0000227
optic placodes
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
BTO:0005351
EHDAA2:0001303
EHDAA:2912
EMAPA:16674
NCIT:C34233
TAO:0001202
UMLS:C0231109
VHOG:0000167
ZFA:0001202
uberon
eye cup
eyecup
ocular cup
ophtalmic cup
UBERON:0003072
optic cup
ZFA
ZFA
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].
MP:0004269
ZFA:0001202
(...) 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]
2012-09-17
VHOG:0000167
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C0231109
ncithesaurus:Optic_Cup
eyecup
BTO:0005351
ocular cup
VHOG:0000167
ophtalmic cup
BTO:0005351
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
AAO:0011055
EFO:0003494
EHDAA2:0000982
EHDAA:2908
EMAPA:16672
FMA:296767
NCIT:C34202
TAO:0000122
UMLS:C1517770
VHOG:0000166
XAO:0000240
ZFA:0000122
uberon
lens placodes
placoda lentis
UBERON:0003073
lens placode
NCBIBook:NBK53175
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
ZFIN:curator
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000122
TAO
ZFIN:curator
(...) 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]
2012-09-17
VHOG:0000166
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
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)
NCBIBook:NBK53175
UMLS:C1517770
ncithesaurus:Lens_Placodes
lens placodes
ZFA:0000122
placoda lentis
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]
(...) 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]
AAO:0011072
BTO:0001765
DHBA:10153
DMBA:15565
EHDAA:346
EHDAA:902
EMAPA:35593
FMA:293879
NCIT:C34225
RETIRED_EHDAA2:0001252
TAO:0000132
UMLS:C0920623
VHOG:0000068
XAO:0000249
ZFA:0000132
uberon
lamina neuralis
presumptive central nervous system
UBERON:0003075
neural plate
Wikipedia
Bgee:AN
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]
ISBN:0815318960
OMD:neural+plate
ZFIN:curator
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]
2012-08-14
TAO:0000132
TAO
ZFIN:curator
(...) 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]
2012-09-17
VHOG:0000068
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
UMLS:C0920623
ncithesaurus:Neural_Plate
lamina neuralis
(...) 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]
AAO:0011082
TAO:0007037
VHOG:0001383
XAO:0000250
ZFA:0007037
uberon
UBERON:0003076
posterior neural tube
lexical
(...) 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]
2012-09-17
VHOG:0001383
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
AAO:0010568
EFO:0003515
EMAPA:16183
EMAPA:16751
FMA:293145
NCIT:C34244
TAO:0000255
UMLS:C1284009
VHOG:0000114
XAO:0000259
ZFA:0000255
paraxial mesenchyme
somitic mesoderm
uberon
mesoderma paraxiale
UBERON:0003077
paraxial mesoderm
EHDAA2
Bgee:AN
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
GO:0048339
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]
2012-06-20
AAO:0010568
AAO
AAO:EJS
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]
2012-09-17
VHOG:0000114
VHOG
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
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)
ZFA
UMLS:C1284009
ncithesaurus:Paraxial_Mesoderm
paraxial mesenchyme
ZFA:0000255
somitic mesoderm
ISBN:9780878932504
mesoderma paraxiale
TODO - add grouping class for the anterior end of the neural tube at all stages
(...) 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]
AAO:0011012
TAO:0007038
VHOG:0001384
XAO:0000307
ZFA:0007038
uberon
UBERON:0003080
anterior neural tube
lexical
(...) 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]
2012-09-17
VHOG:0001384
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
subclass of mesoderm in ZFA.
UBERON:0006258
AAO:0010574
EHDAA2:0000919
EHDAA:379
EMAPA:16179
FMA:293149
NCIT:C34199
TAO:0000121
UMLS:C1517749
VHOG:0000118
XAO:0000311
ZFA:0000121
LPM
lateral mesoderm
uberon
lateral plate
lateral plate mesenchyme
mesoderma laminae lateralis
UBERON:0003081
lateral plate mesoderm
EHDAA2
EHDAA2
VHOG
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].
MP:0010117
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
2012-06-20
AAO:0010574
AAO
AAO:EJS
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]
2012-09-17
VHOG:0000118
VHOG
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
2012-09-17
VHOG:0000118
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
subclass of mesoderm in ZFA.
ZFA
UMLS:C1517749
ncithesaurus:Lateral_Mesoderm
LPM
ZFA:0000121
lateral mesoderm
GO:0048368
lateral plate mesenchyme
EHDAA2:0000919
mesoderma laminae lateralis
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
AAO:0011044
BTO:0001887
NCIT:C34276
TAO:0000028
UMLS:C1514450
XAO:0000336
ZFA:0000028
uberon
cardiac field
fused heart primordium
UBERON:0003084
heart primordium
Obol
ZFA
ZFA
XAO
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.
ZFIN:curator
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]
2012-08-14
TAO:0000028
TAO
ZFIN:curator
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]
2012-06-20
AAO:0011044
AAO
XAO:curator
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
2012-08-14
TAO:0000028
TAO
UMLS:C1514450
ncithesaurus:Primordium_of_the_Heart
cardiac field
ZFA:0000028
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].
Skeletogenic portion of somites.[AAO]
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
part_of somite in XAO
AAO:0010571
AEO:0000212
EHDAA2:0003439
EMAPA:31159
FMA:295652
NCIT:C34287
TAO:0001080
UMLS:C0183176
VHOG:0000680
XAO:0000397
ZFA:0001080
sclerotomes
uberon
sclerotomus
UBERON:0003089
sclerotome
EHDAA2
EHDAA2
ZFA
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].
XB:curator
Skeletogenic portion of somites.[AAO]
2012-06-20
AAO:0010571
AAO
AAO:EJS
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
2012-09-17
VHOG:0000680
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
part_of somite in XAO
XAO
UMLS:C0183176
ncithesaurus:Sclerotome
sclerotomes
TAO:0001080
sclerotomus
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
AAO:0010580
EFO:0003645
EHDAA2:0004420
EMAPA:16091
TAO:0001194
VHOG:0000063
XAO:0001001
ZFA:0001194
CNC
cephalic neural crest
cranial NCC population
head NCC population
uberon
crista neuralis cranialis
head crest
head neural crest
UBERON:0003099
cranial neural crest
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.
MGI:anna
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
2012-06-20
AAO:0010580
AAO
AAO:EJS
Neural crest that is part of the head.[TAO]
2012-08-14
TAO:0001194
TAO
ZFIN:curator
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0000063
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
CNC
XAO:0001001
cephalic neural crest
EMAPA:16091
crista neuralis cranialis
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
consider obsoleting. See issue/1305
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
AAO:0010337
AEO_RETIRED:0000010
EHDAA2_RETIRED:0003010
TAO:0000292
VSAO:0000001
XAO:0003028
ZFA:0000292
galen:SurfaceRegion
anatomical surface feature
uberon
surface feature
surface region
surface structures
UBERON:0003102
surface structure
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]
2012-08-14
TAO:0000292
TAO
ZFIN:curator
anatomical surface feature
EHDAA2:0003010
surface structures
ZFA:0000292
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
AAO:0010015
AEO:0000024
BILA:0000024
CARO:0000024
EHDAA2:0003024
HAO:0000024
TADS:0000598
TAO:0000496
TGMA:0001837
VHOG:0001723
XAO:0003041
ZFA:0000496
uberon
organ
UBERON:0003103
compound organ
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.
CARO:0000024
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
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]
mesenchymal
AAO:0010427
AEO:0000145
BTO:0001393
CALOHA:TS-0620
EHDAA2:0003145
EV:0100007
NCIT:C13301
TAO:0000393
UMLS:C0162415
VHOG:0000170
XAO:0003046
ZFA:0000393
mesenchymal tissue
mesenchyme tissue
portion of mesenchymal tissue
portion of mesenchyme tissue
uberon
mesenchyma
UBERON:0003104
mesenchyme
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].
BTO:0001393
ZFIN:curator
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000393
TAO
ZFIN:curator
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]
2012-06-20
AAO:0010427
AAO
AAO:EJS
UMLS:C0162415
ncithesaurus:Mesenchyme
mesenchyma
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
6
UBERON:0004349
AAO:0010368
EHDAA2:0004075
EMAPA:32766
FMA:293047
TAO:0001601
VHOG:0001205
XAO:0000453
ZFA:0001609
6th arch
gill arch 4
sixth branchial arch
visceral arch 6
uberon
6th pharyngeal arch
6th visceral arch
branchial arch 4
fourth branchial arch
sixth pharyngeal arch
sixth visceral arch
UBERON:0003117
pharyngeal arch 6
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles
MP:0006347
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
2012-06-20
AAO:0010368
AAO
ISBN:0-02-377110-0
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
2012-09-17
VHOG:0001205
VHOG
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
6th arch
EHDAA2:0004075
gill arch 4
ZFA:0001609
visceral arch 6
ZFA:0001609
6th pharyngeal arch
VHOG:0001205
6th visceral arch
VHOG:0001205
branchial arch 4
AAO:0010368
ZFA:0001609
fourth branchial arch
sixth pharyngeal arch
VHOG:0001205
sixth visceral arch
XAO:0000453
The vessels formed within the first pair of branchial arches in embryogenesis
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
UBERON:0004371
AAO:0010415
EHDAA2:0000007
EMAPA:16202
EMAPA:16685
TAO:0005005
VHOG:0000149
XAO:0000342
ZFA:0005005
1st arch artery
AA1
aortic arch 1
first aortic arch
first branchial arch artery
mandibular aortic arch
uberon
1st aortic arch artery
1st branchial arch artery
1st pharyngeal arch artery
first arch artery
UBERON:0003118
pharyngeal arch artery 1
The vessels formed within the first pair of branchial arches in embryogenesis
MP:0010355
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
ZFA
1st arch artery
EMAPA:16685
AA1
ZFA:0005005
aortic arch 1
ZFA:0005005
first aortic arch
XAO:0000342
mandibular aortic arch
ZFA:0005005
1st aortic arch artery
EMAPA:16685
1st branchial arch artery
EMAPA:16685
1st pharyngeal arch artery
EMAPA:16685
first arch artery
EMAPA:16685
The vessels formed within the sixth pair of branchial arches in embryogenesis
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
UBERON:0004351
AAO:0010422
EHDAA2:0000102
EMAPA:17005
TAO:0005016
VHOG:0000144
XAO:0000353
ZFA:0005016
6th arch artery
AA6
aortic arch 6
sixth aortic arch
sixth branchial arch artery
uberon
6th aortic arch artery
6th branchial arch artery
6th pharyngeal arch artery
pulmonary arch
UBERON:0003123
pharyngeal arch artery 6
The vessels formed within the sixth pair of branchial arches in embryogenesis
MP:0006355
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
2012-08-14
TAO:0005016
TAO
ZFIN:curator
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
2012-06-20
AAO:0010422
AAO
ISBN:0-02-377110-0
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
6th arch artery
EMAPA:17005
AA6
ZFA:0005016
aortic arch 6
ZFA:0005016
sixth aortic arch
XAO:0000353
6th aortic arch artery
EMAPA:17005
6th branchial arch artery
EMAPA:17005
6th pharyngeal arch artery
EMAPA:17005
pulmonary arch
ISBN:0073040584
Upper portion of the skull that excludes the mandible (when present in the organism).
cranial
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
BTO:0001328
EFO:0000831
EHDAA:6029
EMAPA:17680
FMA:71325
MA:0000316
MAT:0000340
MIAA:0000340
OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA
VHOG:0000334
bones of cranium
ossa cranii
set of bones of cranium
skull minus mandible
upper part of skull
uberon
calvarium
epicranial plate
skeletal system of head
UBERON:0003128
cranium
FMA-inferred
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
FMA
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
WP
bones of cranium
FMA:71325
ossa cranii
FMA:71325
FMA:TA
set of bones of cranium
FMA:71325
calvarium
BTO:0001328
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
BTO:0001295
CALOHA:TS-2344
EHDAA2:0000325
EMAPA:17680
FMA:46565
GAID:82
MESH:D012886
NCIT:C12789
OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA
UMLS:C0037303
WikipediaCategory:Skull
galen:Skull
uberon
cranial skeleton
skeletal system of head
UBERON:0003129
skull
FMA
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
FMA
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
WP
UMLS:C0037303
ncithesaurus:Skull
An epithelium that is part of a lower jaw [Automatically generated definition].
EHDAA2:0001019
EHDAA:7999
EMAPA:35516
VHOG:0000802
epithelial tissue of lower jaw
epithelial tissue of ventral mandibular arch
epithelium of ventral mandibular arch
lower jaw epithelial tissue
lower jaw epithelium
ventral mandibular arch epithelial tissue
ventral mandibular arch epithelium
uberon
UBERON:0003236
epithelium of lower jaw
An epithelium that is part of a lower jaw [Automatically generated definition].
OBOL:automatic
epithelial tissue of lower jaw
OBOL:automatic
epithelial tissue of ventral mandibular arch
OBOL:automatic
epithelium of ventral mandibular arch
OBOL:automatic
lower jaw epithelial tissue
OBOL:automatic
lower jaw epithelium
OBOL:automatic
ventral mandibular arch epithelial tissue
OBOL:automatic
ventral mandibular arch epithelium
OBOL:automatic
An endoderm that is part of a foregut [Automatically generated definition].
TODO - check
EHDAA2:0004568
EHDAA:524
foregut endoderm
uberon
UBERON:0003258
endoderm of foregut
An endoderm that is part of a foregut [Automatically generated definition].
OBOL:automatic
foregut endoderm
OBOL:automatic
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
lower jaw
mandible
AAO:0000274
EHDAA2:0004606
EHDAA:8005
EMAPA:17906
EMAPA:17910
FMA:54398
MA:0001906
TAO:0001273
VHOG:0000428
XAO:0003084
ZFA:0001273
lower jaw skeleton
uberon
mandibles
mandibular series
UBERON:0003278
skeleton of lower jaw
EHDAA2
VHOG-modified
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
2012-08-14
TAO:0001273
TAO
ZFIN:curator
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
2012-09-17
VHOG:0000428
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
FMA
lower jaw
MA:0001906
lower jaw
ZFA:0001273
mandible
ZFA:0001273
lower jaw skeleton
AAO:0000274
mandibles
TAO:0001273
mandibular series
ZFA:0001273
A gland that is part of a foregut [Automatically generated definition].
EHDAA2:0000567
EHDAA:950
EMAPA:16557
VHOG:0000650
foregut gland
uberon
UBERON:0003294
gland of foregut
A gland that is part of a foregut [Automatically generated definition].
OBOL:automatic
foregut gland
OBOL:automatic
Racemose mucous glands beneath the mucous membrane of the pharynx.
BTO:0004849
EHDAA2:0001461
EHDAA:2967
FMA:55075
pharynx gland
uberon
glandulae pharyngeae
UBERON:0003295
pharyngeal gland
BTO
Racemose mucous glands beneath the mucous membrane of the pharynx.
pharynx gland
EHDAA2:0001461
glandulae pharyngeae
BTO:0004849
A gland that is part of a integumental system [Automatically generated definition].
EHDAA2:0000837
EHDAA:6522
EMAPA:17758
MA:0000144
VHOG:0000654
integumental gland
integumental system gland
integumentary gland
uberon
UBERON:0003297
gland of integumental system
A gland that is part of a integumental system [Automatically generated definition].
OBOL:automatic
integumental gland
integumental system gland
integumentary gland
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
UBERON:0003305
EHDAA2:0003241
EHDAA:170
EMAPA:16115
mesoderm blood islands
uberon
mesenchyme blood island
UBERON:0003304
mesoderm blood island
EHDAA2
EHDAA2
A blood island that is part of a mesoderm.
OBOL:automatic
in EHDAA2, gives rise to blood and dorsal aorta
EHDAA2
mesoderm blood islands
EHDAA2:0003241
mesenchyme blood island
OBOL:automatic
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
EHDAA2:0000485
EHDAA:2910
EMAPA:16673
VHOG:0001084
mesenchyme of eye
uberon
UBERON:0003314
eye mesenchyme
EHDAA2
Mesenchyme that is part of a developing camera-type eye.
OBOL:automatic
mesenchyme of eye
OBOL:automatic
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
EHDAA2:0001024
EHDAA:8003
EMAPA:17916
VHOG:0001069
lower jaw mesenchyme
mesenchyme of ventral mandibular arch
ventral mandibular arch mesenchyme
uberon
UBERON:0003324
mesenchyme of lower jaw
EHDAA2
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
OBOL:automatic
lower jaw mesenchyme
OBOL:automatic
mesenchyme of ventral mandibular arch
OBOL:automatic
ventral mandibular arch mesenchyme
OBOL:automatic
A mucosa that is part of a oral opening [Automatically generated definition].
EMAPA:26937
mucosa of oral opening
mucosa of oral part of face
mucosa of organ of oral opening
mucosa of organ of oral part of face
mucosa of organ of oral region
mucosa of organ of subdivision of mouth
mucosa of subdivision of mouth
mucous membrane of oral opening
mucous membrane of oral part of face
mucous membrane of oral region
mucous membrane of subdivision of mouth
oral opening mucosa
oral opening mucosa of organ
oral opening mucous membrane
oral opening organ mucosa
oral part of face mucosa
oral part of face mucosa of organ
oral part of face mucous membrane
oral part of face organ mucosa
oral region mucosa
oral region mucosa of organ
oral region mucous membrane
oral region organ mucosa
organ mucosa of oral opening
organ mucosa of oral part of face
organ mucosa of oral region
organ mucosa of subdivision of mouth
subdivision of mouth mucosa
subdivision of mouth mucosa of organ
subdivision of mouth mucous membrane
subdivision of mouth organ mucosa
uberon
UBERON:0003343
mucosa of oral region
A mucosa that is part of a oral opening [Automatically generated definition].
OBOL:automatic
mucosa of oral opening
OBOL:automatic
mucosa of oral part of face
OBOL:automatic
mucosa of organ of oral opening
OBOL:automatic
mucosa of organ of oral part of face
OBOL:automatic
mucosa of organ of oral region
OBOL:automatic
mucosa of organ of subdivision of mouth
OBOL:automatic
mucosa of subdivision of mouth
OBOL:automatic
mucous membrane of oral opening
OBOL:automatic
mucous membrane of oral part of face
OBOL:automatic
mucous membrane of oral region
OBOL:automatic
mucous membrane of subdivision of mouth
OBOL:automatic
oral opening mucosa
OBOL:automatic
oral opening mucosa of organ
OBOL:automatic
oral opening mucous membrane
OBOL:automatic
oral opening organ mucosa
OBOL:automatic
oral part of face mucosa
OBOL:automatic
oral part of face mucosa of organ
OBOL:automatic
oral part of face mucous membrane
OBOL:automatic
oral part of face organ mucosa
OBOL:automatic
oral region mucosa
OBOL:automatic
oral region mucosa of organ
OBOL:automatic
oral region mucous membrane
OBOL:automatic
oral region organ mucosa
OBOL:automatic
organ mucosa of oral opening
OBOL:automatic
organ mucosa of oral part of face
OBOL:automatic
organ mucosa of oral region
OBOL:automatic
organ mucosa of subdivision of mouth
OBOL:automatic
subdivision of mouth mucosa
OBOL:automatic
subdivision of mouth mucosa of organ
OBOL:automatic
subdivision of mouth mucous membrane
OBOL:automatic
subdivision of mouth organ mucosa
OBOL:automatic
A layer of epithelial cells on the surface of the mucosa.
BTO:0003752
uberon
lamina epithelialis mucosa
lamina epithelialis mucosae
UBERON:0003350
lies on top of lamina propria
epithelium of mucosa
A layer of epithelial cells on the surface of the mucosa.
BTO:0003752
lamina epithelialis mucosa
BTO:0003752
lamina epithelialis mucosae
BTO:0003752
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
BSA:0000112
BTO:0005240
EMAPA:16708
MA:0002725
RETIRED_EHDAA2:0001460
TAO:0001174
XAO:0003202
ZFA:0001174
epithelial tissue of pharynx
epithelium of pharynx
pharynx epithelial tissue
pharynx epithelium
uberon
UBERON:0003351
pharyngeal epithelium
ZFA
ZFA
An epithelium that is part of a pharynx [Automatically generated definition].
OBOL:automatic
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
2012-08-14
TAO:0001174
TAO
ZFIN:curator
epithelial tissue of pharynx
OBOL:automatic
epithelium of pharynx
OBOL:automatic
pharynx epithelial tissue
OBOL:automatic
pharynx epithelium
OBOL:automatic
An epithelium that is part of a right lung [Automatically generated definition].
EMAPA:17663
MA:0003132
epithelial tissue of right lung
right lung epithelial tissue
right lung epithelium
uberon
UBERON:0003364
epithelium of right lung
An epithelium that is part of a right lung [Automatically generated definition].
OBOL:automatic
epithelial tissue of right lung
OBOL:automatic
right lung epithelial tissue
OBOL:automatic
right lung epithelium
OBOL:automatic
An epithelium that is part of a left lung [Automatically generated definition].
EMAPA:17655
MA:0003131
epithelial tissue of left lung
left lung epithelial tissue
left lung epithelium
uberon
UBERON:0003365
epithelium of left lung
An epithelium that is part of a left lung [Automatically generated definition].
OBOL:automatic
epithelial tissue of left lung
OBOL:automatic
left lung epithelial tissue
OBOL:automatic
left lung epithelium
OBOL:automatic
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
EMAPA:18807
MA:0001268
ocular smooth muscle
uberon
UBERON:0003386
smooth muscle of eye
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
MGI:cwg
MP:0005247
ocular smooth muscle
MA:0001268
A gland that is part of a digestive tract [Automatically generated definition].
EMAPA:18815
MA:0003202
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
uberon
UBERON:0003408
gland of digestive tract
A gland that is part of a digestive tract [Automatically generated definition].
OBOL:automatic
digestive tract gland
OBOL:automatic
gland of digestive tract
OBOL:automatic
gland of lower gastrointestinal tract
OBOL:automatic
gut gland
MA:0003202
lower gastrointestinal tract gland
OBOL:automatic
An adipose tissue that is part of a dermis [Automatically generated definition].
MA:0000798
adipose tissue of dermis
dermis fat tissue
dermis fatty tissue
fat tissue of dermis
fatty tissue of dermis
uberon
UBERON:0003426
dermis adipose tissue
An adipose tissue that is part of a dermis [Automatically generated definition].
OBOL:automatic
adipose tissue of dermis
OBOL:automatic
dermis fat tissue
OBOL:automatic
dermis fatty tissue
OBOL:automatic
fat tissue of dermis
OBOL:automatic
fatty tissue of dermis
OBOL:automatic
An artery that is part of a respiratory system [Automatically generated definition].
EMAPA:37569
MA:0001804
uberon
UBERON:0003469
respiratory system artery
An artery that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37569
MA:th
The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
EMAPA:37429
FMA:49567
MA:0001916
arteria labialis inferior
inferior labial artery
inferior labial branch of facial artery
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
uberon
UBERON:0003471
artery of lower lip
FMA
The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
EMAPA:37429
MA:th
arteria labialis inferior
inferior labial artery
FMA:49567
inferior labial branch of facial artery
FMA:49567
ramus labialis inferior (arteria facialis)
FMA:TA
ramus labialis inferior arteriae facialis
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
EMAPA:37241
MA:0001902
MESH:D013895
uberon
thoracic artery
UBERON:0003473
thoracic cavity artery
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
MA
EMAPA:37241
MA:th
thoracic artery
MESH:A07.231.114.891
A vein that is part of a respiratory system [Automatically generated definition].
EMAPA:37584
MA:0001809
MA:0001810
apparatus respiratorius vein
respiratory system vein
vein of apparatus respiratorius
vein of respiratory system
uberon
UBERON:0003476
respiratory system venous blood vessel
A vein that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37584
MA:th
apparatus respiratorius vein
OBOL:automatic
respiratory system vein
OBOL:automatic
vein of apparatus respiratorius
OBOL:automatic
vein of respiratory system
OBOL:automatic
The inferior labial vein is the vein receiving blood from the lower lip.
EMAPA:37202
FMA:52541
MA:0002253
inferior labial vein
lower lip vein
vena labialis inferior
uberon
venae labiales inferiores
UBERON:0003478
vein of lower lip
The inferior labial vein is the vein receiving blood from the lower lip.
EMAPA:37202
MA:th
inferior labial vein
FMA:52541
lower lip vein
OBOL:automatic
vena labialis inferior
venae labiales inferiores
A vein that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37242
MA:0001903
cavity of chest vein
cavity of thorax vein
chest cavity vein
pectoral cavity vein
vein of cavity of chest
vein of cavity of thorax
vein of chest cavity
vein of pectoral cavity
vein of thoracic cavity
uberon
UBERON:0003479
thoracic cavity vein
A vein that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37242
MA:th
cavity of chest vein
OBOL:automatic
cavity of thorax vein
OBOL:automatic
chest cavity vein
OBOL:automatic
pectoral cavity vein
OBOL:automatic
vein of cavity of chest
OBOL:automatic
vein of cavity of thorax
OBOL:automatic
vein of chest cavity
OBOL:automatic
vein of pectoral cavity
OBOL:automatic
vein of thoracic cavity
OBOL:automatic
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
EMAPA:37575
MA:0001808
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
uberon
UBERON:0003489
respiratory system capillary endothelium
true
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37575
MA:th
apparatus respiratorius blood capillary endothelium
OBOL:automatic
apparatus respiratorius capillary endothelium
OBOL:automatic
apparatus respiratorius capillary vessel endothelium
OBOL:automatic
apparatus respiratorius endothelium of blood capillary
OBOL:automatic
apparatus respiratorius endothelium of capillary
OBOL:automatic
apparatus respiratorius endothelium of capillary vessel
OBOL:automatic
blood capillary endothelium of apparatus respiratorius
OBOL:automatic
blood capillary endothelium of respiratory system
OBOL:automatic
capillary endothelium of apparatus respiratorius
OBOL:automatic
capillary endothelium of respiratory system
OBOL:automatic
capillary vessel endothelium of apparatus respiratorius
OBOL:automatic
capillary vessel endothelium of respiratory system
OBOL:automatic
endothelium of blood capillary of apparatus respiratorius
OBOL:automatic
endothelium of blood capillary of respiratory system
OBOL:automatic
endothelium of capillary of apparatus respiratorius
OBOL:automatic
endothelium of capillary of respiratory system
OBOL:automatic
endothelium of capillary vessel of apparatus respiratorius
OBOL:automatic
endothelium of capillary vessel of respiratory system
OBOL:automatic
respiratory system blood capillary endothelium
OBOL:automatic
respiratory system capillary vessel endothelium
OBOL:automatic
respiratory system endothelium of blood capillary
OBOL:automatic
respiratory system endothelium of capillary
OBOL:automatic
respiratory system endothelium of capillary vessel
OBOL:automatic
A venule that is part of a respiratory system [Automatically generated definition].
EMAPA:37587
MA:0001813
apparatus respiratorius venule
venule of apparatus respiratorius
venule of respiratory system
uberon
UBERON:0003494
respiratory system venule
A venule that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37587
MA:th
apparatus respiratorius venule
OBOL:automatic
venule of apparatus respiratorius
OBOL:automatic
venule of respiratory system
OBOL:automatic
An arteriole that is part of a respiratory system [Automatically generated definition].
EMAPA:37568
MA:0001803
uberon
UBERON:0003495
respiratory system arteriole
true
An arteriole that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37568
MA:th
A blood vessel that is part of a head [Automatically generated definition].
EMAPA:36610
MA:0000575
adult head blood vessel
blood vessel of adult head
blood vessel of head
uberon
UBERON:0003496
head blood vessel
true
A blood vessel that is part of a head [Automatically generated definition].
OBOL:automatic
adult head blood vessel
OBOL:automatic
blood vessel of adult head
OBOL:automatic
blood vessel of head
OBOL:automatic
A blood vessel that is part of a heart [Automatically generated definition].
EMAPA:35397
MA:0002483
blood vessel of heart
uberon
cardiac blood vessel
UBERON:0003498
heart blood vessel
A blood vessel that is part of a heart [Automatically generated definition].
OBOL:automatic
blood vessel of heart
OBOL:automatic
cardiac blood vessel
EMAPA:35397
A blood vessel that is part of a brain [Automatically generated definition].
EMAPA:35182
MA:0002769
blood vessel of brain
uberon
UBERON:0003499
brain blood vessel
A blood vessel that is part of a brain [Automatically generated definition].
OBOL:automatic
blood vessel of brain
OBOL:automatic
A blood vessel that is part of a cornea [Automatically generated definition].
follow up on tracker item
EMAPA:36611
MA:0001241
blood vessel of cornea
cornea blood vessel
uberon
UBERON:0003500
corneal blood vessel
A blood vessel that is part of a cornea [Automatically generated definition].
blood vessel of cornea
OBOL:automatic
cornea blood vessel
OBOL:automatic
A blood vessel that is part of a retina [Automatically generated definition].
EMAPA:36520
GAID:509
MA:0001317
MESH:D012171
XAO:0004153
blood vessel of inner layer of eyeball
blood vessel of retina
blood vessel of tunica interna of eyeball
inner layer of eyeball blood vessel
retinal blood vessel
tunica interna of eyeball blood vessel
uberon
UBERON:0003501
retina blood vessel
A blood vessel that is part of a retina [Automatically generated definition].
OBOL:automatic
blood vessel of inner layer of eyeball
OBOL:automatic
blood vessel of retina
OBOL:automatic
blood vessel of tunica interna of eyeball
OBOL:automatic
inner layer of eyeball blood vessel
OBOL:automatic
retinal blood vessel
OBOL:automatic
tunica interna of eyeball blood vessel
OBOL:automatic
A blood vessel that is part of a neck [Automatically generated definition].
EMAPA:37236
MA:0000583
blood vessel of neck
blood vessel of neck (volume)
neck (volume) blood vessel
uberon
UBERON:0003502
neck blood vessel
A blood vessel that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37236
MA:th
blood vessel of neck
OBOL:automatic
blood vessel of neck (volume)
OBOL:automatic
neck (volume) blood vessel
OBOL:automatic
A blood vessel that is part of a respiratory system [Automatically generated definition].
EMAPA:35731
EMAPA:35995
MA:0001799
apparatus respiratorius blood vessel
blood vessel of apparatus respiratorius
blood vessel of respiratory system
uberon
UBERON:0003504
respiratory system blood vessel
A blood vessel that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius blood vessel
OBOL:automatic
blood vessel of apparatus respiratorius
OBOL:automatic
blood vessel of respiratory system
OBOL:automatic
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
EMAPA:35144
MA:0000061
uberon
UBERON:0003509
only in MA - supertype of artery, arteriole, aorta.
arterial blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
A blood vessel that is part of a iris [Automatically generated definition].
EMAPA:37387
MA:0001290
ZFA:0005568
blood vessel of iris
uberon
UBERON:0003511
iris blood vessel
A blood vessel that is part of a iris [Automatically generated definition].
OBOL:automatic
EMAPA:37387
MA:th
blood vessel of iris
OBOL:automatic
A blood vessel that is part of a lung [Automatically generated definition].
EMAPA:32867
MA:0002457
blood vessel of lung
uberon
pulmonary vascular element
UBERON:0003512
lung blood vessel
A blood vessel that is part of a lung [Automatically generated definition].
OBOL:automatic
blood vessel of lung
OBOL:automatic
pulmonary vascular element
EMAPA:32867
A blood vessel that is part of a trunk [Automatically generated definition].
EMAPA:37237
MA:0000511
blood vessel of torso
blood vessel of trunk
torso blood vessel
uberon
UBERON:0003513
trunk blood vessel
A blood vessel that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37237
MA:th
blood vessel of torso
OBOL:automatic
blood vessel of trunk
OBOL:automatic
torso blood vessel
OBOL:automatic
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37240
MA:0000554
blood vessel of cavity of chest
blood vessel of cavity of thorax
blood vessel of chest cavity
blood vessel of pectoral cavity
blood vessel of thoracic cavity
cavity of chest blood vessel
cavity of thorax blood vessel
chest cavity blood vessel
pectoral cavity blood vessel
uberon
UBERON:0003519
thoracic cavity blood vessel
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37240
MA:th
blood vessel of cavity of chest
OBOL:automatic
blood vessel of cavity of thorax
OBOL:automatic
blood vessel of chest cavity
OBOL:automatic
blood vessel of pectoral cavity
OBOL:automatic
blood vessel of thoracic cavity
OBOL:automatic
cavity of chest blood vessel
OBOL:automatic
cavity of thorax blood vessel
OBOL:automatic
chest cavity blood vessel
OBOL:automatic
pectoral cavity blood vessel
OBOL:automatic
A capillary that is part of a respiratory system [Automatically generated definition].
EMAPA:37574
MA:0001807
apparatus respiratorius blood capillary
apparatus respiratorius capillary
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
blood capillary of respiratory system
capillary of apparatus respiratorius
capillary of respiratory system
capillary vessel of apparatus respiratorius
capillary vessel of respiratory system
respiratory system blood capillary
respiratory system capillary vessel
uberon
UBERON:0003526
respiratory system capillary
A capillary that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37574
MA:th
apparatus respiratorius blood capillary
OBOL:automatic
apparatus respiratorius capillary
OBOL:automatic
apparatus respiratorius capillary vessel
OBOL:automatic
blood capillary of apparatus respiratorius
OBOL:automatic
blood capillary of respiratory system
OBOL:automatic
capillary of apparatus respiratorius
OBOL:automatic
capillary of respiratory system
OBOL:automatic
capillary vessel of apparatus respiratorius
OBOL:automatic
capillary vessel of respiratory system
OBOL:automatic
respiratory system blood capillary
OBOL:automatic
respiratory system capillary vessel
OBOL:automatic
A gray matter that is part of a brain [Automatically generated definition].
EMAPA:35184
MA:0000810
NCIT:C49333
UMLS:C1707348
brain grey matter
brain grey substance
gray matter of brain
grey matter of brain
grey substance of brain
uberon
UBERON:0003528
brain gray matter
A gray matter that is part of a brain [Automatically generated definition].
OBOL:automatic
UMLS:C1707348
ncithesaurus:Cerebral_Gray_Matter
brain grey matter
MA:0000810
brain grey substance
OBOL:automatic
gray matter of brain
OBOL:automatic
grey matter of brain
OBOL:automatic
grey substance of brain
OBOL:automatic
A portion of connective tissue that is part of a head [Automatically generated definition].
EMAPA:16098
MA:0000577
adult head connective tissue
adult head portion of connective tissue
adult head textus connectivus
connective tissue of adult head
connective tissue of head
head portion of connective tissue
head textus connectivus
portion of connective tissue of adult head
portion of connective tissue of head
textus connectivus of adult head
textus connectivus of head
uberon
UBERON:0003566
head connective tissue
A portion of connective tissue that is part of a head [Automatically generated definition].
OBOL:automatic
adult head connective tissue
OBOL:automatic
adult head portion of connective tissue
OBOL:automatic
adult head textus connectivus
OBOL:automatic
connective tissue of adult head
OBOL:automatic
connective tissue of head
OBOL:automatic
head portion of connective tissue
OBOL:automatic
head textus connectivus
OBOL:automatic
portion of connective tissue of adult head
OBOL:automatic
portion of connective tissue of head
OBOL:automatic
textus connectivus of adult head
OBOL:automatic
textus connectivus of head
OBOL:automatic
A portion of connective tissue that is part of a neck [Automatically generated definition].
EMAPA:37250
MA:0000585
connective tissue of neck
connective tissue of neck (volume)
neck (volume) connective tissue
neck (volume) portion of connective tissue
neck (volume) textus connectivus
neck portion of connective tissue
neck textus connectivus
portion of connective tissue of neck
portion of connective tissue of neck (volume)
textus connectivus of neck
textus connectivus of neck (volume)
uberon
UBERON:0003568
neck connective tissue
A portion of connective tissue that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37250
MA:th
connective tissue of neck
OBOL:automatic
connective tissue of neck (volume)
OBOL:automatic
neck (volume) connective tissue
OBOL:automatic
neck (volume) portion of connective tissue
OBOL:automatic
neck (volume) textus connectivus
OBOL:automatic
neck portion of connective tissue
OBOL:automatic
neck textus connectivus
OBOL:automatic
portion of connective tissue of neck
OBOL:automatic
portion of connective tissue of neck (volume)
OBOL:automatic
textus connectivus of neck
OBOL:automatic
textus connectivus of neck (volume)
OBOL:automatic
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
EMAPA:35968
EMAPA:35977
MA:0001814
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
connective tissue of respiratory system
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
respiratory system textus connectivus
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
uberon
UBERON:0003570
respiratory system connective tissue
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius connective tissue
OBOL:automatic
apparatus respiratorius portion of connective tissue
OBOL:automatic
apparatus respiratorius textus connectivus
OBOL:automatic
connective tissue of apparatus respiratorius
OBOL:automatic
connective tissue of respiratory system
OBOL:automatic
portion of connective tissue of apparatus respiratorius
OBOL:automatic
portion of connective tissue of respiratory system
OBOL:automatic
respiratory system portion of connective tissue
OBOL:automatic
respiratory system textus connectivus
OBOL:automatic
textus connectivus of apparatus respiratorius
OBOL:automatic
textus connectivus of respiratory system
OBOL:automatic
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
EMAPA:37548
MA:0002409
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
uberon
UBERON:0003580
lower respiratory tract connective tissue
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
OBOL:automatic
EMAPA:37548
MA:th
connective tissue of lower respiratory tract
OBOL:automatic
lower respiratory tract portion of connective tissue
OBOL:automatic
lower respiratory tract textus connectivus
OBOL:automatic
portion of connective tissue of lower respiratory tract
OBOL:automatic
textus connectivus of lower respiratory tract
OBOL:automatic
A portion of connective tissue that is part of a dermis [Automatically generated definition].
EMAPA:36509
MA:0000799
connective tissue of dermis
dermis portion of connective tissue
dermis textus connectivus
portion of connective tissue of dermis
textus connectivus of dermis
uberon
UBERON:0003585
dermis connective tissue
A portion of connective tissue that is part of a dermis [Automatically generated definition].
OBOL:automatic
connective tissue of dermis
OBOL:automatic
dermis portion of connective tissue
OBOL:automatic
dermis textus connectivus
OBOL:automatic
portion of connective tissue of dermis
OBOL:automatic
textus connectivus of dermis
OBOL:automatic
A portion of connective tissue that is part of a trunk [Automatically generated definition].
EMAPA:37252
MA:0000513
connective tissue of torso
connective tissue of trunk
portion of connective tissue of torso
portion of connective tissue of trunk
textus connectivus of torso
textus connectivus of trunk
torso connective tissue
torso portion of connective tissue
torso textus connectivus
trunk portion of connective tissue
trunk textus connectivus
uberon
UBERON:0003586
trunk connective tissue
A portion of connective tissue that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37252
MA:th
connective tissue of torso
OBOL:automatic
connective tissue of trunk
OBOL:automatic
portion of connective tissue of torso
OBOL:automatic
portion of connective tissue of trunk
OBOL:automatic
textus connectivus of torso
OBOL:automatic
textus connectivus of trunk
OBOL:automatic
torso connective tissue
OBOL:automatic
torso portion of connective tissue
OBOL:automatic
torso textus connectivus
OBOL:automatic
trunk portion of connective tissue
OBOL:automatic
trunk textus connectivus
OBOL:automatic
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37255
MA:0000555
cavity of chest connective tissue
cavity of chest portion of connective tissue
cavity of chest textus connectivus
cavity of thorax connective tissue
cavity of thorax portion of connective tissue
cavity of thorax textus connectivus
chest cavity connective tissue
chest cavity portion of connective tissue
chest cavity textus connectivus
connective tissue of cavity of chest
connective tissue of cavity of thorax
connective tissue of chest cavity
connective tissue of pectoral cavity
connective tissue of thoracic cavity
pectoral cavity connective tissue
pectoral cavity portion of connective tissue
pectoral cavity textus connectivus
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
textus connectivus of cavity of chest
textus connectivus of cavity of thorax
textus connectivus of chest cavity
textus connectivus of pectoral cavity
textus connectivus of thoracic cavity
thoracic cavity portion of connective tissue
thoracic cavity textus connectivus
uberon
UBERON:0003593
thoracic cavity connective tissue
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37255
MA:th
cavity of chest connective tissue
OBOL:automatic
cavity of chest portion of connective tissue
OBOL:automatic
cavity of chest textus connectivus
OBOL:automatic
cavity of thorax connective tissue
OBOL:automatic
cavity of thorax portion of connective tissue
OBOL:automatic
cavity of thorax textus connectivus
OBOL:automatic
chest cavity connective tissue
OBOL:automatic
chest cavity portion of connective tissue
OBOL:automatic
chest cavity textus connectivus
OBOL:automatic
connective tissue of cavity of chest
OBOL:automatic
connective tissue of cavity of thorax
OBOL:automatic
connective tissue of chest cavity
OBOL:automatic
connective tissue of pectoral cavity
OBOL:automatic
connective tissue of thoracic cavity
OBOL:automatic
pectoral cavity connective tissue
OBOL:automatic
pectoral cavity portion of connective tissue
OBOL:automatic
pectoral cavity textus connectivus
OBOL:automatic
portion of connective tissue of cavity of chest
OBOL:automatic
portion of connective tissue of cavity of thorax
OBOL:automatic
portion of connective tissue of chest cavity
OBOL:automatic
portion of connective tissue of pectoral cavity
OBOL:automatic
portion of connective tissue of thoracic cavity
OBOL:automatic
textus connectivus of cavity of chest
OBOL:automatic
textus connectivus of cavity of thorax
OBOL:automatic
textus connectivus of chest cavity
OBOL:automatic
textus connectivus of pectoral cavity
OBOL:automatic
textus connectivus of thoracic cavity
OBOL:automatic
thoracic cavity portion of connective tissue
OBOL:automatic
thoracic cavity textus connectivus
OBOL:automatic
A skin gland that is part of a camera-type eye [Automatically generated definition].
EMAPA:37530
MA:0002451
camera-type eye skin gland
camera-type eye skin glands
camera-type eye skin glands set
skin gland of camera-type eye
skin gland of vertebrate eye
skin glands of camera-type eye
skin glands of vertebrate eye
skin glands set of camera-type eye
skin glands set of vertebrate eye
vertebrate eye skin gland
vertebrate eye skin glands
vertebrate eye skin glands set
uberon
UBERON:0003605
eye skin gland
A skin gland that is part of a camera-type eye [Automatically generated definition].
OBOL:automatic
EMAPA:37530
MA:th
camera-type eye skin gland
OBOL:automatic
camera-type eye skin glands
OBOL:automatic
camera-type eye skin glands set
OBOL:automatic
skin gland of camera-type eye
OBOL:automatic
skin gland of vertebrate eye
OBOL:automatic
skin glands of camera-type eye
OBOL:automatic
skin glands of vertebrate eye
OBOL:automatic
skin glands set of camera-type eye
OBOL:automatic
skin glands set of vertebrate eye
OBOL:automatic
vertebrate eye skin gland
OBOL:automatic
vertebrate eye skin glands
OBOL:automatic
vertebrate eye skin glands set
OBOL:automatic
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
MA:0002858
cardiac elastic tissue
elastic connective tissue of heart
elastic tissue of heart
heart elastic connective tissue
heart textus connectivus elasticus
textus connectivus elasticus of heart
uberon
UBERON:0003610
heart elastic tissue
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
MP:0009863
cardiac elastic tissue
MP:0009863
elastic connective tissue of heart
OBOL:automatic
elastic tissue of heart
OBOL:automatic
heart elastic connective tissue
OBOL:automatic
heart textus connectivus elasticus
OBOL:automatic
textus connectivus elasticus of heart
OBOL:automatic
An elastic tissue that is part of a respiratory system [Automatically generated definition].
EMAPA:37579
MA:0001820
apparatus respiratorius elastic connective tissue
apparatus respiratorius elastic tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
elastic tissue of respiratory system
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
uberon
UBERON:0003611
respiratory system elastic tissue
An elastic tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37579
MA:th
apparatus respiratorius elastic connective tissue
OBOL:automatic
apparatus respiratorius elastic tissue
OBOL:automatic
apparatus respiratorius textus connectivus elasticus
OBOL:automatic
elastic connective tissue of apparatus respiratorius
OBOL:automatic
elastic connective tissue of respiratory system
OBOL:automatic
elastic tissue of apparatus respiratorius
OBOL:automatic
elastic tissue of respiratory system
OBOL:automatic
respiratory system elastic connective tissue
OBOL:automatic
respiratory system textus connectivus elasticus
OBOL:automatic
textus connectivus elasticus of apparatus respiratorius
OBOL:automatic
textus connectivus elasticus of respiratory system
OBOL:automatic
An elastic tissue that is part of a circulatory system [Automatically generated definition].
MA:0002857
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system elastic tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
elastic tissue of cardiovascular system
elastic tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
uberon
UBERON:0003613
cardiovascular system elastic tissue
An elastic tissue that is part of a circulatory system [Automatically generated definition].
OBOL:automatic
cardiovascular system elastic connective tissue
OBOL:automatic
cardiovascular system textus connectivus elasticus
OBOL:automatic
circulatory system elastic connective tissue
OBOL:automatic
circulatory system elastic tissue
OBOL:automatic
circulatory system textus connectivus elasticus
OBOL:automatic
elastic connective tissue of cardiovascular system
OBOL:automatic
elastic connective tissue of circulatory system
OBOL:automatic
elastic tissue of cardiovascular system
OBOL:automatic
elastic tissue of circulatory system
OBOL:automatic
textus connectivus elasticus of cardiovascular system
OBOL:automatic
textus connectivus elasticus of circulatory system
OBOL:automatic
Elastic tissue layer that lines a blood vessel layer.
elastic lamina
elastic laminae
EMAPA:36300
MA:0002856
blood vessel elastic connective tissue
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
elastic tissue of blood vessel
textus connectivus elasticus of blood vessel
vascular elastic lamina
vascular elastic laminae
vascular elastic tissue
uberon
UBERON:0003614
blood vessel elastic tissue
Elastic tissue layer that lines a blood vessel layer.
elastic lamina
MP:0006083
elastic laminae
MP:0006083
blood vessel elastic connective tissue
OBOL:automatic
blood vessel textus connectivus elasticus
OBOL:automatic
elastic connective tissue of blood vessel
OBOL:automatic
elastic tissue of blood vessel
OBOL:automatic
textus connectivus elasticus of blood vessel
OBOL:automatic
vascular elastic lamina
vascular elastic laminae
vascular elastic tissue
MP:0006083
Elastic tissue that is part of a lung [Automatically generated definition].
MA:0002860
elastic connective tissue of lung
elastic tissue of lung
lung elastic connective tissue
lung textus connectivus elasticus
textus connectivus elasticus of lung
pulmonary elastic fiber
uberon
UBERON:0003615
lung elastic tissue
Elastic tissue that is part of a lung [Automatically generated definition].
OBOL:automatic
elastic connective tissue of lung
OBOL:automatic
elastic tissue of lung
OBOL:automatic
lung elastic connective tissue
OBOL:automatic
lung textus connectivus elasticus
OBOL:automatic
textus connectivus elasticus of lung
OBOL:automatic
pulmonary elastic fiber
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
EMAPA:37565
MA:0001800
uberon
UBERON:0003643
respiratory system arterial blood vessel
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37565
MA:th
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
FMA definition includes vasculature
AAO:0000325
AEO:0000123
EHDAA2:0003123
FMA:9642
GAID:609
MESH:D009417
NCIT:C13052
OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ
UMLS:C0027757
nerve tissue
nervous tissue
portion of neural tissue
uberon
UBERON:0003714
neural tissue
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
FMA:9642
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
2012-06-20
AAO:0000325
AAO
AAO:LAP
FMA definition includes vasculature
FMA
UMLS:C0027757
ncithesaurus:Nervous_Tissue
nerve tissue
FMA:9642
nervous tissue
FMA:9642
portion of neural tissue
FMA:9642
A mucous membrane that lines the mouth.
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
BTO:0002860
CALOHA:TS-0716
EMAPA:26937
FMA:59660
GAID:951
MA:0002794
MESH:D009061
NCIT:C77637
UMLS:C0026639
mouth mucosa
mouth mucous membrane
mouth organ mucosa
mucosa of mouth
mucous membrane of mouth
oral mucous membrane
oral part of viscerocranial mucosa
tunica mucosa oris
uberon
buccal mucosa
mucosal lining of mouth
oral mucosa
tunica mucosa oris
UBERON:0003729
mouth mucosa
A mucous membrane that lines the mouth.
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
UMLS:C0026639
ncithesaurus:Oral_Mucosa
mouth mucosa
FMA:59660
mouth mucous membrane
OBOL:accepted
mouth organ mucosa
OBOL:accepted
mucosa of mouth
OBOL:accepted
mucous membrane of mouth
FMA:59660
oral part of viscerocranial mucosa
FMA:59660
tunica mucosa oris
FMA:59660
FMA:TA
buccal mucosa
GAID:951
mucosal lining of mouth
MA:0002794
oral mucosa
GAID:951
tunica mucosa oris
Any muscle organ that is part of a respiratory system [Automatically generated definition].
EMAPA:35733
MA:0001828
apparatus respiratorius muscle organ
muscle organ of apparatus respiratorius
muscle organ of respiratory system
respiratory system muscle organ
uberon
UBERON:0003831
respiratory system muscle
Any muscle organ that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius muscle organ
OBOL:automatic
muscle organ of apparatus respiratorius
OBOL:automatic
muscle organ of respiratory system
OBOL:automatic
respiratory system muscle organ
OBOL:automatic
A blood vessel that is part of a thorax [Automatically generated definition].
EMAPA:37238
MA:0000558
blood vessel of thorax
thorax blood vessel
uberon
upper body blood vessel
UBERON:0003834
thoracic segment blood vessel
A blood vessel that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37238
MA:th
blood vessel of thorax
OBOL:automatic
thorax blood vessel
OBOL:automatic
upper body blood vessel
MA:0000558
A portion of connective tissue that is part of a thorax [Automatically generated definition].
EMAPA:37253
MA:0000560
connective tissue of thorax
portion of connective tissue of thorax
textus connectivus of thorax
thorax connective tissue
thorax portion of connective tissue
thorax textus connectivus
uberon
upper body connective tissue
UBERON:0003837
thoracic segment connective tissue
A portion of connective tissue that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37253
MA:th
connective tissue of thorax
OBOL:automatic
portion of connective tissue of thorax
OBOL:automatic
textus connectivus of thorax
OBOL:automatic
thorax connective tissue
OBOL:automatic
thorax portion of connective tissue
OBOL:automatic
thorax textus connectivus
OBOL:automatic
upper body connective tissue
MA:0000560
An anatomical space that surrounded_by a neural tube.
(...) 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]
UBERON:0005713
AAO:0011073
EHDAA2:0001269
EHDAA:2889
EHDAA:914
EMAPA:16167
VHOG:0001119
XAO:0000252
cavity of neural tube
lumen of neural tube
neural tube neural lumen
prosencoel
uberon
central lumen
neural lumen
neurocoel
UBERON:0003842
neural tube lumen
An anatomical space that surrounded_by a neural tube.
OBOL:automatic
(...) 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]
2012-09-17
VHOG:0001119
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
cavity of neural tube
lumen of neural tube
neural tube neural lumen
EHDAA2:0001269
neural lumen
EHDAA:2889
neurocoel
VHOG:0001119
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
EFO:0003591
EHDAA2:0001101
EHDAA:360
TAO:0000935
VHOG:0000796
ZFA:0000935
mesencephalic neural crest
neural crest midbrain
uberon
UBERON:0003849
mesencephalic neural crest
ZFA
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
OBOL:automatic
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0000796
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
mesencephalic neural crest
ZFA:0000935
neural crest midbrain
ZFA:0000935
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
EHDAA2:0001628
EHDAA:362
EMAPA:35747
TAO:0007063
VHOG:0001210
ZFA:0007063
neural crest hindbrain
rhombencephalic neural crest
uberon
rhombomere neural crest
UBERON:0003852
rhombencephalon neural crest
ZFA
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
OBOL:automatic
Cranial neural crest that is part of the hindbrain.[TAO]
2012-08-14
TAO:0007063
TAO
ZFIN:curator
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0001210
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
neural crest hindbrain
ZFA:0007063
rhombencephalic neural crest
ZFA:0007063
rhombomere neural crest
EMAPA:35747
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]
EHDAA:696
EMAPA:16163
EMAPA:16881
VHOG:0001006
neural crest spinal cord
uberon
spinal neural crest
UBERON:0003853
spinal cord neural crest
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
OBOL:automatic
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
2012-09-17
VHOG:0001006
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
neural crest spinal cord
VHOG:0001006
spinal neural crest
VHOG:0001006
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
FMA:312957
TAO:0007021
VHOG:0000439
ZFA:0007021
neural plate of spinal cord
uberon
UBERON:0003854
spinal cord neural plate
ZFA
A neural plate that develops_from a future spinal cord.
OBOL:automatic
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
2012-09-17
VHOG:0000439
VHOG
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
2012-09-17
VHOG:0000439
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
neural plate of spinal cord
OBOL:automatic
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
uberon
body cavity precursor
UBERON:0003886
future coelemic cavity lumen
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
OBOL:automatic
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
EHDAA:251
EMAPA:16088
NCIT:C34195
UMLS:C1512940
VHOG:0000316
somatic coelom
uberon
UBERON:0003887
intraembryonic coelom
Wikipedia
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
MGI:anna
MP:0012187
(...) 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]
2012-09-17
VHOG:0000316
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
UMLS:C1512940
ncithesaurus:Intraembryonic_Coelom
somatic coelom
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
AAO:0011095
BTO:0000929
CALOHA:TS-0685
EHDAA2:0001253
EHDAA:4763
EMAPA:17171
EMAPA:18590
FMA:58628
MA:0000277
NCIT:C33166
TAO:0000046
UMLS:C1518263
VHOG:0000535
XAO:0003216
ZFA:0000046
neural layer of retina
neural retina
neuroretina
stratum nervosum (retina)
stratum nervosum retinae
uberon
neural retinal epithelium
UBERON:0003902
retinal neural layer
Bgee:AN
The part of the retina that contains neurons and photoreceptor cells[GO].
GO:0003407
(...) 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]
2012-09-17
VHOG:0000535
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C1518263
ncithesaurus:Neural_Retina
neural layer of retina
FMA:58628
neural retina
XAO:0003216
ZFA:0000046
neuroretina
ZFA:0000046
stratum nervosum (retina)
FMA:58628
stratum nervosum retinae
FMA:58628
FMA:TA
neural retinal epithelium
MA:000027
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
AEO:0000114
EHDAA2:0003114
FBbt:00007474
epithelial or endothelial tube
uberon
UBERON:0003914
epithelial tube
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.
GO:0060562
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
uberon
UBERON:0003915
endothelial tube
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
OBOL:automatic
A blood vessel that carries blood from the capillaries toward the heart
EMAPA:35932
FMA:86188
MA:0000066
segment of venous tree organ
venous tree organ segment
uberon
UBERON:0003920
Compare to: vein
venous blood vessel
A blood vessel that carries blood from the capillaries toward the heart
segment of venous tree organ
FMA:86188
venous tree organ segment
FMA:86188
A duct that is part of a digestive system [Automatically generated definition].
TAO:0005162
ZFA:0005162
duct of digestive system
duct of gastrointestinal system
gastrointestinal system duct
uberon
UBERON:0003928
digestive system duct
A duct that is part of a digestive system [Automatically generated definition].
OBOL:automatic
duct of digestive system
OBOL:automatic
duct of gastrointestinal system
OBOL:automatic
gastrointestinal system duct
OBOL:automatic
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
BTO:0000956
EHDAA2:0004567
EMAPA:32928
MA:0003201
NCIT:C12963
TAO:0005123
UMLS:C0836205
XAO:0003200
ZFA:0005123
digestive tract epithelial tissue
epithelial tissue of digestive tract
epithelial tissue of gut
epithelium of digestive tract
epithelium of gut
gastrodermis
gut epithelial tissue
gut epithelium
uberon
alimentary tract epithelium
UBERON:0003929
digestive tract epithelium
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
2012-08-14
TAO:0005123
TAO
ZFIN:curator
UMLS:C0836205
ncithesaurus:Gut_Epithelium
digestive tract epithelial tissue
OBOL:automatic
epithelial tissue of digestive tract
OBOL:automatic
epithelial tissue of gut
OBOL:automatic
epithelium of digestive tract
OBOL:automatic
epithelium of gut
OBOL:automatic
gastrodermis
BGEE:ANN
NCBITaxon:6073
gut epithelial tissue
OBOL:automatic
gut epithelium
EHDAA2:0004567
MA:0003201
ZFA:0005123
alimentary tract epithelium
OBOL:automatic
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
EMAPA:37841
cutaneous elastic fiber
dermal elastic fiber
uberon
UBERON:0003967
cutaneous elastic tissue
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
MP:0008418
EMAPA:37841
MA:th
cutaneous elastic fiber
MP:0008418
dermal elastic fiber
MP:0008418
The connection between the embryo proper and extraembryonic tissues
uberon
UBERON:0004015
embryonic-extraembryonic boundary
The connection between the embryo proper and extraembryonic tissues
MP:0003890
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'.
AAO:0011028
AEO:0001017
EHDAA2_RETIRED:0003428
EHDAA:1719
EHDAA:1725
EHDAA:1731
EHDAA:1737
EMAPA:32838
FMA:295656
NCIT:C61572
UMLS:C0180383
XAO:0000220
cutis plate
dermatomal mesenchyme
uberon
epimere mesoderm
mesenchyma dermatomiale
UBERON:0004016
dermatome
AEO
EHDAA2-abduced
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
AEO:0001017
AEO:JB
UMLS:C0180383
ncithesaurus:Dermatome
cutis plate
dermatomal mesenchyme
mesenchyma dermatomiale
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
germinal neuroepithelial layer
germinal neuroepithelium
original neural tube
uberon
UBERON:0004022
germinal neuroepithelium
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
MP:0004261
germinal neuroepithelial layer
germinal neuroepithelium
NCBIBook:NBK10047
original neural tube
NCBIBook:NBK10047
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
ependymal layer
EMAPA:17152
EMAPA:35362
EMAPA_RETIRED:16783
MA:0003193
neural tube ependymal layer
neural tube ventricular germinal zone
neural tube ventricular zone
neural tube ependymal zone
uberon
UBERON:0004060
neural tube ventricular layer
NCBIBook:NBK10047
NCBIBook:NBK10047
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
MP:0009689
The layer of undifferentiated, proliferating cells that line the neural tube lumen
MP:0009689
ependymal layer
NCBIBook:NBK10047
neural tube ependymal layer
NCBIBook:NBK10047
neural tube ventricular germinal zone
NCBIBook:NBK10047
neural tube ventricular zone
MP:0009689
neural tube ependymal zone
MP:0009689
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.
EMAPA:17148
EMAPA:35360
neural tube intermediate zone
uberon
future brain marginal layer
UBERON:0004061
neural tube mantle layer
NCBIBook:NBK10047
by division
NCBIBook:NBK10047
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.
MP:0009690
neural tube intermediate zone
MP:0009690
future brain marginal layer
EMAPA:35360
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
EMAPA:17151
neural tube marginal zone
uberon
brain marginal zone
UBERON:0004062
neural tube marginal layer
forms from axons
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
MP:0009691
neural tube marginal zone
MP:0009691
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
in HP covers eyelid, eyebrow.
FMA:260119
content of orbital part of eye
eye region
orbital part of face
uberon
ocular and peri-ocular region
ocular region
orbital content
orbital part of eye
UBERON:0004088
orbital region
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
in HP covers eyelid, eyebrow.
HP:0000284
content of orbital part of eye
FMA:260119
eye region
orbital part of face
orbital content
FMA:260119
orbital part of eye
FMA:72951
2
2
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
AEO:0000080
EHDAA2:0003080
FMA:242873
foramen
foramina
uberon
opening
ostia
ostium
UBERON:0004111
anatomical conduit
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
FMA
foramen
EHDAA2:0003080
foramina
ostia
A vasculature that is part of a iris [Automatically generated definition].
ZFA:0005568
iris blood vessels
iris vascular network
iris vasculature
vascular network of iris
uberon
UBERON:0004118
vasculature of iris
A vasculature that is part of a iris [Automatically generated definition].
OBOL:automatic
iris blood vessels
ZFA:0005568
iris vascular network
OBOL:automatic
vascular network of iris
OBOL:automatic
An anatomical structure that develops (entirely or partially) from the endoderm.
Grouping term for query purposes
uberon
UBERON:0004119
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
Grouping term for query purposes
FBbt:00025998
mesodermal derivative
uberon
UBERON:0004120
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
mesodermal derivative
FBbt:00025998
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
FBbt:00025990
ectodermal deriviative
uberon
UBERON:0004121
ectoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectodermal deriviative
FBbt:00025990
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
AAO:0011039
EHDAA2:0001320
EMAPA:16540
FMA:293357
NCIT:C34236
TAO:0000050
UMLS:C0231106
VHOG:0000165
XAO:0000228
ZFA:0000050
uberon
evagination
eye vesicle
ocular vesicle
optic vesicles
UBERON:0004128
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]
optic vesicle
ZFA
GO-def
ZFA
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].
GO:0003404
(...) 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]
2012-09-17
VHOG:0000165
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C0231106
ncithesaurus:Optic_Vesicle
eye vesicle
XAO:0000228
ocular vesicle
VHOG:0000165
optic vesicles
ZFA:0000050
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
EHDAA2:0000215
EMAPA:16106
VHOG:0000975
myocardial plate
uberon
cardiac crescent
cardiogenic crescent
heart rudiment
UBERON:0004139
cardiogenic plate
The first recognizable structure derived from the heart field
GO:0003142
(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]
2012-09-17
VHOG:0000975
VHOG
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
myocardial plate
EHDAA2:0000215
cardiac crescent
EMAPA:16106
cardiogenic crescent
GO:0003142
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]
XAO:0004185
first heart field
primary heart field
uberon
FHF
PHF
heart field
UBERON:0004140
primary heart field
GO:0003128
BGEE:ann
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.
GO:0003138
GOC:mtg_heart
GOC:rl
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]
GO
first heart field
XAO:0004185
primary heart field
XAO:0004185
FHF
XAO:0004185
PHF
XAO:0004185
heart field
XAO:0004185
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.
AAO:0010411
EFO:0003526
EMAPA:32685
NCIT:C34161
TAO:0000360
XAO:0000337
ZFA:0000360
embryonic heart tube
endocardial heart tube
endocardial tube
uberon
UBERON:0004141
heart tube
ZFA-modified
An epithelial tube that will give rise to the mature heart.
GO:0003143
GOC:mtg_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.
MP:0012700
embryonic heart tube
GO:0003143
endocardial heart tube
MP:0012700
endocardial tube
XAO:0000337
The outflow tract septum is a partition in the outflow tract
uberon
UBERON:0004142
outflow tract septum
The outflow tract septum is a partition in the outflow tract
GO:0003148
The outflow tract is the portion of the heart through which blood flows into the arteries
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
EHDAA2:0001351
EHDAA:464
EHDAA:798
EMAPA:16346
MA:0000100
VHOG:0000670
XAO:0004139
cardiac outflow tract
heart outflow tract
uberon
arterial (outflow) pole
UBERON:0004145
outflow tract
The outflow tract is the portion of the heart through which blood flows into the arteries
GO:0003151
cardiac outflow tract
arterial (outflow) pole
A cardiac chamber surrounds an enclosed cavity within the heart
FMA:7095
OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw
chamber of heart
heart chamber
uberon
UBERON:0004151
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
cardiac chamber
A cardiac chamber surrounds an enclosed cavity within the heart
GO:0003205
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
BTO:0004605
EMAPA:37665
FMA:7143
MA:0000747
haematological system organ
haemopoietic system organ
hematopoeitic organ
hematopoietic system organ
organ of haematological system
organ of haemopoietic system
organ of hematopoietic system
organ of organa haemopoietica
organa haemopoietica organ
hematopoeitic or lymphoid organ
lymph organ
lymphoid organ
uberon
UBERON:0004177
hemopoietic organ
Organ that is part of the hematopoietic system.
GOC:Obol
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
FMA
EMAPA:37665
MA:th
haematological system organ
OBOL:automatic
haemopoietic system organ
OBOL:automatic
hematopoietic system organ
OBOL:automatic
organ of haematological system
OBOL:automatic
organ of haemopoietic system
OBOL:automatic
organ of hematopoietic system
OBOL:automatic
organ of organa haemopoietica
OBOL:automatic
organa haemopoietica organ
OBOL:automatic
lymph organ
MA:0000747
lymphoid organ
BTO:0004605
FMA:7143
A portions of the gut that is derived from endoderm.
EMAPA:32930
endodermal gut
gut endoderm
uberon
UBERON:0004185
endodermal part of digestive tract
A portions of the gut that is derived from endoderm.
GO:0061031
gut endoderm
EMAPA:32930
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
BTO:0001660
EMAPA:35734
MA:0001830
respiratory smooth muscle
smooth muscle of respiratory system
uberon
airway smooth muscle
airway smooth muscle cell
UBERON:0004225
respiratory system smooth muscle
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
respiratory smooth muscle
BTO:0001660
smooth muscle of respiratory system
OBOL:automatic
airway smooth muscle
BTO:0001660
airway smooth muscle cell
BTO:0001660
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
EMAPA:35520
MA:0002410
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
uberon
UBERON:0004233
lower respiratory tract smooth muscle
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
OBOL:automatic
involuntary muscle of lower respiratory tract
OBOL:automatic
lower respiratory tract involuntary muscle
OBOL:automatic
lower respiratory tract non-striated muscle
OBOL:automatic
lower respiratory tract smooth muscle tissue
OBOL:automatic
non-striated muscle of lower respiratory tract
OBOL:automatic
smooth muscle of lower respiratory tract
OBOL:automatic
smooth muscle tissue of lower respiratory tract
OBOL:automatic
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
see notes for muscle of iris.
BTO:0000655
EMAPA:35448
FMA:312338
MA:0001270
involuntary muscle of iris
iridial smooth muscle
iris involuntary muscle
iris non-striated muscle
iris smooth muscle tissue
non-striated muscle of iris
smooth muscle of iris
smooth muscle tissue of iris
uberon
UBERON:0004234
iris smooth muscle
MA
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
OBOL:automatic
involuntary muscle of iris
OBOL:automatic
iridial smooth muscle
iris involuntary muscle
OBOL:automatic
iris non-striated muscle
OBOL:automatic
iris smooth muscle tissue
OBOL:automatic
non-striated muscle of iris
OBOL:automatic
smooth muscle of iris
OBOL:automatic
smooth muscle tissue of iris
OBOL:automatic
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
EMAPA:36287
FMA:312251
MA:0000706
uberon
UBERON:0004236
arteriole smooth muscle
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
OBOL:automatic
smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
UBERON:0010508
BTO:0001431
CALOHA:TS-1107
EMAPA:35177
MA:0000710
MESH:D009131
NCIT:C33853
TAO:0005321
UMLS:C1519956
ZFA:0005321
blood vessel involuntary muscle
blood vessel non-striated muscle
blood vessel smooth muscle tissue
involuntary muscle of blood vessel
non-striated muscle of blood vessel
smooth muscle of blood vessel
smooth muscle tissue of blood vessel
vascular smooth muscle
vascular smooth muscle tissue
uberon
UBERON:0004237
blood vessel smooth muscle
smooth muscle found within, and composing the majority of the wall of blood vessels.
UMLS:C1519956
ncithesaurus:Vascular_Smooth_Muscle_Tissue
blood vessel involuntary muscle
OBOL:automatic
blood vessel non-striated muscle
OBOL:automatic
blood vessel smooth muscle tissue
OBOL:automatic
involuntary muscle of blood vessel
OBOL:automatic
non-striated muscle of blood vessel
OBOL:automatic
smooth muscle of blood vessel
OBOL:automatic
smooth muscle tissue of blood vessel
OBOL:automatic
vascular smooth muscle
ZFA:0005321
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
EMAPA:37708
MA:0000492
involuntary muscle of outflow tract
non-striated muscle of outflow tract
outflow tract involuntary muscle
outflow tract non-striated muscle
outflow tract smooth muscle tissue
smooth muscle of outflow tract
smooth muscle tissue of outflow tract
uberon
UBERON:0004246
outflow tract smooth muscle
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
OBOL:automatic
EMAPA:37708
MA:th
involuntary muscle of outflow tract
OBOL:automatic
non-striated muscle of outflow tract
OBOL:automatic
outflow tract involuntary muscle
OBOL:automatic
outflow tract non-striated muscle
OBOL:automatic
outflow tract smooth muscle tissue
OBOL:automatic
smooth muscle of outflow tract
OBOL:automatic
smooth muscle tissue of outflow tract
OBOL:automatic
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
UBERON:0015797
EMAPA:18187
EMAPA:35776
MA:0002710
MA:0003139
integumental system muscle
muscle of integumental system
muscle organ of skin
skin muscle organ
uberon
UBERON:0004253
skin muscle
Any muscle organ that is part of a skin of body [Automatically generated definition].
OBOL:automatic
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
MA
integumental system muscle
MA:0003139
muscle of integumental system
EMAPA:18187
muscle organ of skin
OBOL:automatic
skin muscle organ
OBOL:automatic
A blood vessel that is part of a back [Automatically generated definition].
EMAPA:37243
MA:0000493
blood vessel of back
uberon
UBERON:0004258
back blood vessel
A blood vessel that is part of a back [Automatically generated definition].
OBOL:automatic
EMAPA:37243
MA:th
blood vessel of back
OBOL:automatic
A portion of connective tissue that is part of a back [Automatically generated definition].
EMAPA:37256
MA:0000495
uberon
mesenchyne of back
UBERON:0004267
back connective tissue
A portion of connective tissue that is part of a back [Automatically generated definition].
OBOL:automatic
EMAPA:37256
MA:th
mesenchyne of back
OBOL:automatic
A muscle that is part of the eye region.
AAO:0000156
EMAPA:35335
MA:0000271
OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA
uberon
UBERON:0004277
eye muscle
MA
A muscle that is part of the eye region.
OBOL:automatic
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]
skeletal
AEO:0000168
EHDAA2:0001843
EHDAA:5047
EMAPA:17213
FMA:23875
GAID:177
MA:0003006
MAT:0000032
MESH:D012863
MIAA:0000032
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
VSAO:0000026
XAO:0004053
galen:Skeleton
set of all bones
set of bones of body
uberon
UBERON:0004288
skeleton
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
VSAO:0000026
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
2012-08-14
VSAO:0000026
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
AAO:0010572
AEO:0000214
EHDAA2:0003259
EMAPA:31109
FMA:295654
NCIT:C34140
TAO:0001513
UMLS:C1511786
VHOG:0000676
ZFA:0001513
uberon
dermamyotome
dermomyotomes
UBERON:0004290
dermomyotome
AEO
AEO
EHDAA2
ZFA
The bilaminar epithelium formed from the myotome and dermatome.
AEO:0000214
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]
2012-08-14
TAO:0001513
TAO
ZFIN:curator
Portion of somites that gives rise to dermis and muscles.[AAO]
2012-06-20
AAO:0010572
AAO
AAO:EJS
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
2012-09-17
VHOG:0000676
VHOG
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
UMLS:C1511786
ncithesaurus:Dermomyotome
dermamyotome
VHOG:0000676
dermomyotomes
VHOG:0000676
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]
TAO:0000115
ZFA:0000115
heart cone
rudimentary heart
uberon
UBERON:0004291
heart rudiment
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.
GO:0003313
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]
2012-08-14
TAO:0000115
TAO
ZFIN:curator
heart cone
GO:0003313
rudimentary heart
ZFA:0000115
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
EMAPA:37573
MA:0001806
smooth muscle tissue of blood vessel of respiratory system
uberon
UBERON:0004297
respiratory system blood vessel smooth muscle
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37573
MA:th
smooth muscle tissue of blood vessel of respiratory system
OBOL:automatic
The embryonic structure that gives rise to the corneal ectoderm
EHDAA:938
EMAPA:16322
RETIRED_EHDAA2:0001308
VHOG:0001296
uberon
UBERON:0004348
optic eminence
The embryonic structure that gives rise to the corneal ectoderm
MP:0006305
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
1
AAO:0010364
CALOHA:TS-2089
EHDAA2:0000006
EHDAA:573
EMAPA:16118
FMA:293019
MFMO:0000095
NCIT:C34175
TAO:0001595
UMLS:C1517197
VHOG:0000296
XAO:0000097
ZFA:0001612
1st pharyngeal arch
branchial arch 1
first branchial arch
first pharyngeal arch
first visceral arch
mandibular arch
visceral arch 1
uberon
1st arch
1st visceral arch
arcus pharyngeus primus
UBERON:0004362
pharyngeal arch 1
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
2012-06-20
AAO:0010364
AAO
XAO:EJS
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
MP:0006337,MGI:smb
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
2012-09-17
VHOG:0000296
VHOG
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
UMLS:C1517197
ncithesaurus:First_Pharyngeal_Arch
branchial arch 1
first branchial arch
first visceral arch
visceral arch 1
1st arch
EHDAA2:0000006
1st visceral arch
VHOG:0000296
arcus pharyngeus primus
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
add specific artery derivatives
Do not confuse with arch of aorta.
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
UBERON:0004342
AAO:0010414
EFO:0003695
EHDAA2:0000186
EHDAA:398
EHDAA:7327
EMAPA:16684
NCIT:C32123
TAO:0005004
UMLS:C0003489
VHOG:0000122
XAO:0000341
ZFA:0005004
PAA
aortic arch
aortic arches
branchial aortic arches
branchial arch artery
embryonic aortic arch artery
pharyngeal arch artery
uberon
a. arcuum pharyngeorum
aortic arch artery
arteriae arcuum pharyngeorum
branchial aortic arches
pharyngeal arch arteries
pharyngeal arch artery
UBERON:0004363
pharyngeal arch artery
ZFA
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
MP:0002672
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
2012-09-17
VHOG:0000122
VHOG
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
2012-09-17
VHOG:0000122
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
UMLS:C0003489
ncithesaurus:Aortic_Arch
PAA
MP:0002672
aortic arch
ZFA:0005004
aortic arches
ZFA:0005004
branchial aortic arches
ZFIN:ZDB-PUB-080512-6
branchial arch artery
EMAPA:16684
embryonic aortic arch artery
EMAPA:16684
MP:0002672
pharyngeal arch artery
MP:0002672
a. arcuum pharyngeorum
aortic arch artery
EMAPA:16684
arteriae arcuum pharyngeorum
branchial aortic arches
ZFA:0005004
ZFIN:ZDB-PUB-080512-6
pharyngeal arch arteries
pharyngeal arch artery
VHOG:0000122
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
FMA:58273
MA:0001240
NCIT:C32226
TAO:0002155
UMLS:C0229127
ZFA:0001684
Bowman's anterior elastic lamina
Bowman's layer
Bowman's membrane
anterior elastic lamina
anterior limiting lamina
anterior limiting lamina of cornea
lamina limitans anterior (cornea)
lamina limitans anterior corneae
uberon
Reichert's membrane
anterior limiting membrane
UBERON:0004370
anterior limiting lamina of cornea
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.
ncithesaurus:Bowman_s_Membrane
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
2012-08-14
TAO:0002155
TAO
ZFIN:ZDB-PUB-061010-3
UMLS:C0229127
ncithesaurus:Bowman_s_Membrane
Bowman's anterior elastic lamina
FMA:58273
Bowman's layer
FMA:58273
Bowman's membrane
FMA:58273
anterior elastic lamina
ZFA:0001684
anterior limiting lamina
MA:0001240
anterior limiting lamina of cornea
FMA:58273
lamina limitans anterior (cornea)
FMA:58273
lamina limitans anterior corneae
FMA:58273
FMA:TA
Reichert's membrane
anterior limiting membrane
ZFA:0001684
An embryo at the neurula stage.
UBERON:0007013
BILA:0000061
BTO:0001766
NCIT:C34229
UMLS:C1518306
neurula
uberon
UBERON:0004455
neurula embryo
An embryo at the neurula stage.
UMLS:C1518306
ncithesaurus:Neurula
neurula
BTO:0001766
Sum of all sensory systems in an organism.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
FMA:78499
sense organ system
uberon
UBERON:0004456
entire sense organ system
Sum of all sensory systems in an organism.
sense organ system
FMA:78499
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
EMAPA:18171
FMA:71287
head musculature
muscle group of head
muscles of head
musculi capitis
set of muscles of head
uberon
UBERON:0004461
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
skeletal musculature of head
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
OBOL:automatic
head musculature
FMA:71287
muscle group of head
FMA:71287
muscles of head
FMA:71287
musculi capitis
FMA:71287
FMA:TA
set of muscles of head
FMA:71287
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
BTO:0000508
EMAPA:37260
FMA:71293
muscle group of thorax
muscles of thorax
musculi thoracis
set of muscles of thorax
thoracic musculature
uberon
UBERON:0004464
musculature of thorax
Any collection of muscles that is part of a thorax [Automatically generated definition].
OBOL:automatic
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
BTO
EMAPA:37260
MA:th
muscle group of thorax
FMA:71293
muscles of thorax
FMA:71293
musculi thoracis
FMA:71293
FMA:TA
set of muscles of thorax
FMA:71293
thoracic musculature
FMA:71293
Any collection of muscles that is part of a neck [Automatically generated definition].
AAO:0000091
EMAPA:36050
FMA:71290
MESH:D009334
cervical muscles
muscle group of neck
muscles of neck
musculi cervicis
musculi colli
neck musculature
set of muscles of neck
uberon
UBERON:0004465
musculature of neck
Any collection of muscles that is part of a neck [Automatically generated definition].
OBOL:automatic
cervical muscles
AAO:0000091
muscle group of neck
FMA:71290
muscles of neck
FMA:71290
musculi cervicis
FMA:71290
FMA:TA
musculi colli
FMA:71290
FMA:TA
neck musculature
FMA:71290
set of muscles of neck
FMA:71290
Any collection of muscles that is part of a back [Automatically generated definition].
FMA:71291
muscle group of back
muscles of back
musculi dorsi
set of muscles of back
uberon
UBERON:0004469
musculature of back
Any collection of muscles that is part of a back [Automatically generated definition].
OBOL:automatic
muscle group of back
FMA:71291
muscles of back
FMA:71291
musculi dorsi
FMA:71291
FMA:TA
set of muscles of back
FMA:71291
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
FMA:71288
entire facial musculature
facial muscles
muscle group of face
musculi faciei
uberon
set of facial muscles
set of muscles of face
UBERON:0004473
musculature of face
Any collection of muscles that is part of a face.
OBOL:automatic
entire facial musculature
facial muscles
FMA:71288
muscle group of face
FMA:71288
musculi faciei
FMA:71288
FMA:TA
set of facial muscles
FMA:71288
set of muscles of face
FMA:71288
Any collection of muscles that is part of a trunk [Automatically generated definition].
currently defined by location rather than attachment
AAO:0011572
EFO:0003531
FMA:50187
muscle group of trunk
set of muscles of trunk
uberon
muscular system of trunk
UBERON:0004479
musculature of trunk
Any collection of muscles that is part of a trunk [Automatically generated definition].
OBOL:automatic
muscle group of trunk
FMA:50187
set of muscles of trunk
FMA:50187
muscular system of trunk
FMA:50187
A vasculature that is part of a muscle organ [Automatically generated definition].
FMA:87123
muscular organ vasculature
uberon
UBERON:0004521
vasculature of muscle organ
A vasculature that is part of a muscle organ [Automatically generated definition].
OBOL:automatic
muscular organ vasculature
FMA:87123
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
FMA:239607
uberon
UBERON:0004522
vasculature of musculoskeletal system
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
OBOL:automatic
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
AAO:0011001
BILA:0000016
BTO:0000088
CALOHA:TS-1297
EFO:0000791
EHDAA2:0000216
EHDAA:394
EMAPA:16104
EMAPA:16370
EV:0100017
FMA:7161
GAID:467
MA:0000010
MAT:0000016
MESH:D002319
MIAA:0000016
NCIT:C12686
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
TAO:0000010
UMLS:C0007226
VHOG:0000302
WikipediaCategory:Cardiovascular_system
XAO:0000100
XAO:0001010
ZFA:0000010
uberon
CV system
Herz und Gefaesssystem
UBERON:0004535
cardiovascular system
Anatomical system that has as its parts the heart and blood vessels.
BTO:0000088
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]
2012-09-17
VHOG:0000302
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
UMLS:C0007226
ncithesaurus:Cardiovascular_System
CV system
BTO:0000088
Herz und Gefaesssystem
BTO:0000088
A vascular network consisting of blood vessels.
TAO:0001079
ZFA:0001079
blood vascular network
set of blood vessels
uberon
blood system
blood vessel system
blood vessels
UBERON:0004537
blood vasculature
A vascular network consisting of blood vessels.
blood vessels
TAO:0001079
An eye that is part of a left side of organism [Automatically generated definition].
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EMAPA:37362
FMA:12515
MA:0002949
NCIT:C119334
left eyeball
left orbital part of face
left orbital region
uberon
UBERON:0004548
left eye
An eye that is part of a left side of organism [Automatically generated definition].
OBOL:automatic
EMAPA:37362
MA:th
left eyeball
FMA:12515
left orbital part of face
FMA:54450
left orbital region
FMA:54450
An eye that is part of a right side of organism [Automatically generated definition].
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EMAPA:37363
FMA:12514
MA:0002950
NCIT:C119333
right eyeball
right orbital part of face
right orbital region
uberon
UBERON:0004549
right eye
An eye that is part of a right side of organism [Automatically generated definition].
OBOL:automatic
EMAPA:37363
MA:th
right eyeball
FMA:12514
right orbital part of face
FMA:54449
right orbital region
FMA:54449
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
FMA:45623
systemic arterial circulatory system
uberon
UBERON:0004571
systemic arterial system
MA-inferred
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
systemic arterial circulatory system
FMA:45623
The part of the cardiovascular system consisting of all arteries.
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]
BTO:0004690
EHDAA2:0000143
EHDAA:396
EMAPA:16201
EMAPA:16371
MA:0002719
VHOG:0000273
uberon
UBERON:0004572
arterial system
MA
The part of the cardiovascular system consisting of all arteries.
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]
2012-09-17
VHOG:0000273
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
EMAPA:37126
FMA:66464
systemic arterial subtree
uberon
UBERON:0004573
systemic artery
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
EMAPA:37126
MA:th
systemic arterial subtree
FMA:66464
The part of the venous system that drains the general body tissues[Kardong]
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The 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]
FMA:45626
systemic venous circulatory system
uberon
UBERON:0004581
systemic venous system
The part of the venous system that drains the general body tissues[Kardong]
ISBN:0073040584
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
FMA
FMA:45626
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]
2012-09-17
VHOG:0000277
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
systemic venous circulatory system
FMA:45626
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.
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]
BTO:0004692
EHDAA2:0002171
EHDAA:486
EMAPA:16240
MA:0002720
NCIT:C33858
UMLS:C1267406
VHOG:0000277
vein system
uberon
UBERON:0004582
venous system
MA
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.
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]
2012-09-17
VHOG:0000277
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
UMLS:C1267406
ncithesaurus:Venous_System
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
BTO:0000766
CALOHA:TS-2155
EMAPA:35176
MA:0000709
NCIT:C53395
TAO:0005257
UMLS:C1706972
ZFA:0005257
uberon
UBERON:0004638
blood vessel endothelium
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
UMLS:C1706972
ncithesaurus:Blood_Vessel_Endothelium
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
EMAPA:37496
FMA:10636
MA:0001939
costocervical trunk
trunk of costocervical artery
uberon
truncus costocervicalis
UBERON:0004688
costo-cervical trunk
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
EMAPA:37496
MA:th
costocervical trunk
FMA:10636
trunk of costocervical artery
FMA:10636
truncus costocervicalis
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
EMAPA:36503
MA:0000704
uberon
UBERON:0004695
arterial system smooth muscle
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
OBOL:automatic
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
EMAPA:36613
MA:0000715
uberon
UBERON:0004696
venous system smooth muscle
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
OBOL:automatic
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
MA:0000490
VHOG:0001524
uberon
UBERON:0004699
outflow tract endothelium
An endothelium that is part of a outflow tract [Automatically generated definition].
OBOL:automatic
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
2012-09-17
VHOG:0001524
VHOG
DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)
An endothelium that is part of an arterial system [Automatically generated definition].
EMAPA:35145
MA:0000703
NCIT:C49329
UMLS:C1706849
uberon
UBERON:0004700
arterial system endothelium
An endothelium that is part of an arterial system [Automatically generated definition].
OBOL:automatic
UMLS:C1706849
ncithesaurus:Arterial_System_Endothelium
An endothelium that is part of a venous system [Automatically generated definition].
EMAPA:35907
MA:0000714
NCIT:C49320
UMLS:C1710626
uberon
UBERON:0004701
venous system endothelium
An endothelium that is part of a venous system [Automatically generated definition].
OBOL:automatic
UMLS:C1710626
ncithesaurus:Venous_System_Endothelium
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
EMAPA:35732
MA:0001805
uberon
UBERON:0004702
respiratory system blood vessel endothelium
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
BTO:0001744
CALOHA:TS-0497
EMAPA:18638
GAID:536
MA:0002154
MESH:D007601
NCIT:C12738
UMLS:C0022427
uberon
jugular
vena jugularis
UBERON:0004711
jugular vein
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
UMLS:C0022427
ncithesaurus:Jugular_Vein
vena jugularis
BTO:0001744
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
AEO:0000194
BTO:0003834
EHDAA2:0000001
EHDAA2:0003235
EMAPA:36040
NCIT:C34131
UMLS:C1516779
embryo plus adnexa
uberon
UBERON:0004716
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].
BTO:0003834
UMLS:C1516779
ncithesaurus:Conceptus
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Melissa Haendel
2009-06-18T09:00:04Z
NLX:147842
TAO:0001328
ZFA:0001328
neural tube metameric segment
neural tube segment
neuromere
neuromeres
uberon
neural metamere
neural segment
UBERON:0004731
neuromere
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
A metameric segment of the central nervous system.[ZFA]
2012-08-14
TAO:0001328
TAO
ZFIN:curator
neural tube metameric segment
neuromeres
TAO:0001328
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)
FBbt:00005140
uberon
neuromere
UBERON:0004732
segmental subdivision of nervous system
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
FBbt:00005140
neuromere
FBbt:00005140
An organ subunit that is part of a hindbrain [Automatically generated definition].
FMA:61998
hindbrain segment
segment of hindbrain
uberon
UBERON:0004733
segmental subdivision of hindbrain
An organ subunit that is part of a hindbrain [Automatically generated definition].
OBOL:automatic
hindbrain segment
FMA:61998
segment of hindbrain
FMA:61998
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
UBERON:0007012
BILA:0000060
BTO:0001403
FBbt:00005317
FMA:293108
GAID:1302
MESH:A16.254.412
MIAA:0000179
NCIT:C34057
NCIT:C34058
UMLS:C0017199
UMLS:C1284022
gastrula embryo
uberon
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
UBERON:0004734
gastrula
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
NCIT
UMLS:C0017199
ncithesaurus:Gastrula
UMLS:C1284022
ncithesaurus:Trilaminar_Embryonic_Disc
gastrula embryo
BILA:0000060
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
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]
AAO:0011129
TAO:0001890
VSAO:0000128
XAO:0004012
ZFA:0005494
galen:SkeletalStructure
uberon
UBERON:0004765
skeletal element
VSAO
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]
2012-08-14
VSAO:0000128
VSAO
PSPUB:0000170
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
2012-08-14
TAO:0001890
TAO
TAO:VSAO_workshop
Anatomical system that consists of all the joints of the body.
EMAPA:35150
FMA:23878
MA:0003007
VSAO:0000181
joint system
set of all joints of body
uberon
set of all joints
set of joints of body
UBERON:0004770
articular system
FMA
Anatomical system that consists of all the joints of the body.
VSAO:0000181
joint system
FMA:23878
set of all joints of body
FMA:23878
set of joints of body
FMA:23878
A submucosa that is part of a respiratory system [Automatically generated definition].
EMAPA:37578
MA:0001822
apparatus respiratorius submucosa
submucosa of apparatus respiratorius
submucosa of respiratory system
uberon
UBERON:0004777
respiratory system submucosa
A submucosa that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37578
MA:th
apparatus respiratorius submucosa
OBOL:automatic
submucosa of apparatus respiratorius
OBOL:automatic
submucosa of respiratory system
OBOL:automatic
the mucous membrane lining the respiratory tract
TODO - split respiratory tract mucosa from respiratory system mucosa
BTO:0000973
EMAPA:18334
EMAPA:37577
FMA:302092
GAID:304
MA:0001827
MESH:D020545
apparatus respiratorius mucosa
apparatus respiratorius mucosa of organ
apparatus respiratorius mucous membrane
mucosa of apparatus respiratorius
mucosa of organ of apparatus respiratorius
mucosa of organ of respiratory system
mucosa of respiratory system
mucous membrane of apparatus respiratorius
mucous membrane of respiratory system
respiratory system mucosa of organ
respiratory system mucous membrane
uberon
laryngeal mucous membrane
respiratory mucosa
respiratory tract mucosa
UBERON:0004785
respiratory system mucosa
the mucous membrane lining the respiratory tract
MESH:A04.760
MGI:cwg
MP:0002277
EMAPA:37577
MA:th
apparatus respiratorius mucosa
OBOL:automatic
apparatus respiratorius mucosa of organ
OBOL:automatic
apparatus respiratorius mucous membrane
OBOL:automatic
mucosa of apparatus respiratorius
OBOL:automatic
mucosa of organ of apparatus respiratorius
OBOL:automatic
mucosa of organ of respiratory system
OBOL:automatic
mucosa of respiratory system
OBOL:automatic
mucous membrane of apparatus respiratorius
OBOL:automatic
mucous membrane of respiratory system
OBOL:automatic
respiratory system mucosa of organ
OBOL:automatic
respiratory system mucous membrane
OBOL:automatic
laryngeal mucous membrane
EMAPA:18334
respiratory mucosa
BTO:0000973
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
EMAPA:36296
MA:0002854
uberon
UBERON:0004797
blood vessel layer
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
BTO:0000419
CALOHA:TS-0023
EMAPA:32827
MA:0001480
VHOG:0000981
epithelial tissue of respiratory tract
epithelium of respiratory tract
respiratory tract epithelial tissue
uberon
airway epithelium
respiratory epithelium
UBERON:0004802
respiratory tract epithelium
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
ISBN:0-683-40008-8
MGI:anna
MP:0010942
epithelial tissue of respiratory tract
OBOL:automatic
epithelium of respiratory tract
OBOL:automatic
respiratory tract epithelial tissue
OBOL:automatic
airway epithelium
BTO:0000419
respiratory epithelium
BTO:0000419
An epithelium that is part of a respiratory system [Automatically generated definition].
CALOHA:TS-0023
EMAPA:32826
MA:0001823
VHOG:0000981
apparatus respiratorius epithelial tissue
apparatus respiratorius epithelium
epithelial tissue of apparatus respiratorius
epithelial tissue of respiratory system
epithelium of apparatus respiratorius
epithelium of respiratory system
respiratory system epithelial tissue
uberon
UBERON:0004807
respiratory system epithelium
An epithelium that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius epithelial tissue
OBOL:automatic
apparatus respiratorius epithelium
OBOL:automatic
epithelial tissue of apparatus respiratorius
OBOL:automatic
epithelial tissue of respiratory system
OBOL:automatic
epithelium of apparatus respiratorius
OBOL:automatic
epithelium of respiratory system
OBOL:automatic
respiratory system epithelial tissue
OBOL:automatic
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
EMAPA:37549
MA:0001481
epithelial tissue of lower respiratory tract
epithelium of lower respiratory tract
lower respiratory tract epithelial tissue
uberon
UBERON:0004815
lower respiratory tract epithelium
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
OBOL:automatic
EMAPA:37549
MA:th
epithelial tissue of lower respiratory tract
OBOL:automatic
epithelium of lower respiratory tract
OBOL:automatic
lower respiratory tract epithelial tissue
OBOL:automatic
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
EMAPA:37566
MA:0001801
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system artery endothelium
respiratory system endothelium of artery
uberon
UBERON:0004848
respiratory system arterial endothelium
true
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37566
MA:th
apparatus respiratorius arterial endothelium
OBOL:automatic
apparatus respiratorius artery endothelium
OBOL:automatic
apparatus respiratorius endothelium of artery
OBOL:automatic
arterial endothelium of apparatus respiratorius
OBOL:automatic
arterial endothelium of respiratory system
OBOL:automatic
artery endothelium of apparatus respiratorius
OBOL:automatic
artery endothelium of respiratory system
OBOL:automatic
endothelium of artery of apparatus respiratorius
OBOL:automatic
endothelium of artery of respiratory system
OBOL:automatic
respiratory system artery endothelium
OBOL:automatic
respiratory system endothelium of artery
OBOL:automatic
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
EMAPA:37585
MA:0001811
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
respiratory system endothelium of vein
respiratory system vein endothelium
vein endothelium of apparatus respiratorius
vein endothelium of respiratory system
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
uberon
UBERON:0004849
respiratory system venous endothelium
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37585
MA:th
apparatus respiratorius endothelium of vein
OBOL:automatic
apparatus respiratorius vein endothelium
OBOL:automatic
apparatus respiratorius venous endothelium
OBOL:automatic
endothelium of vein of apparatus respiratorius
OBOL:automatic
endothelium of vein of respiratory system
OBOL:automatic
respiratory system endothelium of vein
OBOL:automatic
respiratory system vein endothelium
OBOL:automatic
vein endothelium of apparatus respiratorius
OBOL:automatic
vein endothelium of respiratory system
OBOL:automatic
venous endothelium of apparatus respiratorius
OBOL:automatic
venous endothelium of respiratory system
OBOL:automatic
An endothelium that is part of the cardiovascular system.
consider merging with 'endothelium'
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
BTO:0001853
EMAPA:35201
GAID:519
MA:0000717
MESH:D004730
NCIT:C13053
TAO:0002171
UMLS:C0014261
VHOG:0001217
XAO:0000356
ZFA:0001639
uberon
endothelia
vascular endothelia
UBERON:0004852
cardiovascular system endothelium
An endothelium that is part of the cardiovascular system.
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001217
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C0014261
ncithesaurus:Vascular_Endothelium
endothelia
ZFA:0001639
vascular endothelia
XAO:0000356
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
EMAPA:35334
MA:0000267
eye-associated gland
gland of eye
uberon
UBERON:0004859
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
eye gland
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
eye-associated gland
gland of eye
OBOL:automatic
A vasculature that is part of a retina [Automatically generated definition].
FMA:76552
MESH:D012171
XAO:0004153
retina vasculature
retina vasculature of camera-type eye
retinal blood vessels
retinal blood vessels set
retinal vasculature
set of blood vessels of retina
set of retinal blood vessels
vasa sanguinea retinae
uberon
UBERON:0004864
vasculature of retina
A vasculature that is part of a retina [Automatically generated definition].
OBOL:automatic
retina vasculature
GO:0061298
retina vasculature of camera-type eye
GO:0061298
retinal blood vessels
FMA:76552
retinal blood vessels set
FMA:76552
retinal vasculature
OBOL:automatic
set of blood vessels of retina
OBOL:automatic
set of retinal blood vessels
FMA:76552
vasa sanguinea retinae
FMA:76552
FMA:TA
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
visceral mesoderm
AAO:0011102
BILA:0000044
FMA:295568
XAO:0000276
inner layer of lateral plate mesoderm
uberon
splanchnic mesoderm
UBERON:0004872
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
BILA
visceral mesoderm
BILA:0000044
splanchnic mesoderm
ISBN:9780878932504
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
TODO - check relationship to LPM
EHDAA2:0001903
EHDAA:383
EMAPA:16181
FMA:295564
NCIT:C34303
UMLS:C1519472
VHOG:0000558
uberon
ventral splanchnic mesoderm
UBERON:0004873
splanchnopleure
EHDAA2
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
UMLS:C1519472
ncithesaurus:Splanchnopleure
ventral splanchnic mesoderm
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
AAO:0000478
EFO:0003426
TAO:0000091
ZFA:0000091
axial chorda mesoderm
chorda mesoderm
dorsal mesoderm
presumptive notochord
uberon
UBERON:0004880
chordamesoderm
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
ZFIN:ZDB-PUB-961014-576
axial chorda mesoderm
ZFA:0000091
dorsal mesoderm
presumptive notochord
ZFA:0000091
The mass of tissue made up of mesenchymal cells in the lung.
EMAPA:32866
lung-associated mesenchyme
mesenchyme of lung
pulmonary mesenchyme
uberon
UBERON:0004883
lung mesenchyme
The mass of tissue made up of mesenchymal cells in the lung.
GO:0060484
lung-associated mesenchyme
GO:0060484
mesenchyme of lung
OBOL:automatic
pulmonary mesenchyme
GO:0060484
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
FBbt:00005811
joint
uberon
UBERON:0004905
articulation
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
ectodermal gut
gut ectoderm
uberon
UBERON:0004906
ectodermal part of digestive tract
A portion of the gut that is derived from ectoderm.
GO:0007439
gut ectoderm
EMAPA:32930
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.
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
A proximal-distal subdivision of the digestive tract.
alimentary system subdivision
FMA:71131
subdivision of alimentary system
FMA:71131
A part of a wall of an organ that forms a layer.
FMA:82485
uberon
UBERON:0004923
organ component layer
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
BTO:0002113
FMA:75144
pharyngeal submucosa
pharynx submucosa
tela submucosa pharyngea
tela submucosa pharyngis
uberon
pharyngobasilar fascia
submucous coat of pharynx
submucous layer of pharynx
UBERON:0004924
submucosa of pharynx
The tissue underlying the tunica mucosa of the pharynx.
BTO:0002113
pharyngeal submucosa
FMA:75144
pharynx submucosa
OBOL:automatic
tela submucosa pharyngea
FMA:75144
FMA:TA
tela submucosa pharyngis
BTO:0002113
submucous coat of pharynx
BTO:0002113
submucous layer of pharynx
BTO:0002113
A mucosa that is part of a lower lip [Automatically generated definition].
FMA:59833
NCIT:C12225
UMLS:C0226939
lower labial mucosa
lower lip mucosa
lower lip mucosa of organ
lower lip mucous membrane
lower lip organ mucosa
mucosa of organ of lower lip
mucous membrane of lower lip
organ mucosa of lower lip
uberon
UBERON:0005032
mucosa of lower lip
A mucosa that is part of a lower lip [Automatically generated definition].
OBOL:automatic
UMLS:C0226939
ncithesaurus:Mucosa_of_the_Lower_Lip
lower labial mucosa
UBERON:cjm
lower lip mucosa
OBOL:automatic
lower lip mucosa of organ
OBOL:automatic
lower lip mucous membrane
OBOL:automatic
lower lip organ mucosa
OBOL:automatic
mucosa of organ of lower lip
OBOL:automatic
mucous membrane of lower lip
OBOL:automatic
organ mucosa of lower lip
OBOL:automatic
A gland that is part of a hemolymphoid system [Automatically generated definition].
hemopoietic or lymphoid organ
EMAPA:18766
MA:0002962
hemopoietic or lymphoid gland
uberon
haemolymphoid system gland
UBERON:0005058
hemolymphoid system gland
A gland that is part of a hemolymphoid system [Automatically generated definition].
OBOL:automatic
hemopoietic or lymphoid organ
GO:0048534
hemopoietic or lymphoid gland
haemolymphoid system gland
EMAPA:18766
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].
AAO:0011071
EMAPA:35594
FMA:295624
NCIT:C34224
UMLS:C0814992
XAO:0000248
uberon
UBERON:0005061
neural groove
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
GO:0001842
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].
UMLS:C0814992
ncithesaurus:Neural_Groove
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
EHDAA2:0001249
FMA:295618
NCIT:C34223
UMLS:C0814993
XAO:0004087
medullary fold
uberon
UBERON:0005062
neural fold
One of the two elevated edges of the neural groove[GO,MP].
GO:0001842
MP:0011256
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].
UMLS:C0814993
ncithesaurus:Neural_Fold
medullary fold
MP:0011256
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]
EFO:0003498
TAO:0000133
ZFA:0000133
uberon
neural tube rod
UBERON:0005068
neural rod
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].
GO:0014024
ZFA:0000133
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]
2012-08-14
TAO:0000133
TAO
ZFIN:curator
neural tube rod
GO:0014027
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
hindbrain-spinal cord boundary region
uberon
UBERON:0005076
hindbrain-spinal cord boundary
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
OBOL:automatic
A hole in a tube[GO].
AEO:0000078
EHDAA2:0004618
RETIRED_EHDAA2:0003078
uberon
UBERON:0005082
tube lumen
A hole in a tube[GO].
GO:0060609
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
AEO:0000218
uberon
epithelial placode
UBERON:0005085
ectodermal placode
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
GO:0060788
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
GO
epithelial placode
AEO:0000112
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
EMAPA:32715
FBbt:00005073
FMA:30316
musculus
uberon
muscle
muscle element
UBERON:0005090
muscle structure
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
GO:0061061
musculus
FMA:30316
A bud is a protrusion that forms from an epithelial sheet by localized folding.
BTO:0001639
uberon
UBERON:0005153
epithelial bud
A bud is a protrusion that forms from an epithelial sheet by localized folding.
GO:0060572
An epithelial sheet bent on a linear axis.
uberon
UBERON:0005157
epithelial fold
An epithelial sheet bent on a linear axis.
GO:0060571
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.'
AAO:0011000
CARO:0001000
FBbt:00007060
FMA:83115
multi-cell-component structure
multi-cell-part structure
uberon
cell part cluster
UBERON:0005162
multi cell part structure
FMA
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
CARO:0001000
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.'
CARO
FMA
multi-cell-component structure
CARO:0001000
multi-cell-part structure
CARO:0001000
cell part cluster
FMA:83115
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:0001901
back organ
dorsal region organ
uberon
UBERON:0005174
dorsal region element
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:th
back organ
MA:0001901
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.
EMAPA:37270
MA:0000516
trunk organ
uberon
UBERON:0005177
trunk region element
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.
EMAPA:37270
MA:th
trunk organ
MA:0000516
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:0000557
thoracic cavity organ
uberon
UBERON:0005178
thoracic cavity element
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:th
thoracic cavity organ
MA:0000557
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:0000563
uberon
upper body organ
UBERON:0005181
thoracic segment organ
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:th
upper body organ
MA:0000563
A vein that is part of a thorax [Automatically generated definition].
EMAPA:37197
MA:0002235
NCIT:C53142
UMLS:C0226629
uberon
UBERON:0005194
thoracic vein
A vein that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37197
MA:th
UMLS:C0226629
ncithesaurus:Thoracic_Vein
An external ectoderm that is part of a optic eminence [Automatically generated definition].
EMAPA:16539
RETIRED_EHDAA2:0001311
VHOG:0000520
uberon
UBERON:0005216
optic eminence surface ectoderm
true
An external ectoderm that is part of a optic eminence [Automatically generated definition].
OBOL:automatic
An ectoderm that is part of a optic eminence [Automatically generated definition].
EHDAA:940
EMAPA:16539
RETIRED_EHDAA2:0001309
VHOG:0001105
uberon
UBERON:0005234
optic eminence ectoderm
An ectoderm that is part of a optic eminence [Automatically generated definition].
OBOL:automatic
A gland that is part of a stomodeum.
check this
VHOG:0000658
stomatodaeum gland
uberon
UBERON:0005250
stomatodeum gland
A gland that is part of a stomodeum.
OBOL:automatic
stomatodaeum gland
VHOG:0000658
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
EFO:0003492
EHDAA2:0000732
EHDAA:179
EMAPA:16098
EMAPA_RETIRED:16269
FMA:76622
TAO:0000113
VHOG:0000332
ZFA:0000113
cephalic mesenchyme
uberon
cranial mesenchyme
desmocranium
UBERON:0005253
head mesenchyme
EHDAA2
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.
ISBN:0683400088
MP:0011260
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]
2012-08-14
TAO:0000113
TAO
ZFIN:curator
cephalic mesenchyme
MP:0011260
cranial mesenchyme
MGI:anna
desmocranium
FMA:76622
Mesenchyme that is part of a developing trunk.
EFO:0003485
EHDAA2:0002092
EHDAA:377
EMAPA:16177
TAO:0000081
VHOG:0000281
ZFA:0000081
uberon
trunk and cervical mesenchyme
UBERON:0005256
trunk mesenchyme
EHDAA2
Mesenchyme that is part of a developing trunk.
OBOL:automatic
trunk and cervical mesenchyme
EHDAA2:0002092
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
The 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. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
BTO:0000758
CALOHA:TS-0607
CALOHA:TS-2365
DHBA:10662
EHDAA2:0001207
EHDAA:5526
EMAPA:17082
HBA:9512
MA:0000205
VHOG:0000456
uberon
myelencephalon (medulla oblongata)
UBERON:0005290
myelencephalon
definitional
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].
BTO:0000758
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
2012-09-17
VHOG:0000456
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]
2012-09-17
VHOG:0000456
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
myelencephalon (medulla oblongata)
DHBA:10662
A portion of tissue that is part of an embryo.
CALOHA:TS-2100
portion of embryonic tissue
uberon
developing tissue
UBERON:0005291
embryonic tissue
A portion of tissue that is part of an embryo.
OBOL:automatic
portion of embryonic tissue
OBOL:automatic
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
BTO:0003360
CALOHA:TS-2119
EFO:0001406
MAT:0000061
MIAA:0000061
extra-embryonic tissue
uberon
UBERON:0005292
extraembryonic tissue
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The endothelial lining of the endocardium.
FMA:83596
endocardium endothelium
endothelium of endocardium
uberon
UBERON:0005316
endocardial endothelium
The endothelial lining of the endocardium.
UBERON:cjm
endocardium endothelium
FMA:83596
endothelium of endocardium
FMA:83596
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
BTO:0000137
pulmonary artery endothelial tube
uberon
UBERON:0005317
pulmonary artery endothelium
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
GO:0061155
pulmonary artery endothelial tube
GO:0061155
merge with RVOT?
EHDAA2:0001359
EHDAA:4401
EMAPA:17330
MA:0000102
VHOG:0001395
uberon
UBERON:0005339
outflow tract pulmonary component
An array of photoreceptors and any supporting cells found in an eye.
FBbt:00004200
light-sensitive tissue
uberon
UBERON:0005388
photoreceptor array
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
lens
uberon
UBERON:0005389
transparent eye structure
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.
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
AAO:0010217
BTO:0000168
CALOHA:TS-0116
EFO:0000818
EHDAA:6385
EMAPA:18609
EV:0100379
FMA:70504
GAID:478
MA:0001925
MAT:0000501
MESH:D002339
NCIT:C12687
OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA
TAO:0000097
UMLS:C0007272
VHOG:0000266
ZFA:0000097
galen:CarotidArtery
carotid
carotid artery
subdivision of common carotid artery
uberon
common carotid arterial subdivision
UBERON:0005396
carotid artery segment
FMA
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000097
TAO
ZFIN:curator
UMLS:C0007272
ncithesaurus:Carotid_Artery
carotid
AAO:0010217
carotid artery
MA:0001925
subdivision of common carotid artery
FMA:70504
common carotid arterial subdivision
FMA:70504
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
developmental tissue
MIAA:0000019
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
(...) 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]
EHDAA2:0001304
EMAPA:16675
TAO:0001071
VHOG:0000490
ZFA:0001071
future neural retina
future retinal neural layer
inner layer optic cup
optic cup inner layer
presumptive retinas
uberon
future NR
future neural epithelium
future neural layer
presumptive retina
UBERON:0005425
presumptive neural retina
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
ZFIN:curator
(...) 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]
2012-09-17
VHOG:0000490
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
inner layer optic cup
ZFA:0001071
optic cup inner layer
EHDAA2:0001304
presumptive retinas
ZFA:0001071
future neural epithelium
EMAPA:16675
future neural layer
EMAPA:16675
presumptive retina
TAO:0001071
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
(...) 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]
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
EHDAA2:0000983
EHDAA:4737
EMAPA:17163
TAO:0002205
VHOG:0001163
ZFA:0001679
hollow lens vesicle
solid lens vesicle
uberon
immature lens
lens mass
presumptive lens
UBERON:0005426
lens vesicle
Portion of tissue that gives rise to the lens.
ZFIN:curator
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
2012-09-17
VHOG:0001163
VHOG
(...) 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]
2012-09-17
VHOG:0001163
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
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
ZFA
hollow lens vesicle
solid lens vesicle
ZFA:0001679
immature lens
ZFA:0001679
lens mass
ZFA:0001679
ZFIN:ZDB-PUB-091023-49
presumptive lens
ZFA:0001679
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
TAO:0002188
ZFA:0001688
uberon
UBERON:0005427
corneal primordium
ZFA
Obol
ZFA
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
ZFIN:ZDB-PUB-061010-3
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
EHDAA2:0004145
EHDAA:9826
EMAPA:36461
FMA:71008
RETIRED_EHDAA2:0000133
saccus aorticus
uberon
UBERON:0005432
aortic sac
EHDAA2
EHDAA2
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates
MP:0012510
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
saccus aorticus
Portion of tissue on the side of the lumen of the neural tube.
EHDAA2:0001257
EHDAA:2873
EHDAA:912
EMAPA:16166
TAO:0001435
VHOG:0000513
ZFA:0001435
lateral wall neural tube
uberon
UBERON:0005496
neural tube lateral wall
Portion of tissue on the side of the lumen of the neural tube.
ZFA:0001435
lateral wall neural tube
ZFA:0001435
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
EHDAA2:0001512
EHDAA:424
EHDAA:436
EMAPA:16215
FMA:321916
TAO:0000149
ZFA:0000149
primitive heart tube
early primitive heart tube
uberon
UBERON:0005498
primitive heart tube
ZFA
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
ZFA:0000149
primitive heart tube
EMAPA:16215
early primitive heart tube
EMAPA:16208
A neural tube lateral wall that is part of a rhombomere.
EMAPA:32819
EMAPA:35364
uberon
future hindbrain lateral wall
UBERON:0005501
rhombomere lateral wall
A neural tube lateral wall that is part of a rhombomere.
OBOL:automatic
future hindbrain lateral wall
EMAPA:35364
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
UBERON:3010717
AAO:0011059
EFO:0002578
EMAPA:36007
XAO:0001002
uberon
lateral diverticula
lung diverticulum
lung endoderm
UBERON:0005597
lung primordium
XAO
XAO
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
XAO:0001002
lateral diverticula
XAO:0001002
lung diverticulum
AAO:3010717
lung endoderm
EFO:0002578
A somite that is part of a trunk.
AAO:0010385
EHDAA2:0003438
EMAPA:16184
XAO:0000314
uberon
UBERON:0005598
trunk somite
A somite that is part of a trunk.
OBOL:automatic
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
lens epithelium
EHDAA2:0000984
EHDAA:9059
EMAPA:17304
EMAPA:17839
FMA:70612
MA:0001302
NCIT:C33641
RETIRED_EHDAA2:0000976
UMLS:C1182652
VHOG:0001425
lens subcapsular epithelium
subcapsular lens epithelium
uberon
anterior epithelium of lens vesicle
anterior surface of lens
UBERON:0005614
lens anterior epithelium
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
UMLS:C1182652
ncithesaurus:Subcapsular_Epithelium_of_the_Lens
lens subcapsular epithelium
subcapsular lens epithelium
FMA:70612
anterior epithelium of lens vesicle
EMAPA:17304
anterior surface of lens
FMA:58889
An epithelium that is part of a anterior chamber of eyeball.
EHDAA2:0000130
uberon
UBERON:0005638
anterior chamber epithelium
An epithelium that is part of a anterior chamber of eyeball.
OBOL:automatic
An epithelium that is part of a lens vesicle.
EHDAA2:0000987
EMAPA:17165
VHOG:0000532
uberon
UBERON:0005656
lens vesicle epithelium
An epithelium that is part of a lens vesicle.
OBOL:automatic
An endothelium that is part of a right lung.
EHDAA2:0001755
uberon
UBERON:0005672
right lung endothelium
An endothelium that is part of a right lung.
OBOL:automatic
An endothelium that is part of a left lung.
EHDAA2:0000961
uberon
UBERON:0005673
left lung endothelium
An endothelium that is part of a left lung.
OBOL:automatic
An anatomical cavity that is part of a lens vesicle.
(...) 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]
cavity of lens
lens cavity
EHDAA2:0000986
EMAPA:17164
VHOG:0000531
cavity of lens vesicle
uberon
UBERON:0005688
lens vesicle cavity
An anatomical cavity that is part of a lens vesicle.
OBOL:automatic
(...) 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]
2012-09-17
VHOG:0000531
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
lens cavity
EHDAA2:0000986
cavity of lens vesicle
EMAPA:17164
Mesenchyme that is part of a optic eminence.
EHDAA:942
EMAPA:16324
RETIRED_EHDAA2:0001310
VHOG:0001073
uberon
UBERON:0005702
optic eminence mesenchyme
Mesenchyme that is part of a optic eminence.
OBOL:automatic
A venous system that is part of a hindbrain.
EHDAA2:0000776
EMAPA:18632
VHOG:0001322
uberon
rhombencephalon venous system
UBERON:0005720
hindbrain venous system
A venous system that is part of a hindbrain.
OBOL:automatic
rhombencephalon venous system
VHOG:0001322
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
BTO:0002010
EMAPA:36299
NCIT:C33818
UMLS:C0225342
adventitia externa
tunica adventitia
tunica adventitia of vessel
uberon
external coat
tunica adventitia vasorum
tunica externa vasorum
UBERON:0005734
tunica adventitia of blood vessel
cjm
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
ISBN:0073040584
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
UMLS:C0225342
ncithesaurus:Tunica_Adventitia
adventitia externa
tunica adventitia
tunica adventitia of vessel
external coat
tunica adventitia vasorum
tunica externa vasorum
A tunica intima that is part of a artery.
EMAPA:36293
EV:0100028
FMA:14272
galen:IntimaOfArtery
arterial intima
tunica interna (intima)(arteriae)
uberon
UBERON:0005740
tunica intima of artery
A tunica intima that is part of a artery.
OBOL:automatic
arterial intima
EV:0100028
tunica interna (intima)(arteriae)
FMA:14272
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
BTO:0002010
FMA:45635
tunica advetitia
tunica externa
uberon
UBERON:0005742
adventitia
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
tunica advetitia
tunica externa
FMA:45635
A acellular anatomical structure that is the bounding layer of a anatomical structure.
FMA:63871
uberon
UBERON:0005764
acellular membrane
A acellular anatomical structure that is the bounding layer of a anatomical structure.
OBOL:automatic
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.
AAO:0010596
FMA:63872
GAID:915
NCIT:C13191
UMLS:C0004799
basement membrane of connective tissue
membrana basalis
uberon
basement membrane
UBERON:0005769
basement membrane of epithelium
FMA
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.
UMLS:C0004799
ncithesaurus:Basement_Membrane
basement membrane of connective tissue
FMA:63872
membrana basalis
basement membrane
FMA:63872
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
EHDAA2_RETIRED:0003148
EHDAA:8979
mesenchyme condensation
uberon
UBERON:0005856
developing mesenchymal condensation
AEO
cjm
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
mesenchyme condensation
EMAPA:25351
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
check develops_from
EHDAA2:0001061
EHDAA:5871
EMAPA:17355
FMA:293051
NCIT:C34204
UMLS:C1512982
uberon
mandibular process
mandibular swelling
prominentia mandibularis
UBERON:0005867
mandibular prominence
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
ISBN:0-683-40008-8
MP:0010939
UMLS:C1512982
ncithesaurus:Mandibular_Prominence
mandibular process
mandibular swelling
prominentia mandibularis
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
EMAPA:16060
FMA:9689
MA:0000005
uberon
UBERON:0005906
See notes for serous membrane
serous sac
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
FMA:9689
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
FMA:69065
endoderm-derived epithelium
endoepithelium
uberon
UBERON:0005911
endo-epithelium
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
FMA:69065
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
AAO:0000963
EMAPA:17214
EMAPA:18043
MA:0000308
NCIT:C32172
UMLS:C0222645
VSAO:0000056
XAO:0004011
uberon
skeleton axiale
UBERON:0005944
axial skeleton plus cranial skeleton
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
FMA:71221
VSAO:0000056
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
2012-08-14
VSAO:0000056
VSAO
PSPUB:0000170
UMLS:C0222645
ncithesaurus:Axial_Skeleton
skeleton axiale
The laminar structure of the heart
uberon
UBERON:0005983
heart layer
The laminar structure of the heart
MP:0010545
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
TODO - change relation from part_of
MESH:D003331
uberon
UBERON:0005985
coronary vessel
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
MP:0010551
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]
EMAPA:37883
body hair or bristle
uberon
adnexae cutis
skin adnexa
skin adnexal structure
skin appendage
UBERON:0006003
integumentary adnexa
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
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]
MP:0010678
EMAPA:37883
MA:th
body hair or bristle
GO:GO
adnexae cutis
skin adnexa
skin appendage
uberon
UBERON:0006056
posterior surface of head
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
EHDAA2:0000189
EHDAA:536
EMAPA:16259
FMA:313607
VHOG:0000380
uberon
oral membrane
oral plate
oropharyngeal membrane
pharyngeal membrane
UBERON:0006211
buccopharyngeal membrane
EHDAA2
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
MP:0012521
oral membrane
MP:0012521
oral plate
MP:0012521
oropharyngeal membrane
pharyngeal membrane
MP:0012521
The embryonic precursor of the brain.
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
BAMS:Enc
BTO:0004726
EFO:0003431
EHDAA:300
EHDAA:830
EMAPA:16089
FMA:312967
RETIRED_EHDAA2:0000591
TAO:0000146
ZFA:0000146
brain rudiment
presumptive brain
encephalon
uberon
embryonic brain
UBERON:0006238
future brain
The embryonic precursor of the brain.
NLX:94995
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
brain rudiment
TAO:0000146
presumptive brain
ZFA:0000146
encephalon
NLX:94995
embryonic brain
BTO:0004726
EFO:0003438
EHDAA2:0000674
EHDAA:898
EMAPA:16092
EMAPA:16755
TAO:0000417
ZFA:0000417
presumptive spinal cord
presumptive spinal cord neural keel
presumptive spinal cord neural plate
presumptive spinal cord neural rod
uberon
UBERON:0006241
future spinal cord
EHDAA2
presumptive spinal cord
ZFA:0000417
presumptive spinal cord neural keel
TAO:0000417
presumptive spinal cord neural plate
TAO:0000417
presumptive spinal cord neural rod
TAO:0000417
An anatomical junctions that overlaps the mouth and foregut.
EHDAA:534
EMAPA:16258
RETIRED_EHDAA2:0001205
VHOG:0000592
uberon
UBERON:0006264
mouth-foregut junction
An anatomical junctions that overlaps the mouth and foregut.
OBOL:automatic
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
EHDAA2:0001278
EHDAA:264
EMAPA:16101
NCIT:C34231
UMLS:C1518429
VHOG:0001212
uberon
UBERON:0006267
notochordal plate
EHDAA2
EHDAA2
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.
VHOG:0001212
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]
2012-09-17
VHOG:0001212
VHOG
UMLS:C1518429
ncithesaurus:Notochordal_Plate
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
EHDAA2:0001279
EHDAA:224
EMAPA:16102
FMA:293135
NCIT:C34232
UMLS:C1518430
VHOG:0001213
uberon
chordamesoderm
presumptive notochord
UBERON:0006268
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.
notochordal process
EHDAA2
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
UMLS:C1518430
ncithesaurus:Notochordal_Process
A segment of the eyeball that is filled with refractive media
BTO:0002085
EMAPA:37529
FMA:58071
MA:0002459
NCIT:C32301
UMLS:C0459556
eye chamber
eyeball chamber
uberon
chamber of eye
UBERON:0006311
chamber of eyeball
A segment of the eyeball that is filled with refractive media
EMAPA:37529
MA:th
UMLS:C0459556
ncithesaurus:Chamber_of_the_Eye
eye chamber
MA:0002459
eyeball chamber
FMA:58071
chamber of eye
BTO:0002085
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
ocular refraction
MA:0001911
uberon
UBERON:0006312
ocular refractive media
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
BIRNLEX:20
EMAPA:37441
FMA:280556
GAID:266
MESH:D001826
galen:BodyFluid
body fluid
uberon
UBERON:0006314
bodily fluid
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
MESH:A12.207
EMAPA:37441
MA:th
body fluid
GAID:266
2
2
An artery that connects two larger arteries.
EMAPA:18598
MA:0001938
NCIT:C52851
UMLS:C1707451
uberon
UBERON:0006347
Grouping for anterior and posterior
communicating artery
An artery that connects two larger arteries.
ncithesaurus:Communicating_Artery
UMLS:C1707451
ncithesaurus:Communicating_Artery
A portion of organism substance that secreted_by a zone of skin.
MA:0002537
skin fluid/secretion
uberon
skin fluid
skin substance
UBERON:0006535
skin secretion
A portion of organism substance that secreted_by a zone of skin.
OBOL:automatic
skin fluid/secretion
MA:0002537
A portion of organism substance that secreted_by a respiratory system.
EMAPA:36550
MA:0002533
NCIT:C13722
UMLS:C1514899
uberon
respiratory system fluid
respiratory system secretion
UBERON:0006538
respiratory system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
OBOL:automatic
UMLS:C1514899
ncithesaurus:Respiratory_System_Fluid_or_Secretion
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.
branchial
pharyngeal
FBbt:00005380
MAT:0000049
MIAA:0000049
uberon
anterior part of foregut
pharyngeal tube
UBERON:0006562
pharynx
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
GO:0060465
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]
FMA:85030
uberon
UBERON:0006563
tunica media of pulmonary trunk
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]
FMA:85030
FMA:FMA
Presumptive structure of the blastula that will develop into endoderm.
AAO:0000471
EFO:0003437
TAO:0000416
ZFA:0000416
uberon
UBERON:0006595
presumptive endoderm
Presumptive structure of the blastula that will develop into endoderm.
AAO:0000468
EFO:0003439
TAO:0000568
ZFA:0000568
future blood
uberon
UBERON:0006596
presumptive blood
Portion of embryonic tissue determined by fate mapping to become a structure.
Consider merging with anlage
AAO:0000479
TAO:0001116
ZFA:0001116
future structure
presumptive structures
uberon
UBERON:0006598
presumptive structure
Portion of embryonic tissue determined by fate mapping to become a structure.
GOC:CVS
GOC:YMB
ZFA:0001116
presumptive structures
ZFA:0001116
Presumptive structure of the blastula that will develop into ectoderm.
AAO:0000470
EFO:0003466
TAO:0001376
XAO:0004132
ZFA:0001376
uberon
presumptive epidermis
UBERON:0006601
presumptive ectoderm
Presumptive structure of the blastula that will develop into ectoderm.
presumptive epidermis
ZFA:0001376
Presumptive structure of the blastula that will develop into mesoderm.
AAO:0000476
EFO:0003467
TAO:0001377
ZFA:0001377
uberon
UBERON:0006603
presumptive mesoderm
Presumptive structure of the blastula that will develop into mesoderm.
An anatomical boundary that adjacent_to a epithelium.
FMA:70997
epithelium surface
uberon
UBERON:0006677
surface of epithelium
An anatomical boundary that adjacent_to a epithelium.
OBOL:automatic
epithelium surface
FMA:70997
the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm
EFO:0001403
EMAPA:37835
FMA:58342
GAID:896
MESH:D016850
ZFA:0005570
cornea limbus
corneal limbus
corneal-scleral limbus
corneoscleral junction
limbus corneae
sclerocorneal junction
sclerocorneal limbus
uberon
limbus corneae
UBERON:0006761
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
corneo-scleral junction
the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm
MP:0013477
EMAPA:37835
MA:th
corneal limbus
FMA:58342
corneal limbus
GAID:896
corneal-scleral limbus
corneoscleral junction
GAID:896
limbus corneae
sclerocorneal junction
FMA:58342
sclerocorneal limbus
GAID:896
limbus corneae
A vasculature that is part of a organ.
FMA:74612
organ vasculature
set of blood vessels of organ
uberon
UBERON:0006876
vasculature of organ
A vasculature that is part of a organ.
OBOL:automatic
organ vasculature
FMA:74612
set of blood vessels of organ
FMA:74612
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
AAO:0011051
EFO:0003337
EFO:0003603
EHDAA2:0001118
EHDAA:655
EMAPA:16099
EMAPA_RETIRED:16270
FMA:293859
TAO:0000998
VHOG:0000185
XAO:0000053
ZFA:0000998
head mesenchyme derived from mesoderm
head mesenchyme from head mesoderm
head mesenchyme from mesoderm
mesenchyme derived from head mesoderm
mesenchyme from head mesoderm
uberon
cranial mesoderm
head mesoderm
UBERON:0006904
head mesenchyme from mesoderm
ZFA
EHDAA2
XAO
A head mesenchyme that develops_from a mesoderm.
OBOL:automatic
head mesenchyme from head mesoderm
EHDAA2:0001118
mesenchyme derived from head mesoderm
EHDAA:1057
cranial mesoderm
UBERON:0005280
head mesoderm
AAO:0011051
UBERON:0005280
Mesenchyme that is part of a mandibular prominence.
EHDAA2:0001062
EHDAA:5861
EHDAA:5873
EMAPA:17357
mesenchyme of mandibular process
mesenchyme of mandibular prominence
uberon
UBERON:0006905
mandibular process mesenchyme
Mesenchyme that is part of a mandibular prominence.
OBOL:automatic
mesenchyme of mandibular process
EMAPA:17357
mesenchyme of mandibular prominence
An anatomical space that surrounded_by a digestive tract.
BTO:0000349
EMAPA:32908
FMA:45677
digestive tract lumen
gut cavity
gut lumen
lumen of alimentary tract
lumen of digestive tract
lumen of gut
uberon
UBERON:0006909
lumen of digestive tract
An anatomical space that surrounded_by a digestive tract.
OBOL:automatic
digestive tract lumen
gut cavity
BTO:0000349
gut lumen
FMA:45677
lumen of alimentary tract
lumen of digestive tract
lumen of gut
FMA:45677
An epithelium that is part of a lip.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
BTO:0004468
TAO:0005334
ZFA:0005334
uberon
UBERON:0006913
lip epithelium
An epithelium that is part of a lip.
OBOL:automatic
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
2012-08-14
TAO:0005334
TAO
ZFIN:ZDB-PUB-060921-12
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
BTO:0002072
NCIT:C12848
UMLS:C0221909
uberon
UBERON:0006914
squamous epithelium
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
FBbt
UMLS:C0221909
ncithesaurus:Squamous_Epithelium
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].
EFO:0003709
TAO:0005077
ZFA:0005077
uberon
UBERON:0006965
vascular cord
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].
GO:0072360
ZFA:0005077
A capillary that is part of the coronary system.
ZFA:0005813
heart capillary
uberon
UBERON:0006966
coronary capillary
A capillary that is part of the coronary system.
heart capillary
GO:0003248
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
BILA:0000010
CARO:0001002
EHDAA2_RETIRED:0003192
FMA:24137
NCIT:C34022
UMLS:C1515977
uberon
UBERON:0006984
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.
anatomical surface
via morphological boundary in CARO
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
CARO:0001002
UMLS:C1515977
ncithesaurus:Anatomic_Surface
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
review EHDAA2 placement
AAO:0011021
BILA:0000051
EFO:0000315
EHDAA2:0000214
EHDAA:385
FMA:293143
VHOG:0001641
XAO:0000235
cardiogenic splanchnopleure
uberon
cardiac mesoderm
cardiogenic mesoderm
cardiogenic region
heart primordia
UBERON:0007005
cardiogenic splanchnic mesoderm
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].
XAO:0000235
cardiogenic splanchnopleure
EHDAA2:0000214
cardiac mesoderm
XAO:0000235
cardiogenic mesoderm
cardiogenic region
heart primordia
XAO:0000235
Organism at the cleavage stage.
BILA:0000058
uberon
UBERON:0007010
cleaving embryo
Organism at the cleavage stage.
OBOL:automatic
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
juvenile
BILA:0000076
TAO:0002047
juvenile organism
juveniles
uberon
UBERON:0007021
sexually immature organism
A multicellular organism that is at the juvenile stage.
OBOL:automatic
Whole organism that is not fully grown or sexually mature.[TAO]
2012-08-14
TAO:0002047
TAO
TAO:wd
juvenile organism
BILA:0000076
juveniles
TAO:0002047
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
adult
BILA:0000078
FBbt:00003004
HAO:0000087
NCIT:C17600
TAO:0002046
UMLS:C0001675
galen:Adult
adults
uberon
UBERON:0007023
adult organism
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
OBOL:automatic
Whole organism that is fully grown or sexually mature.[TAO]
2012-08-14
TAO:0002046
TAO
TAO:wd
UMLS:C0001675
ncithesaurus:Adult
adults
TAO:0002046
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
BILA:0000084
NCIT:C34268
UMLS:C1514442
future digestive tract
future digestive tube
future gut
primitive gut
uberon
embryonic digestive tube
primordial digestive tube
primordial gut
UBERON:0007026
presumptive gut
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
NCBIBook:NBK10107
UMLS:C1514442
ncithesaurus:Primordial_Gut
Cranial neural crest that migrates into the mandibular arch.
TAO:0007064
XAO:0000024
ZFA:0007064
uberon
UBERON:0007098
mandibular neural crest
ZFA
ZFA
Cranial neural crest that migrates into the mandibular arch.
ZFA:0007064
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
FBbt:00003154
SPD:0000130
TADS:0000147
dorsal tube
heart
uberon
adult heart
UBERON:0007100
Gene notes: Bmp, Nkx, Gata
primary circulatory organ
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
GO:0007507
dorsal tube
heart
GO:0007507
adult heart
FBbt:00003154
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]
EFO:0003497
TAO:0000131
ZFA:0000131
uberon
presumptive central nervous system
UBERON:0007135
neural keel
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.
ZFIN:ZDB-PUB-961014-576
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]
2012-08-14
TAO:0000131
TAO
ZFIN:curator
presumptive central nervous system
ZFA:0000131
multicellular organism that can produce both male and female gametes.
AAO:0010035
BILA:0000029
CARO:0000029
HAO:0000029
TADS:0000601
WBbt:0007849
monoecious organism
uberon
dioecious organism
hermaphrodite
UBERON:0007197
hermaphroditic organism
multicellular organism that can produce both male and female gametes.
dioecious organism
BILA:0000029
hermaphrodite
WBbt:0007849
Mesenchyme that develops_from a cranial neural crest.
EFO:0003572
EHDAA2:0000735
EMAPA:16169
EMAPA:16271
EMAPA_RETIRED:16271
TAO:0000787
ZFA:0000787
head mesenchyme from cranial neural crest
head mesenchyme from neural crest
head neural crest derived mesenchyme
uberon
UBERON:0007213
mesenchyme derived from head neural crest
ZFA
Mesenchyme that develops_from a cranial neural crest.
OBOL:automatic
head mesenchyme from neural crest
EHDAA2:0000735
relationship to Meckel's cartilage to be added
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
EHDAA2:0000031
EHDAA:583
EMAPA:16382
VHOG:0000510
ventral pharyngeal arch 1
uberon
ventral mandibular arch
ventral visceral arch 1
UBERON:0007237
1st arch mandibular component
EHDAA2
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
2012-09-17
VHOG:0000510
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
ventral pharyngeal arch 1
VHOG:0000510
ventral mandibular arch
VHOG:0000510
ventral visceral arch 1
VHOG:0000510
A tunica media that is part of a artery.
EMAPA:36294
EV:0100029
FMA:14273
NCIT:C49321
UMLS:C1710627
arterial media
tunica media (arteriae)
uberon
UBERON:0007239
tunica media of artery
A tunica media that is part of a artery.
OBOL:automatic
UMLS:C1710627
ncithesaurus:Venous_System_Smooth_Muscle_Tissue
arterial media
EV:0100029
tunica media (arteriae)
FMA:14273
A tunica adventitia that is part of a artery.
EMAPA:36295
EV:0100030
FMA:14274
arterial adventitia
tunica externa (adventitia)(arteriae)
uberon
UBERON:0007240
tunica adventitia of artery
A tunica adventitia that is part of a artery.
OBOL:automatic
arterial adventitia
EV:0100030
tunica externa (adventitia)(arteriae)
FMA:14274
A tunica adventitia that is part of a vein.
EMAPA:36310
EV:0100034
FMA:14355
tunica externa (adventitia)(venae)
venous adventitia
uberon
UBERON:0007241
tunica adventitia of vein
A tunica adventitia that is part of a vein.
OBOL:automatic
tunica externa (adventitia)(venae)
FMA:14355
venous adventitia
EV:0100034
A tunica intima that is part of a vein.
EMAPA:36308
EV:0100032
FMA:14353
tunica interna (intima)(venae)
venous intima
uberon
UBERON:0007242
tunica intima of vein
A tunica intima that is part of a vein.
OBOL:automatic
tunica interna (intima)(venae)
FMA:14353
venous intima
EV:0100032
A tunica media that is part of a vein.
EMAPA:36309
EV:0100033
FMA:14354
tunica media (venae)
venous media
uberon
UBERON:0007243
tunica media of vein
A tunica media that is part of a vein.
OBOL:automatic
tunica media (venae)
FMA:14354
venous media
EV:0100033
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.
TODO - unify naming conventions
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].
BAMS:HB
CALOHA:TS-2118
EFO:0003440
EHDAA2:0001630
FMA:295640
TAO:0000569
ZFA:0000569
presumptive rhombencephalon
uberon
embryonic rhombencephalon
future hindbrain
rhombencephalon
UBERON:0007277
presumptive hindbrain
XAO-abduced
cjm
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
NPX:PDR
presumptive rhombencephalon
ZFA:0000569
embryonic rhombencephalon
CALOHA:TS-2118
future hindbrain
rhombencephalon
EHDAA2:0001630
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
TAO:0002233
ZFA:0001724
uberon
UBERON:0007280
presumptive endocardium
A presumptive structure that has the potential to develop into a endocardium.
OBOL:automatic
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
2012-08-14
TAO:0002233
TAO
ZFIN:curator
Embryonic structure that gives rise to the midbrain hindbrain boundary.
EFO:0003446
TAO:0001187
XAO:0004086
ZFA:0001187
presumptive MHB
presumptive midbrain-hindbrain boundary
uberon
UBERON:0007281
presumptive midbrain hindbrain boundary
ZFA
Embryonic structure that gives rise to the midbrain hindbrain boundary.
ZFA:0001187
presumptive MHB
presumptive midbrain-hindbrain boundary
ZFA:0001187
A presumptive structure that has the potential to develop into a presomitic mesoderm.
EFO:0003421
TAO:0000053
ZFA:0000053
uberon
presumptive segmental plates
UBERON:0007282
presumptive segmental plate
https://github.com/obophenotype/uberon/wiki/The-neural-crest
EDHAA2
A presumptive structure that has the potential to develop into a presomitic mesoderm.
OBOL:automatic
presumptive segmental plates
ZFA:0000053
A presumptive structure that has the potential to develop into a neural plate.
consider merging
Region of the gastrula which gives rise to the neural plate.[TAO]
EFO:0003424
TAO:0000063
ZFA:0000063
prospective neuroectoderm
prospective vegetal ectoderm
uberon
UBERON:0007284
presumptive neural plate
A presumptive structure that has the potential to develop into a neural plate.
OBOL:automatic
Region of the gastrula which gives rise to the neural plate.[TAO]
2012-08-14
TAO:0000063
TAO
ZFIN:curator
prospective neuroectoderm
ZFA:0000063
prospective vegetal ectoderm
ZFA:0000063
The part of the blastula that has the potential to develop into a paraxial mesoderm.
EFO:0003443
TAO:0000591
XAO:0004134
ZFA:0000591
future paraxial mesenchyme
future paraxial mesoderm
uberon
UBERON:0007285
presumptive paraxial mesoderm
The part of the blastula that has the potential to develop into a paraxial mesoderm.
UBERON:cjm
future paraxial mesenchyme
UBERON:cjm
A vasculature that is part of a chordate pharynx.
TAO:0005003
ZFA:0005003
branchial vasculature
uberon
UBERON:0007303
pharyngeal vasculature
A vasculature that is part of a chordate pharynx.
OBOL:automatic
branchial vasculature
ZFA:0005003
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.
BSA:0000073
BTO:0000313
FBbt:00004993
HAO:0000298
TADS:0000109
WBbt:0005733
epidermis
epidermis (sensu Metazoa)
outer epidermal layer
outer epithelial layer
uberon
hypoderm
hypodermis
UBERON:0007376
outer epithelium
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].
GO:0008544
epidermis
GO:0008544
hypoderm
BTO:0000313
hypodermis
GO:0008544
WBbt:0005733
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]
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[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
AAO:0010600
TAO:0001182
ZFA:0001182
dermal deep region
stratum compactum
uberon
UBERON:0007377
stratum compactum of dermis
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
ISBN:0073040584
ZFIN:ZDB-PUB-040726-12
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0001182
TAO
ZFIN:curator
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
2012-08-14
TAO:0001182
TAO
dermal deep region
ZFA:0001182
stratum compactum
AAO:0010600
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
EFO:0003425
TAO:0000086
ZFA:0000086
EVL
enveloping layer
uberon
UBERON:0007383
enveloping layer of ectoderm
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]
2012-08-14
TAO:0000086
TAO
ZFIN:curator
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
2012-08-14
TAO:0000086
TAO
EVL
ZFA:0000086
enveloping layer
ZFIN:ZDB-PUB-961014-576
The space within an epithelial sphere.
EHDAA2:0003079
AEO:0000079
cavity of vesicle
uberon
UBERON:0007473
lumen of epithelial sac
The space within an epithelial sphere.
AEO:JB
cavity of vesicle
AEO:0000079
An epithelial tube that is open at one end only.
AEO:0000115
EHDAA2:0003115
uberon
UBERON:0007499
epithelial sac
AEO
An epithelial tube that is open at one end only.
AEO:JB
UBERONREF:0000001
An epithelial tube open at both ends that allows fluid flow.
AEO_RETIRED:0000116
RETIRED_EHDAA2:0003116
uberon
UBERON:0007500
epithelial tube open at both ends
AEO
An epithelial tube open at both ends that allows fluid flow.
AEO:JB
UBERONREF:0000001
A closed epithelium with a lumen.
EHDAA2:0003119
AEO:0000119
EHDAA2:0003119
uberon
UBERON:0007503
epithelial vesicle
AEO
A closed epithelium with a lumen.
AEO:JB
Mesenchyme with little extracellular matrix.
EHDAA2:0003146
AEO:0000146
EHDAA2:0003146
uberon
UBERON:0007524
dense mesenchyme tissue
AEO
Mesenchyme with little extracellular matrix.
AEO:JB
Mesenchymal cells that are migrating.
this class will be an important part of the NC reorganization
EHDAA2:0003152
AEO:0000152
EHDAA2:0003152
uberon
UBERON:0007530
migrating mesenchyme population
Mesenchymal cells that are migrating.
AEO:JB
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
FMA:64798
uberon
UBERON:0007592
ciliated columnar epithelium
FMA
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
FMA:64798
Epithelium bearing vibratile cilia on the free surface.
uberon
UBERON:0007601
ciliated epithelium
Epithelium bearing vibratile cilia on the free surface.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
BTO:0001338
CALOHA:TS-0998
FMA:66762
synovium
stratum synoviale
synovial layer
synovial membrane
uberon
synovial tissue
UBERON:0007616
layer of synovial tissue
BTO
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].
BTO:0001338
synovium
CALOHA:TS-0998
stratum synoviale
FMA:TA
synovial layer
FMA:66762
synovial membrane
FMA:66762
synovial tissue
BTO:0001338
An anatomical cavity that surrounded_by a synovial joint.
FMA:11356
articular cavity (synovial joint)
cavitas articularis (junctura synovialis)
cavity of synovial joint
uberon
joint cavity
synovial cavity
UBERON:0007617
synovial cavity of joint
An anatomical cavity that surrounded_by a synovial joint.
OBOL:automatic
articular cavity (synovial joint)
FMA:11356
cavitas articularis (junctura synovialis)
FMA:11356
cavity of synovial joint
FMA:11356
joint cavity
FMA:11356
synovial cavity
FMA:11356
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
GAID:907
MESH:D010857
uberon
eye pigment epithelium
UBERON:0007625
pigment epithelium of eye
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
MP:0005200
eye pigment epithelium
MESH:A09.371.670
2
An anatomical structure that connects two structures
junction
FMA:5898
anatomical junction
uberon
UBERON:0007651
anatomical junction
FMA
An anatomical structure that connects two structures
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.
field
AEO:0000170
EFO:0001649
EHDAA2:0003170
FBbt:00005426
developmental field
uberon
future organ
organ field
UBERON:0007688
anlage
FBbt
AEO
FBbt
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.
FBbt:00005426
JB:DEF
.
EFO:0003626
EHDAA2:0001457
EHDAA:962
EMAPA:32754
FMA:293087
TAO:0001104
ZFA:0001104
early pharyngeal arch endoderm
uberon
pharyngeal arch endoderm
pharyngeal endoderm
pharyngeal region endoderm
UBERON:0007690
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
early pharyngeal endoderm
cjm
.
early pharyngeal arch endoderm
EHDAA2:0001457
pharyngeal endoderm
ZFA:0001104
pharyngeal region endoderm
EHDAA2:0001456
A gland that is part of a epidermis.
FMA:59153
epidermal gland
gland of epidermis
uberon
UBERON:0007771
epidermis gland
A gland that is part of a epidermis.
OBOL:automatic
gland of epidermis
FMA:59153
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
transudative
characteristically low in protein and cellular content (unless there has been secondary concentration)
FMA:12276
GAID:1195
MESH:D005122
ncithesaurus:Transudate
uberon
plasma ultrafiltrate
UBERON:0007779
transudate
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
Any fluid produced by a serous gland.
serous fluid
serosal fluid
serous gland fluid
uberon
UBERON:0007794
secretion of serous gland
Any fluid produced by a serous gland.
UBERON:cjm
serosal fluid
Anatomical system that consists of all blood and lymph vessels.
consider merging with vasculature
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
BTO:0001085
CALOHA:TS-2053
EHDAA2:0004520
EMAPA:35905
MA:0002718
NCIT:C33854
UMLS:C0489903
uberon
Gefaesssystem@de
UBERON:0007798
vascular system
MA
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
ncithesaurus:Vascular_System
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
MA
UMLS:C0489903
ncithesaurus:Vascular_System
Gefaesssystem@de
BTO:0001085
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.
CALOHA:TS-2356
EV:0100009
FMA:280881
MA:0000006
NCIT:C12418
UMLS:C0460004
WikipediaCategory:Head_and_neck
galen:HeadAndNeck
uberon
cephalic area
cephalic part of animal
cephalic region
head and neck
head or neck
UBERON:0007811
craniocervical region
MA
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.
UMLS:C0460004
ncithesaurus:Head_and_Neck
cephalic area
cephalic part of animal
cephalic region
head and neck
FMA:280881
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
EMAPA:37259
MA:0000571
TAO:0000328
ZFA:0000328
head or neck muscle
uberon
head muscles
head or neck muscle
UBERON:0008229
craniocervical region musculature
MA
MA
Musculature system of the pharyngeal and head regions.
ZFA:0000328
ZFA:curator
in MA this is restricted to skeletal muscles
MA
EMAPA:37259
MA:th
head or neck muscle
MA:0000571
head muscles
ZFA:0000328
head or neck muscle
MA:0000571
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
BTO:0004293
uberon
cardiac endothelium
UBERON:0008307
heart endothelium
An endothelium that is part of a heart [Automatically generated definition].
OBOL:automatic
cardiac endothelium
BTO:0004293
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
EHDAA2:0000187
FMA:293041
NCIT:C34248
UMLS:C1519038
embryonic pharyngeal complex
pharyngeal apparatus
pharyngeal system
uberon
pharyngeal arch complex
pharyngeal arch region
pharyngeal arches and clefts
pharyngeal complex
UBERON:0008814
pharyngeal arch system
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
GO:0060037
GOC:dph
UMLS:C1519038
ncithesaurus:Pharyngeal_Apparatus
pharyngeal system
GO:0060037
pharyngeal arch region
EHDAA2:0000187
A head that is part of a embryo.
CALOHA:TS-0246
FBbt:00000155
FMA:293011
uberon
UBERON:0008816
embryonic head
A head that is part of a embryo.
OBOL:automatic
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
vertebrate brain
uberon
UBERON:0008823
neural tube derived brain
ZFA
FMA
A brain that develops_from a neural tube.
OBOL:automatic
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
FMA:45621
pulmonary circulatory system
pulmonary system
uberon
UBERON:0008886
pulmonary vascular system
Obol
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
ISBN:0073040584
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
FMA
FMA:45621
pulmonary circulatory system
FMA:45621
pulmonary system
ISBN:0073040584
Subdivision of endoskeleton derived from pharyngeal arches
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
AAO:0010157
TAO:0001216
VHOG:0000315
VSAO:0000149
XAO:0003176
ZFA:0001216
pharyngeal endoskeleton
viscerocranium
uberon
branchial arch skeleton
gill arch skeleton
pharyngeal arch
pharyngeal arch skeleton
pharyngeal skeleton
visceral cranium
visceral skeletal system
visceral skeleton
UBERON:0008895
splanchnocranium
redundant
Grays
Subdivision of endoskeleton derived from pharyngeal arches
ISBN:0073040584
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
2012-08-14
TAO:0001216
TAO
ZFIN:curator
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
2012-06-20
AAO:0010157
AAO
AAO:EJS
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
2012-09-17
VHOG:0000315
VHOG
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000315
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
VSAO
pharyngeal endoskeleton
viscerocranium
VHOG:0000315
ZFA:0001216
pharyngeal arch
VSAO:0000149
pharyngeal arch skeleton
ZFA:0001216
pharyngeal skeleton
ZFA:0001216
visceral cranium
visceral skeletal system
visceral skeleton
UBERONREF:0000007
EHDAA2:0004069
NCIT:C34283
UMLS:C1514898
uberon
UBERON:0008947
respiratory primordium
Obol
UMLS:C1514898
ncithesaurus:Respiratory_Primordium
System pertaining to blood vessels in the brain.
UBERON:0005284
BTO:0003840
EFO:0003491
EMAPA:35186
FMA:242007
FMA:61935
TAO:0000099
ZFA:0000099
brain vasculature
cerebrovascular system
intracerebral vasculature
uberon
UBERON:0008998
vasculature of brain
System pertaining to blood vessels in the brain.
BTO:0003840
cerebrovascular system
BTO:0003840
intracerebral vasculature
FMA:61935
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
EMAPA:37165
MA:0002207
NCIT:C48946
UMLS:C0226670
uberon
UBERON:0009030
left pulmonary vein
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
ncithesaurus:Left_Pulmonary_Vein
EMAPA:37165
MA:th
UMLS:C0226670
ncithesaurus:Left_Pulmonary_Vein
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
EMAPA:37379
MA:0002208
NCIT:C48947
UMLS:C0226669
uberon
UBERON:0009032
right pulmonary vein
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
ncithesaurus:Right_Pulmonary_Vein
EMAPA:37379
MA:th
UMLS:C0226669
ncithesaurus:Right_Pulmonary_Vein
An organism containing a developing embryo, fetus, or unborn offspring within the body.
BTO:0004733
uberon
gravid
pregnant adult
pregnant adult stage
pregnant organism
pregnant stage
UBERON:0009097
gravid organism
An organism containing a developing embryo, fetus, or unborn offspring within the body.
BTO:0004733
gravid
BTO:0004733
pregnant adult
BTO:0004733
pregnant adult stage
BTO:0004733
pregnant stage
BTO:0004733
A vein that is part of a craniocervical region.
EHDAA2:0004542
craniocervical vein
head and neck veins
vein of head and neck
uberon
UBERON:0009141
craniocervical region vein
A vein that is part of a craniocervical region.
OBOL:automatic
head and neck veins
EHDAA2:0004542
Sum total of mesenchyme in the embryo.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
UBERON:0003313
EHDAA2:0001113
EHDAA:177
EMAPA:16097
uberon
UBERON:0009142
entire embryonic mesenchyme
EHDAA2
Sum total of mesenchyme in the embryo.
EMAPA:16549
RETIRED_EHDAA2:0001454
pharyngeal region
uberon
UBERON:0009145
pharyngeal region of foregut
EHDAA2
pharyngeal region
EMAPA:16549
An ectoderm that is part of a buccopharyngeal membrane.
EHDAA2:0000190
EMAPA:16260
uberon
UBERON:0009479
ectoderm of buccopharyngeal membrane
An ectoderm that is part of a buccopharyngeal membrane.
OBOL:automatic
An endoderm that is part of a buccopharyngeal membrane.
EHDAA2:0000191
EMAPA:16261
uberon
UBERON:0009480
endoderm of buccopharyngeal membrane
An endoderm that is part of a buccopharyngeal membrane.
OBOL:automatic
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
EMAPA:32755
FMA:295694
branchial arch mesenchyme
pharyngeal arch mesenchyme
uberon
UBERON:0009494
pharyngeal arch mesenchymal region
EHDAA2
cjm
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
MP:0011262
branchial arch mesenchyme
MP:0011262
pharyngeal arch mesenchyme
FMA:25054
region of trunk
trunk subdivision
uberon
UBERON:0009569
subdivision of trunk
region of trunk
FMA:25054
trunk subdivision
FMA:25054
EHDAA2:0001172
EMAPA:16977
VHOG:0000910
mantle layer lateral wall midbrain
midbrain lateral wall mantle layer
uberon
mantle layer lateral wall mesencephalon
UBERON:0009581
midbrain mantle layer
mantle layer lateral wall midbrain
VHOG:0000910
mantle layer lateral wall mesencephalon
VHOG:0000910
EMAPA:17580
VHOG:0000911
mantle layer lateral wall spinal cord
spinal cord lateral wall mantle layer
uberon
UBERON:0009583
spinal cord mantle layer
mantle layer lateral wall spinal cord
VHOG:0000911
Mesenchyme that is part of a 1st arch mandibular component.
UBERON:0010043
EHDAA2:0000034
EMAPA:16385
mesenchymal region of mandibular component of first pharyngeal arch
mesenchyme of mandibular component
uberon
mandibular component mesenchyme
mandibular mesenchyme
UBERON:0009584
1st arch mandibular mesenchyme
EMAPA
Mesenchyme that is part of a 1st arch mandibular component.
OBOL:automatic
mesenchymal region of mandibular component of first pharyngeal arch
mesenchyme of mandibular component
EMAPA:16385
Mesenchyme that is part of a developing left lung.
EHDAA2:0000944
EMAPA:16730
EMAPA:17654
left lung mesenchyme
uberon
UBERON:0009602
left lung associated mesenchyme
Mesenchyme that is part of a developing left lung.
OBOL:automatic
left lung mesenchyme
EMAPA:17654
Mesenchyme that is part of a developing right lung.
EHDAA2:0001739
EMAPA:17662
right lung mesenchyme
uberon
UBERON:0009603
right lung associated mesenchyme
Mesenchyme that is part of a developing right lung.
OBOL:automatic
right lung mesenchyme
EMAPA:17662
A neural plate that develops_from a presumptive midbrain.
TAO:0007019
ZFA:0007019
uberon
UBERON:0009611
midbrain neural plate
ZFA
ZFA
A neural plate that develops_from a presumptive midbrain.
OBOL:automatic
A neural plate that develops_from a presumptive hindbrain.
TAO:0007022
ZFA:0007022
uberon
UBERON:0009614
hindbrain neural plate
ZFA
ZFA
A neural plate that develops_from a presumptive hindbrain.
OBOL:automatic
TODO - developmental relationships for lines
TAO:0007044
ZFA:0007044
MHB neural plate
midbrain-hindbrain boundary neural plate
uberon
UBERON:0009615
midbrain hindbrain boundary neural plate
ZFA
https://github.com/obophenotype/uberon/issues/438
Bgee:AN
MHB neural plate
midbrain-hindbrain boundary neural plate
ZFA:0007044
A presumptive structure that has the potential to develop into a midbrain.
TODO - unify naming conventions
BAMS:MES
EFO:0003432
EHDAA2:0000615
EMAPA:16140
TAO:0000148
ZFA:0000148
presumptive mesencephalon
uberon
early midbrain
future midbrain
mesencephalon
UBERON:0009616
presumptive midbrain
ZFA
ZFA
A presumptive structure that has the potential to develop into a midbrain.
OBOL:automatic
presumptive mesencephalon
ZFA:0000148
early midbrain
future midbrain
mesencephalon
EHDAA2:0000615
EHDAA2:0002094
trunk and cervical paraxial mesenchyme
uberon
trunk paraxial mesenchyme
UBERON:0009618
trunk paraxial mesoderm
trunk and cervical paraxial mesenchyme
EHDAA2:0002094
trunk paraxial mesenchyme
EMAPA:37092
MA:0001987
NCIT:C52947
UMLS:C1708633
labial artery
uberon
UBERON:0009657
artery of lip
EMAPA:37092
MA:th
UMLS:C1708633
ncithesaurus:Labial_Artery
labial artery
MA:0001987
An anatomical cavity that surrounded_by a stomodeum.
lumen of stomatodaeum
lumen of stomodeum
stomatodeal cavity
uberon
UBERON:0009715
stomodeal lumen
An anatomical cavity that surrounded_by a stomodeum.
OBOL:automatic
EHDAA2:0004621
EMAPA:32754
FMA:293087
uberon
pharyngeal arch endoderm
UBERON:0009722
entire pharyngeal arch endoderm
pharyngeal arch endoderm
EHDAA2:0004621
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
EHDAA2:0004162
EMAPA:36438
heart mesenchyme
uberon
UBERON:0009751
cardiac mesenchyme
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
MP:0011264
heart mesenchyme
EMAPA:36438
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
acinar
acinus
FMA:55588
uberon
acini
UBERON:0009842
glandular acinus
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
acinus
FMA:55588
acini
Branch or outpocketing of the digestive tract.
FBbt:00100316
uberon
diverticulum of gut
intestinal pouch
UBERON:0009854
digestive tract diverticulum
Branch or outpocketing of the digestive tract.
diverticulum of gut
FBbt:00100316
galen:Diverticulum
pouch
uberon
diverticulum
UBERON:0009856
sac
EFO:0003704
TAO:0005041
ZFA:0005041
ALPM
uberon
UBERON:0009881
anterior lateral plate mesoderm
ZFA
ALPM
ZFA:0005041
Mesenchyme that is part of a developing face.
EMAPA:35337
FMA:302884
face mesenchyme
mesenchyme of face
uberon
UBERON:0009891
facial mesenchyme
Mesenchyme that is part of a developing face.
OBOL:automatic
EHDAA2:0001315
EHDAA:1122
uberon
UBERON:0009920
optic neural crest
EHDAA2
A multicellular organism that existence_starts_with a post-embryonic stage.
MA:0002405
postnatal organism
TS28 mouse
post-hatching organism
post-natal organism
postnatal mouse
uberon
UBERON:0009953
post-embryonic organism
A multicellular organism that existence_starts_with a post-embryonic stage.
OBOL:automatic
TS28 mouse
MA:0002405
post-hatching organism
post-natal organism
postnatal mouse
MA:0002405
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
CARO
An anatomical structure that has more than one cell as a part.
CARO:0010000
multicellular structure
FBbt:00100313
Mesenchyme that is part of a pharyngeal arch 6.
EHDAA2:0004076
EMAPA:32765
FMA:318209
6th pharyngeal arch mesenchyme
uberon
6th branchial arch mesenchyme
pharyngeal arch 6 mesenchyme
UBERON:0010031
6th arch mesenchyme
Mesenchyme that is part of a pharyngeal arch 6.
OBOL:automatic
Mesenchyme that is part of a pharyngeal arch 1.
EMAPA:16128
mesenchyme of 1st arch
uberon
UBERON:0010042
1st arch mesenchyme
Mesenchyme that is part of a pharyngeal arch 1.
OBOL:automatic
mesenchyme of 1st arch
EMAPA:16128
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
EHDAA2:0001459
EMAPA:16550
XAO:0004524
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
pharyngeal arch associated mesenchyme
uberon
UBERON:0010046
entire pharyngeal arch associated mesenchyme
EHDAA2
EHDAA2
cjm
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
XAO:0004524
associated mesenchyme of pharyngeal region
EMAPA:16550
entire branchial arch associated mesenchyme
pharyngeal arch associated mesenchyme
EHDAA2:0001459
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
UBERON:0003293
EHDAA2:0001327
EHDAA:2181
EMAPA:16572
EMAPA:16723
VHOG:0000652
buccal gland
uberon
gland of oral opening
gland of oral region
mouth gland
oral cavity gland
oral region gland
UBERON:0010047
oral gland
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
ISBN:0073040584
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
EHDAA2
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
in NCIT this is glandular
NCIT:C32415
UMLS:C0682577
uberon
UBERON:0010077
cuboidal epithelium
An epithelium consisting of cuboidal epithelial cells.
in NCIT this is glandular
NCIT
UMLS:C0682577
ncithesaurus:Cuboidal_Epithelium
Mesenchyme that has the potential to develop into a dermis.
check development
EHDAA2:0000598
uberon
UBERON:0010083
future dermis
EHDAA2
EHDAA2
XAO
Mesenchyme that has the potential to develop into a dermis.
OBOL:automatic
A developing anatomical structure that has the potential to develop into a myelencephalon.
EHDAA2:0000640
uberon
UBERON:0010096
future myelencephalon
A developing anatomical structure that has the potential to develop into a myelencephalon.
OBOL:automatic
An anatomical cavity that surrounded_by a blood vessel.
FMA:312610
blood vessel lumen
uberon
UBERON:0010161
lumen of blood vessel
An anatomical cavity that surrounded_by a blood vessel.
OBOL:automatic
A roughly circular bulge in a surface.
requires review
AEO:0000205
EHDAA2:0003250
FMA:82506
uberon
UBERON:0010188
protuberance
FMA
A roughly circular bulge in a surface.
EHDAA2:0003250
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
uberon
UBERON:0010199
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
bona-fide anatomical boundary
CARO
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
The core globe-shaped component of the camera-type eye.
See notes for camera-type eye
FMA:12513
MIAA:0000283
VHOG:0001616
bulbus oculi
eye globe
eyeball
uberon
eye
globe
UBERON:0010230
eyeball of camera-type eye
FMA
The core globe-shaped component of the camera-type eye.
UBERON:cjm
eye globe
VHOG:0001616
eyeball
FMA:12513
eye
globe
HP:0100886
MIAA:0000283
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
EHDAA2:0000037
uberon
UBERON:0010252
1st arch mandibular mesenchyme from neural crest
inferred
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
EHDAA2:0004077
neural crest derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from neural crest
uberon
branchial arch 6 mesenchyme from neural crest
UBERON:0010257
6th arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a rhombencephalon neural crest.
EHDAA2:0004423
uberon
UBERON:0010258
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
OBOL:automatic
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
EMAPA:16129
mesenchyme derived from neural crest of mesenchyme of 1st arch
neural crest derived arch 1 mesenchyme
pharyngeal arch 1 mesenchyme from neural crest
uberon
branchial arch 1 mesenchyme from neural crest
UBERON:0010259
1st arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
OBOL:automatic
mesenchyme derived from neural crest of mesenchyme of 1st arch
EMAPA:16129
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
DHBA:12322
EFO:0003567
EHDAA2:0004375
TAO:0000761
ZFA:0000761
basal plate midbrain
basal plate midbrain region
uberon
UBERON:0010285
midbrain basal plate
EHDAA2
EHDAA2
ZFA
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
ZFA:0000761
basal plate midbrain
TAO:0000761
basal plate midbrain region
ZFA:0000761
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
TAO:0007039
ZFA:0007039
uberon
UBERON:0010286
midbrain neural tube
ZFA
Portion of neural tube that gives rise to the midbrain.
ZFA:0007039
.
uberon
UBERON:0010291
layer of sclera
cjm
.
An endothelium that is part of a sclera.
uberon
UBERON:0010294
scleral endothelium
Wikipedia
An endothelium that is part of a sclera.
OBOL:automatic
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
uberon
UBERON:0010299
scleral mesenchyme
Mesenchyme surrounding the developing optic cup which develops into the sclera.
An epithelium that is part of a extraembryonic structure.
extra-embryonic epithelium
uberon
UBERON:0010303
extraembryonic epithelium
An epithelium that is part of a extraembryonic structure.
OBOL:automatic
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]
TAO:0002201
ZFA:0001678
future eye
uberon
UBERON:0010312
immature eye
definitional
Developing anatomical structure that develops into the eyeball and associated structures.
ZFA:0001678
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
2012-08-14
TAO:0002201
TAO
ZFIN:curator
An anatomical structure that develops from the neural crest.
Grouping term for query purposes
uberon
UBERON:0010313
neural crest-derived structure
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
Grouping term for query purposes
uberon
UBERON:0010314
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
uberon
UBERON:0010316
germ layer / neural crest
A skeletal element that is part of a orbital region.
uberon
eye skeleton
ocular skeleton
skeletal element of orbital region
UBERON:0010321
skeletal element of eye region
A skeletal element that is part of a orbital region.
OBOL:automatic
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
AAO:0000109
AAO:0000971
AAO:0010185
TAO:0000737
VSAO:0000049
XAO:0003075
ZFA:0000737
cranial skeleton
osteocranium
uberon
cranium
UBERON:0010323
cranial skeletal system
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
GO_REF:0000034
PSPUB:0000170
VSAO:0000049
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
2012-06-20
AAO:0000109
AAO
AAO:LAP
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
2012-08-14
TAO:0000737
TAO
ZFIN:curator
cranium
ZFA:0000737
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
EHDAA2:0004603
uberon
UBERON:0010336
mandibular process mesenchyme from neural crest
EHDAA2
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
EHDAA2:0004604
uberon
UBERON:0010337
mandibular process mesenchyme from head mesenchyme
EHDAA2
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
EHDAA2:0000036
uberon
UBERON:0010339
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
EMAPA:16130
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
uberon
UBERON:0010341
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
OBOL:automatic
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
EMAPA:16130
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
EHDAA2:0004078
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
uberon
branchial arch 6 mesenchyme from head mesenchyme
UBERON:0010347
6th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
arch mesenchyme from neural crest
branchial arch mesenchyme from neural crest
neural crest derived arch mesenchyme
uberon
UBERON:0010359
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
arch mesenchyme from head mesenchyme
branchial arch mesenchyme from head mesenchyme
head mesenchyme derived arch mesenchyme
uberon
UBERON:0010360
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
OBOL:automatic
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
FMA:69064
ectoderm-derived epithelium
uberon
UBERON:0010371
ecto-epithelium
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
FMA:69064
Mesenchyme that develops_from a splanchnopleure.
EHDAA2:0001122
uberon
UBERON:0010378
mesenchyme from splanchnopleure
EHDAA2
EHDAA2
Mesenchyme that develops_from a splanchnopleure.
OBOL:automatic
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.
EMAPA:35336
MA:0002486
eye surface
eye surface region
ocular surface
uberon
UBERON:0010409
ocular surface region
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.
MP:0013754
eye surface
MA:0002486
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.
FMA:76551
ciliary processes
ciliary processes set
processus ciliares
set of ciliary processes
uberon
ciliary process
processus ciliares
UBERON:0010427
ciliary processes
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.
ciliary processes
FMA:76551
ciliary processes set
FMA:76551
processus ciliares
FMA:TA
set of ciliary processes
FMA:76551
ciliary process
processus ciliares
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
FMA:45572
NCIT:C33419
NCIT:C49316
UMLS:C0836138
UMLS:C1514590
uberon
UBERON:0010498
pseudostratified columnar epithelium
FMA
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
glandular in NCIT; we consider the two NCIT terms synonymous
NCIT
UMLS:C0836138
ncithesaurus:Pseudostratified_Columnar_Epithelium
UMLS:C1514590
ncithesaurus:Pseudostratified_Epithelium
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
FMA:13146
NCIT:C13181
UMLS:C0506992
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
uberon
UBERON:0010499
pseudostratified ciliated columnar epithelium
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
NCIT:NCIT
UMLS:C0506992
ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
FMA:13146
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
MESH:A07.231.432
TAO:0005251
ZFA:0005251
uberon
microcirculatory vessels
UBERON:0010523
microcirculatory vessel
ZFA
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
MESH:A07.231.432
ZFA:0005251
microcirculatory vessels
TAO:0005251
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]
FMA:23879
VSAO:0000042
skeletal subdivision
uberon
subdivision of skeleton (in vivo)
UBERON:0010912
subdivision of skeleton
cjm
UBERONREF:0000003
VSAO
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.
UBERONREF:0000003
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
2012-08-14
VSAO:0000042
incorrect
VSAO
VSAO:curator
skeletal subdivision
VSAO:0000042
subdivision of skeleton (in vivo)
FMA:23879
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.
FMA:7491
solid joint
uberon
UBERON:0011134
nonsynovial joint
FMA
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.
FMA:7491
solid joint
FMA:7491
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
FMA:7483
uberon
UBERON:0011137
axial skeletal system
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
FMA
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
axial skeletal system
FMA:302077
post-cranial axial skeletal system
uberon
UBERON:0011138
postcranial axial skeletal system
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
FMA
cjm
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
axial skeletal system
Subdivision of skull that consists of the facial bones.
EHDAA2:0002206
EHDAA:8361
EMAPA:18022
FMA:53673
MA:0000318
facial skeleton
uberon
facial bone
ossa facialia
ossa faciei
viscerocranium
UBERON:0011156
facial skeleton
FMA
FMA
Subdivision of skull that consists of the facial bones.
MP:0005274
facial skeleton
FMA:53673
facial bone
MA:0000318
ossa facialia
ossa faciei
viscerocranium
MA:0000318
The skull can be divided into two: the neurocranium and the facial skeleton
FMA:54964
skull subdivision
subdivision of skull
uberon
UBERON:0011158
primary subdivision of skull
FMA
The skull can be divided into two: the neurocranium and the facial skeleton
skull subdivision
FMA:54964
subdivision of skull
FMA:54964
uberon
UBERON:0011159
primary subdivision of cranial skeletal system
FMA
A multi cell part structure that is part of a central nervous system.
FMA:83143
cell part cluster of neuraxis
neuraxis layer
uberon
UBERON:0011215
central nervous system cell part cluster
A multi cell part structure that is part of a central nervous system.
OBOL:automatic
cell part cluster of neuraxis
FMA:83143
neuraxis layer
FMA:83143
A subdivision of an anatomical system.
FBbt:00007330
FMA:67509
uberon
UBERON:0011216
organ system subdivision
FBbt
A subdivision of an anatomical system.
Muscles within the eye (bulbus oculi).[AAO]
AAO:0010038
EMAPA:18808
FMA:49150
intrinsic muscle of eyeball
intrinsic ocular muscle
uberon
UBERON:0011222
intra-ocular muscle
EMAPA
Muscles within the eye (bulbus oculi).[AAO]
2012-06-20
AAO:0010038
AAO
AAO:EJS
intrinsic ocular muscle
EMAPA:18808
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
EMAPA:35162
FMA:25056
MA:0000020
back of trunk
dorsal part of trunk
dorsum of trunk
trunk back
uberon
UBERON:0011270
dorsal trunk
FMA
FMA
The part of the trunk that is in the dorsum[cjm].
UBERONREF:0000006
back of trunk
FMA:25056
dorsum of trunk
FMA:25056
trunk back
FMA:25056
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
EHDAA2:0001845
uberon
basal cell layer of skin
outer epithelium of body
UBERON:0011272
embryonic skin basal layer
EHDAA2
EHDAA2
EHDAA2
outer epithelium of body
Wikipathways:WP2062
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
TAO:0005297
ZFA:0005297
cranial blood vessel
set of blood vessels of head
uberon
cranial blood vessels
UBERON:0011362
cranial blood vasculature
A blood vasculature that is part of a head.
OBOL:automatic
Blood vessel part of cranial vasculature.[TAO]
2012-08-14
TAO:0005297
TAO
ZFIN:curator
cranial blood vessel
ZFA:0005297
cranial blood vessels
TAO:0005297
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
VSAO:0000006
XAO:0004021
uberon
UBERON:0011585
cell condensation
VSAO
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
GO_REF:0000034
PSPUB:0000170
VSAO:0000006
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
EMAPA:32905
NCIT:C114916
uberon
UBERON:0011595
jaw region
http://eol.org/collections/11578
EMAPA
FMA-abduced
ZFA-abduced
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
EHDAA2:0001020
lower jaw future lip
uberon
UBERON:0011596
future lower lip
EHDAA2
lower jaw future lip
EHDAA2:0001020
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
EHDAA2:0004137
uberon
UBERON:0011642
oral epithelium from ectoderm
EHDAA2
EHDAA2
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
OBOL:automatic
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
axial subdivision of organism
uberon
body segment
main body segment
UBERON:0011676
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.
A cardiovascular system that is part of a conceptus.
EHDAA2:0000216
FMA:305965
NCIT:C34148
conceptus cardiovascular system
uberon
embryonic circulatory system
fetal circulatory system
UBERON:0011695
embryonic cardiovascular system
A cardiovascular system that is part of a conceptus.
OBOL:automatic
Ectodermal placode that does not develop into a component of the nervous system.
uberon
UBERON:0011814
non-neurogenic ectodermal placode
cjm
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.
FMA:20107
uberon
UBERON:0011821
irregular connective tissue
FMA
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.
FMA:20107
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]
FMA:20109
NCIT:C32882
UMLS:C0738366
irregular dense connective tissue
typus irregularis (textus connectivus collagenosus compactus)
uberon
UBERON:0011822
dense irregular connective tissue
FMA
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.
FMA:20109
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]
2012-08-29
ncithesaurus:Irregular_Dense_Connective_Tissue
NCIT
UMLS:C0738366
ncithesaurus:Irregular_Dense_Connective_Tissue
typus irregularis (textus connectivus collagenosus compactus)
FMA:20109
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
AAO:0000121
NCIT:C32450
UMLS:C1511770
uberon
UBERON:0011823
dense connective tissue
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
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
2012-08-29
ncithesaurus:Dense_Connective_Tissue
NCIT
UMLS:C1511770
ncithesaurus:Dense_Connective_Tissue
FMA:75634
uberon
UBERON:0011824
fibrous connective tissue
FMA
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.
FMA:19783
NCIT:C33007
UMLS:C1253917
textus connectivus collagenosus laxus
textus connectivus laxus
uberon
UBERON:0011825
loose connective tissue
FMA
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.
FMA:19783
UMLS:C1253917
ncithesaurus:Loose_Connective_Tissue
textus connectivus collagenosus laxus
FMA:19783
FMA:TA
textus connectivus laxus
FMA:19783
FMA:TA
An acinus that is part of a exocrine gland.
exocrine gland acinus
uberon
UBERON:0011858
acinus of exocrine gland
An acinus that is part of a exocrine gland.
OBOL:automatic
the FMA class specifically refers to ureter
FMA:63212
MESH:D024022
NCIT:C32339
NIF_Subcellular:sao7547390221
uberon
UBERON:0011860
collection of collagen fibrils
ZFA
the FMA class specifically refers to ureter
FMA
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity
uberon
UBERON:0011862
pulmonary collagen fibril
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity
MP:0011641
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
EMAPA:37417
Haller tunica vascula
anterior part of uveal tract
anterior uveal tract
anterior vascular layer of the eyeball
anterior vascular tunic of the eye
tunica vasculosa bulbosa
ventral uveal tract
uberon
ciliary body and iris
vasculosa oculi
UBERON:0011892
anterior uvea
ZFA
MP
lexical
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
MP:0005194
EMAPA:37417
MA:th
Haller tunica vascula
MP:0005194
tunica vasculosa bulbosa
MP:0005194
vasculosa oculi
MP:0005194
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
coelomic
EHDAA2:0004731
enterocoelom
haemocoelom
schizocoelom
uberon
coelem
coelomic cavity
UBERON:0011997
coelom
EHDAA2
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
UBERON:cjm
enterocoelom
NCBITaxon:33511
coelomic cavity
EHDAA2:0004731
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
uberon
dermatological system
UBERON:0012125
dermatological-muscosal system
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
dermatological system
OBI:MC
A zone of skin that is part of a craniocervical region.
EMAPA:37276
MA:0000574
NCIT:C12294
UMLS:C1522650
uberon
UBERON:0012180
head or neck skin
A zone of skin that is part of a craniocervical region.
OBOL:automatic
EMAPA:37276
MA:th
UMLS:C1522650
ncithesaurus:Skin_of_the_Scalp_and_Neck
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]
uberon
UBERON:0012274
columnar epithelium
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].
FMA:86452
mesoderm-derived epithelium
mesoepithelium
uberon
UBERON:0012275
meso-epithelium
Epithelium that derives from the mesoderm. [Automatically generated definition].
OBOL:automatic
One of five swellings formed during the development of the face
FMA:293103
uberon
embryonic facial process
facial primordium
primordium of face
UBERON:0012314
embryonic facial prominence
One of five swellings formed during the development of the face
An artery of the neck
EMAPA:37075
NCIT:C52850
UMLS:C1707349
uberon
UBERON:0012320
cervical artery
An artery of the neck
EMAPA:37075
MA:th
UMLS:C1707349
ncithesaurus:Cervical_Artery
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
FMA:10659
uberon
profunda cervicalis
UBERON:0012321
deep cervical artery
FMA
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
profunda cervicalis
EMAPA:37567
MA:0001802
uberon
UBERON:0012416
respiratory system arterial smooth muscle
EMAPA:37567
MA:th
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
EMAPA:37586
MA:0001812
uberon
UBERON:0012418
respiratory system venous smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
OBOL:automatic
EMAPA:37586
MA:th
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.
tunica fibrosa
FMA:58102
fibrous layer of eyeball
uberon
corneosclera
fibrous tunic
UBERON:0012430
tunica fibrosa of eyeball
FMA
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.
fibrous layer of eyeball
FMA:58102
corneosclera
fibrous tunic
EHDAA2:0000472
EMAPA:16054
VHOG:0000767
uberon
extraembryonic cavities
UBERON:0012466
extraembryonic cavity
extraembryonic cavities
EHDAA2:0000472
An anatomical space with no opening to another space or to the exterior.
AEO:0000222
closed anatomical space
uberon
UBERON:0012467
enclosed anatomical space
An anatomical space with no opening to another space or to the exterior.
AEO:0000222
A vein that drains a lip.
labial vein of face
lip vein
vena labialis
uberon
labial vein
UBERON:0013136
vein of lip
FMA
A vein that drains a lip.
OBOL:automatic
lip vein
OBOL:automatic
vena labialis
Any vein within the general circulation that transports blood back to the right atrium of the heart.
FMA:66644
NCIT:C33719
UMLS:C0447117
systemic venous tree organ part
uberon
UBERON:0013140
systemic vein
Any vein within the general circulation that transports blood back to the right atrium of the heart.
ncithesaurus:Systemic_Vein
UMLS:C0447117
ncithesaurus:Systemic_Vein
systemic venous tree organ part
FMA:66644
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
FMA:86279
acinus of serous gland
uberon
UBERON:0013232
serous acinus
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
Anatomical cavity that is the lumen of the skull and contains the brain.
EMAPA:37497
FMA:9644
MA:0003061
NCIT:C77638
UMLS:C0230041
cavitas cranii
uberon
intracranial cavity
intracranial space
UBERON:0013411
cranial cavity
Wikipedia
Anatomical cavity that is the lumen of the skull and contains the brain.
UBERON:cjm
EMAPA:37497
MA:th
UMLS:C0230041
ncithesaurus:Cranial_Cavity
cavitas cranii
FMA:9644
FMA:TA
intracranial cavity
intracranial space
A blood vessel endothelium that is part of a lung [Automatically generated definition].
BTO:0004128
CALOHA:TS-0573
uberon
respiratory endothelium
UBERON:0013479
lung endothelium
A blood vessel endothelium that is part of a lung [Automatically generated definition].
OBOL:automatic
respiratory endothelium
BTO:0004128
The space that surrounds an organism.
external to organism
outside of body
uberon
UBERON:0013514
space surrounding organism
The space that surrounds an organism.
uberon
UBERON:0013522
subdivision of tube
2
2
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
FMA:9338
foramen space
uberon
UBERON:0013686
anatomical conduit space
FMA
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
FMA:9338
Vascular endothelium found in blood vessels of the blood-brain-barrier.
BTO:0001852
BTO:0003248
CALOHA:TS-0092
uberon
cerebromicrovascular endothelium
UBERON:0013694
brain endothelium
Vascular endothelium found in blood vessels of the blood-brain-barrier.
CALOHA:TS-0092
cerebromicrovascular endothelium
CALOHA:TS-0092
Musculature of the head and neck, spine, and ribs.
EHDAA2:0000159
EMAPA:18166
uberon
UBERON:0013700
axial musculature
Musculature of the head and neck, spine, and ribs.
HP:0003327
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.
uberon
UBERON:0013701
main body axis
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
AEO:0000103
BTO:0001489
EMAPA:36031
FMA:231424
uberon
body
whole body
UBERON:0013702
body proper
AEO
The region of the organism associated with the visceral organs.
AEO:0000103
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].
FMA:231424
body
AEO:0000103
whole body
BTO:0001489
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
FMA:293127
NCIT:C34230
UMLS:C1518428
uberon
chordal canal
UBERON:0013704
notochordal canal
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
UMLS:C1518428
ncithesaurus:Notochordal_Canal
Fluid contained within the notochordal canal
notochord fluid
portion of notochordal fluid
uberon
UBERON:0013727
Distinct feature of coelocanths
notochordal fluid
Fluid contained within the notochordal canal
A organ component layer that is part of a integumental system.
layer of skin
skin layer
uberon
UBERON:0013754
integumentary system layer
A organ component layer that is part of a integumental system.
OBOL:automatic
A blood that is part of a artery.
FMA:83066
arterial blood
blood in artery
portion of arterial blood
uberon
UBERON:0013755
arterial blood
A blood that is part of a artery.
OBOL:automatic
arterial blood
FMA:83066
blood in artery
FMA:83066
portion of arterial blood
FMA:83066
A blood that is part of a vein.
FMA:83067
blood in vein
portion of venous blood
venous blood
uberon
UBERON:0013756
venous blood
A blood that is part of a vein.
OBOL:automatic
blood in vein
FMA:83067
portion of venous blood
FMA:83067
venous blood
FMA:83067
A blood that is part of a capillary.
FMA:263901
NCIT:C32212
blood in capillary
portion of blood in capillary
portion of capillary blood
uberon
UBERON:0013757
capillary blood
A blood that is part of a capillary.
OBOL:automatic
portion of blood in capillary
FMA:263901
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
digestive organ
digestive system organ
uberon
UBERON:0013765
digestive system element
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
MA:th
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
great vessel
EMAPA:36460
great vessel of thorax
uberon
UBERON:0013768
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
great vessel of heart
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
EMAPA:32735
FMA:293883
mesenchyme from neural crest
neural crest derived mesenchyme
neural crest mesenchyme
uberon
UBERON:0014387
mesenchyme derived from neural crest
Mesenchyme that develops_from the neural crest[Automatically generated definition].
OBOL:automatic
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.
EHDAA2:0002013
FMA:77169
skeleton of thorax
thoracic part of axial skeleton
thoracic skeleton
uberon
UBERON:0014477
thoracic skeleton
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.
thoracic skeleton
EHDAA2:0002013
A neuromere that is part of the presumptive midbrain
mesomere
midbrain segment
segment of midbrain
EHDAA2:0004352
FMA:61997
mesomere of nervous system
neuromere of mesomere group
uberon
future mesencephalon
mesomere group
UBERON:0014776
midbrain neuromere
A neuromere that is part of the presumptive midbrain
mesomere group
EHDAA2:0004352
A neuromere that is part of the presumptive spinal cord
TAO:0001332
ZFA:0001332
spinal cord metameric segment
spinal neuromeres
uberon
spinal cord segment
UBERON:0014777
spinal neuromere
A neuromere that is part of the presumptive spinal cord
spinal neuromeres
TAO:0001332
spinal cord segment
TAO:0001332
A portion of tissue that will develop into vasculature.
EFO:0003708
TAO:0005076
ZFA:0005076
uberon
UBERON:0014903
primordial vasculature
A portion of tissue that will develop into vasculature.
ZFA:0005076
ZFA:curator
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
ocular gland
uberon
orbital gland
UBERON:0015152
gland of ocular region
inferred
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
An eye consisting of multiple light-sensing organs
uberon
UBERON:0015165
multi-unit eye
An eye consisting of multiple light-sensing organs
present on tentacular crown
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A region of somite adjacent to presomitic mesoderm.
TAO:0001462
XAO:0004074
ZFA:0001462
uberon
inter-somited border
intersomitic boundary
intersomitic fissure
intersomitic junction
segmental border
somite boundary
UBERON:0015178
somite border
A region of somite adjacent to presomitic mesoderm.
intersomitic junction
XAO:0004074
somite boundary
ZFA:0001462
Epithelium located in the intersomitic region.
XAO:0004077
intersomitic epithelium
intersomitic membrane
uberon
UBERON:0015179
somite boundary epithelium
Epithelium located in the intersomitic region.
XAO:0004077
XAO:EJS
intersomitic epithelium
XAO:0004077
intersomitic membrane
XAO:0004077
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.
uberon
UBERON:0015212
lateral structure
Any structure that is placed on one side of the left-right axis of a bilaterian.
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.
heart
SPD:0000130
cardiac pump
heart or heart like organ
circulatory vessel
uberon
cardiac structure
UBERON:0015228
circulatory organ
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 basement membrane of epithelium that is part of a respiratory system.
EMAPA:37570
MA:0001815
uberon
UBERON:0015329
respiratory system basement membrane
MA
A basement membrane of epithelium that is part of a respiratory system.
OBOL:automatic
EMAPA:37570
MA:th
EMAPA:37597
MA:0002449
heart/pericardium
uberon
UBERON:0015410
heart plus pericardium
MA
EMAPA:37597
MA:th
heart/pericardium
MA:0002449
A smooth muscle tissue that is part of a hypodermis.
FMA:77862
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
uberon
UBERON:0015783
smooth muscle layer in fatty layer of subcutaneous tissue
A smooth muscle tissue that is part of a hypodermis.
OBOL:automatic
muscle layer in fatty layer of subcutaneous tissue
FMA:77862
stratum musculosum panniculi adiposi telae subcutaneae
FMA:77862
FMA:TA
A epithelium that is part of a camera-type eye.
EMAPA:35957
MA:0003162
uberon
UBERON:0015808
eye epithelium
A epithelium that is part of a camera-type eye.
OBOL:automatic
A epithelium that is part of a foregut.
EMAPA:32922
MA:0003204
uberon
UBERON:0015833
foregut epithelium
A epithelium that is part of a foregut.
OBOL:automatic
A capillary that is part of a lung.
FMA:14121
capillary of lung
uberon
UBERON:0016405
pulmonary capillary
A capillary that is part of a lung.
OBOL:automatic
capillary of lung
FMA:14121
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
UBERON:2001379
TAO:0001379
ZFA:0001379
uberon
UBERON:0016545
pharyngeal ectoderm
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
grey matter layer
FMA:83142
CNS gray matter layer
CNS grey matter layer
gray matter layer of neuraxis
grey matter layer of neuraxis
uberon
UBERON:0016548
central nervous system gray matter layer
A layer of of the central nervous system that is part of gray matter.
gray matter layer of neuraxis
FMA:83142
FMA:68861
rexed lamina
uberon
UBERON:0016570
lamina of gray matter of spinal cord
rexed lamina
FMA:68861
Primordium that develops into the central nervous system
UBERON:3000469
future CNS
presumptive central nervous system
uberon
UBERON:0016879
future central nervous system
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
UBERON:3000477
AAO:0000477
presumptive nervous system
uberon
UBERON:0016880
future nervous system
Primordium that develops into the nervous system
presumptive nervous system
AAO:0000477
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.
AEO:0000195
EHDAA2:0000003
EMAPA:16042
extra-embryonic component
extraembryonic component
uberon
UBERON:0016887
entire extraembryonic component
AEO
AEO
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.
AEO:0000195
AEO:JB
extraembryonic component
AEO:0000195
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
AEO:0000132
uberon
UBERON:0016888
transitional anatomical structure
AEO
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
AEO:0000132
AEO:JB
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
AEO:0001016
uberon
UBERON:0017650
developing mesenchymal structure
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
AEO:0001016
AEO:JB
A zone of skin that is part of a lower lip.
FMA:24767
lower lip skin
uberon
UBERON:0018150
skin of lower lip
A zone of skin that is part of a lower lip.
OBOL:automatic
lower lip skin
FMA:24767
A boundary delimiting a rhombomere.
rhombomere junction
uberon
UBERON:0018239
rhombomere boundary
A boundary delimiting a rhombomere.
GO:0021654
Any portion of submucosa that lines the digestive tract.
uberon
UBERON:0018257
submucosa of digestive tract
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
FMA:45634
NCIT:C75444
uberon
UBERON:0018260
layer of muscle tissue
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
NCIT
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
FMA:73747
ZFA:0005811
cardiac vasculature
uberon
UBERON:0018674
heart vasculature
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
ZFA:0005811
ZFA:CVS
cardiac vasculature
FMA:73747
BTO:0004626
uberon
carotid endothelium
carotid epithelium
UBERON:0019189
carotid artery endothelium
carotid endothelium
BTO:0004626
Any region of epithelium that is part of a skin region.
BTO:0004382
uberon
UBERON:0019204
skin epithelium
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid
chorioretina
choroid and retina
retinachoroid
retinachoroidal region
uberon
UBERON:0019207
chorioretinal region
The part of the eye that consists of both the retina and the optic choroid
UBERON:drseb
DHBA:10654
FMA:268630
gray matter of the hindbrain
uberon
UBERON:0019263
gray matter of hindbrain
gray matter of the hindbrain
DHBA:HGM
DHBA:10649
FMA:83913
uberon
UBERON:0019267
gray matter of midbrain
EMAPA:35952
MA:0003174
uberon
UBERON:0019304
sensory organ epithelium
An exocrine gland that is part of a integumental system.
integumental exocrine gland
integumental system exocrine gland
uberon
UBERON:0019319
exocrine gland of integumental system
An exocrine gland that is part of a integumental system.
GOC:dos
integumental exocrine gland
integumental system exocrine gland
FMA:58315
uberon
surface of region of wall of eyeball
UBERON:0022288
surface of eyeball
surface of region of wall of eyeball
FMA:58315
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
lamina
layer
NLX:149357
uberon
UBERON:0022303
nervous system cell part layer
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
NLX:149357
lamina
CUMBO:CUMBO
layer
CUMBO:CUMBO
Serous membrane layer that is adjacent to and lines an organ.
FMA:15860
visceral wall of serous membrane
uberon
UBERON:0022350
visceral serous membrane
Serous membrane layer that is adjacent to and lines an organ.
visceral wall of serous membrane
FMA:15860
Serous membrane layer that lines to a body cavity.
cavity lining
FMA:15859
MA:0002448
parietal wall of serous membrane
uberon
UBERON:0022351
parietal serous membrane
Serous membrane layer that lines to a body cavity.
cavity lining
MA:0002448
parietal wall of serous membrane
FMA:15859
A specific region of the foregut into the area in which the lung will develop.
lung field
uberon
UBERON:0022361
lung field
A specific region of the foregut into the area in which the lung will develop.
GOC:dph
GOC:mtg_lung
An embryonic or larval epithelium that is committed to form part of the nervous system.
neurepithelium
AEO:0001008
BTO:0000314
EHDAA2_RETIRED:0004654
FMA:64807
embryonic neuroepithelium
neuroepithelium
uberon
UBERON:0034705
developing neuroepithelium
An embryonic or larval epithelium that is committed to form part of the nervous system.
AEO:0001008
AEO:JB
neurepithelium
BTO:0000314
embryonic neuroepithelium
neuroepithelium
AEO:0001008
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
AEO:0001009
uberon
UBERON:0034706
proliferating neuroepithelium
AEO
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
AEO:0001009
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
AEO:0001010
uberon
UBERON:0034707
differentiating neuroepithelium
AEO
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
AEO:0001010
DHBA:12694
EMAPA:32916
marginal zone of hindbrain
uberon
MZH
UBERON:0034709
hindbrain marginal layer
marginal zone of hindbrain
DHBA:12694
MZH
DHBA:12694
EHDAA2:0001267
EMAPA:17585
spinal cord lateral wall ventricular layer
uberon
UBERON:0034710
spinal cord ventricular layer
EHDAA2
spinal cord lateral wall ventricular layer
EHDAA2:0001267
Any substance in the body or expelled from the body that is in a gaseous state.
FMA:84580
gas in anatomical space
portion of gas in anatomical space
uberon
UBERON:0034873
bodily gas
Any substance in the body or expelled from the body that is in a gaseous state.
portion of gas in anatomical space
FMA:84580
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
FMA:84581
respiratory air
respiratory system air
uberon
UBERON:0034874
air in respiratory system
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
respiratory air
FMA:84581
the area of axial mesoderm that develops into the prechordal plate
prechordal mesenchyme
uberon
UBERON:0034878
prechordal mesoderm
the area of axial mesoderm that develops into the prechordal plate
MGI:anna
lumen of gland
uberon
UBERON:0034905
gland lumen
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
uberon
anatomical cluster
UBERON:0034921
multi organ part structure
CARO
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
anatomical cluster
CARO:0020001
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
FMA:62807
uberon
UBERON:0034922
cell cluster
CARO
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
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
uberon
UBERON:0034925
anatomical collection
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
Any organ component layer that consists of smooth muscle tissue.
uberon
UBERON:0034933
layer of smooth muscle tissue
Any organ component layer that consists of smooth muscle tissue.
FMA:55268
organ sector
organ zonal region
organ zone
uberon
organ region with floating fiat boundary
UBERON:0034944
zone of organ
organ sector
FMA:55268
organ zone
FMA:55268
organ region with floating fiat boundary
FMA:55268
Any portion of gas located in a part of the respiratory system.
respiratory gas
respiratory system gas
uberon
UBERON:0034947
gas in respiratory system
Any portion of gas located in a part of the respiratory system.
NCIT:C25787
uberon
duct epithelium
ductal epithelium
UBERON:0034969
epithelial layer of duct
Mesenchyme that is part of a developing jaw [Automatically generated definition].
EMAPA:32907
EMAPA:35454
uberon
UBERON:0034995
jaw mesenchyme
Mesenchyme that is part of a developing jaw [Automatically generated definition].
OBOL:automatic
EMAPA:32904
MA:0003220
uberon
UBERON:0035037
jaw epithelium
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
digestive tract contents
uberon
ingested material entity
UBERON:0035118
material entity in digestive tract
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
digestive tract contents
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
FMA:61695
NCIT:C29667
surface of body
uberon
UBERON:0035159
entire surface of organism
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
FMA:61695
surface of body
FMA:61695
FMA:70505
NCIT:C32552
external carotid arterial subdivision
subdivision of external carotid artery
uberon
UBERON:0035398
branch of external carotid artery
external carotid arterial subdivision
FMA:70505
subdivision of external carotid artery
FMA:70505
FMA:51797
ciliary vein
uberon
UBERON:0035546
uveal vein
ciliary vein
FMA:51797
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
FMA:225275
superficial part of circulatory system
superficial vasculature
dermis vasculature
hypodermis vasculature
uberon
skin vasculature
subcutaneous vasculature
vasculature of skin
UBERON:0035549
vasculature of integument
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
vasculature of skin
FMA:225275
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
FMA:76719
NCIT:C33666
uberon
superfical vein
superficial veins
superficial vessels
UBERON:0035550
superficial vein
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
ncithesaurus:Superficial_Vein
superfical vein
superficial veins
superficial vessels
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
deep part of circulatory system
uberon
UBERON:0035551
deep vasculature
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
FMA:76718
NCIT:C32444
uberon
deep veins
deep vessels
UBERON:0035552
deep vein
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
ncithesaurus:Deep_Vein
deep veins
deep vessels
Any chamber of the left side of the heart
FMA:7166
uberon
UBERON:0035553
left cardiac chamber
Any chamber of the left side of the heart
Any chamber of the right side of the heart
FMA:7165
uberon
UBERON:0035554
right cardiac chamber
Any chamber of the right side of the heart
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
FMA:76554
NCIT:C32574
adnexa oculi
uberon
accessory parts of orbital region
accessory visual structures
accessory visual structures set
adnexal parts of orbital region
appendage of eye
appendages of the eye
eye adnexa
set of accessory visual structures
structurae oculi accessoriae
UBERON:0035639
ocular adnexa
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
HPO:pr
UBERON:cjm
adnexa oculi
accessory visual structures
accessory visual structures
FMA:76554
accessory visual structures set
FMA:76554
appendage of eye
appendages of the eye
set of accessory visual structures
FMA:76554
structurae oculi accessoriae
EHDAA2:0004181
FMA:9464
cardiac chamber cavity
heart cavity
heart lumen
uberon
UBERON:0035763
cavity of cardiac chamber
FMA
cardiac chamber cavity
FMA:9464
heart cavity
FMA:9464
heart lumen
EHDAA2:0004181
The primordial mouth region of the developing head.
FMA:293105
primitive mouth
primordial mouth
uberon
UBERON:0035804
future mouth
The primordial mouth region of the developing head.
MP:0003119
primitive mouth
FMA:293105
FMA:12241
uberon
UBERON:0035809
serous cavity
The sum of epicardial and paracardial fat deposits.
ZFA:0005765
uberon
UBERON:0035814
pericardial fat
The sum of epicardial and paracardial fat deposits.
Any fat deposit surrounding a visceral organ.
uberon
UBERON:0035818
visceral fat
Any fat deposit surrounding a visceral organ.
UBERON:cjm
BTO:0004378
EMAPA:37987
FMA:67473
blood vessel wall
uberon
vascular wall
UBERON:0035965
wall of blood vessel
EMAPA:37987
MA:th
blood vessel wall
FMA:67473
vascular wall
BTO:0004378
EHDAA2:0004070
uberon
UBERON:0036072
respiratory primordium epithelium
EHDAA2
EHDAA2:0004071
respiratory primordium associated mesenchyme
uberon
UBERON:0036073
respiratory primordium mesenchyme
EHDAA2
respiratory primordium associated mesenchyme
EHDAA2:0004071
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
uberon
UBERON:0036146
cardiopharyngeal field
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
BGEE:ann
Material anatomical entity that forms the outermost boundary of an anatomical structure.
AAO:0010270
AEO:0000154
ZFA:0005594
uberon
UBERON:0036215
anatomical surface region
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
BTO:0001708
uberon
UBERON:0036217
coelomic fluid
A bodily fluid that is located in the coelom.
Any gland that is part os the respiratory system.
uberon
UBERON:0036225
respiratory system gland
Any gland that is part os the respiratory system.
UBERON:cjm
A notochord that has persisted beyond the embryonic stage.
uberon
UBERON:0036242
post-embryonic notochord
A notochord that has persisted beyond the embryonic stage.
UBERON:cjm
A transudate found in the serous sac.
serous fluid
FMA:20932
serous sac fluid
uberon
UBERON:0036244
secretion of serous membrane
A transudate found in the serous sac.
FMA:20932
serous fluid
FMA:20932
FMA:53133
cranial orifice
skull orifice
uberon
UBERON:0036253
orifice of skull
cranial orifice
FMA:53133
skull orifice
FMA:53133
A mucosa that is part of a lip region [Automatically generated definition].
NCIT:C12226
labial mucosa
uberon
UBERON:0036294
mucosa of lip
A mucosa that is part of a lip region [Automatically generated definition].
OBOL:automatic
labial mucosa
UBERON:cjm
uberon
UBERON:0036302
vasculature of central nervous system plus retina
FMA:259905
uberon
UBERON:0036303
vasculature of central nervous system
A zone of skin that is part of the face.
eriks
2012-02-05T05:23:01Z
EMAPA:36657
FMA:24758
NCIT:C33561
UMLS:C0222084
face skin
uberon
facial skin
UBERON:1000021
skin of face
A zone of skin that is part of the face.
UBERON:EJS
UMLS:C0222084
ncithesaurus:Skin_of_the_Face
face skin
EMAPA:36657
FMA:24758
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
amphibian_anatomy_curators
uberon/phenoscape-anatomy
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
external integument structure
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
AAO:EJS
Dermal, epidermal, glandular and pigment structures of the external head 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
amphibian_anatomy_curators
uberon/phenoscape-anatomy
head external integument structure
Dermal, epidermal, glandular and pigment structures of the external head integument.
AAO:EJS
Dermal, epidermal, glandular and pigment structures of the body 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
amphibian_anatomy_curators
uberon/phenoscape-anatomy
body external integument structure
Dermal, epidermal, glandular and pigment structures of the body integument.
AAO:EJS
Blood vessels in respiratory skin.
Modified from the original AAO source
amphibian_anatomy_curators
uberon/phenoscape-anatomy
vasculature of respiratory integument
Blood vessels in respiratory skin.
AAO:EJS
Any head that is part of some larva.
FBbt:00001730
uberon
UBERON:6001730
larval head
Any head that is part of some larva.
FBC:auto_generated_definition
Any sense organ that is part of some larva.
FBbt:00002639
larval sense organ
uberon
UBERON:6002639
larval sense organ
Any sense organ that is part of some larva.
FBC:auto_generated_definition
Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730).
FBbt:00007280
larval head sense organ
UBERON:6007280
embryonic/larval head sense organ
Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730).
FBC:auto_generated_definition
A heterotroph that consumes plant and animal matter either in whole or in part via ingestion through a type of "mouth". Animal and plant matter is broken down through an internal digestion process
http://orcid.org/0000-0002-2908-3327
omnivore
An environmental zone which an animal consistently defends against conspecifics or, occasionally, animals of other species
http://orcid.org/0000-0002-2908-3327
territory
The fifth post-naupliar life stage of a copepod
http://orcid.org/0000-0002-2908-3327
copepodid stage 5
Obsolete Class
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:25:21Z
Western Australia Ecoregion
WWF:AA1310
https://www.worldwildlife.org/ecoregions/aa1310
Western Australian Mulga Shrublands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:51:32Z
https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
Australasia Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:52:41Z
Southern central Australia Ecoregion
WWF:AA1309
https://www.worldwildlife.org/ecoregions/aa1309
Tirari-Sturt Stony Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:54:35Z
Eastern central Australia Ecoregion
WWF:AA1308
https://www.worldwildlife.org/ecoregions/aa1308
Simpson Desert Region
http://orcid.org/0000-0002-4366-3088
2019-03-05T17:56:13Z
Western Australia Ecoregion
WWF:AA1307
https://www.worldwildlife.org/ecoregions/aa1307
Pilbara Shrublands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:10:52Z
Western coast of Australia Ecoregion
WWF:AA1301
https://www.worldwildlife.org/ecoregions/aa1301
Carnarvon Xeric Shrublands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:12:28Z
Central Australia Ecoregion
WWF:AA1302
https://www.worldwildlife.org/ecoregions/aa1302
Central Ranges Xeric Shrub Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:15:11Z
Western central Australia
WWF:AA1303
https://www.worldwildlife.org/ecoregions/aa1303
Gibson Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:17:15Z
Northwestern Australia
WWF:AA1304
https://www.worldwildlife.org/ecoregions/aa1304
The Great Sandy-Tanami Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:24:06Z
Southern Australia Ecoregion
WWF:AA1305
https://www.worldwildlife.org/ecoregions/aa1305
Great Victoria Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-05T18:26:16Z
Southern Australia Ecoregion
WWF:AA1306
https://www.worldwildlife.org/ecoregions/aa1306
Nullarbor Plains Xeric Shrubland Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:01:41Z
https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
Afrotropical Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:02:37Z
Southern Africa: Southern Namibia into South Africa
WWF:AT1322
https://www.worldwildlife.org/ecoregions/at1322
Succulent Karoo Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:07:38Z
WWF:AT1321
https://www.worldwildlife.org/ecoregions/at1321
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:11:38Z
WWF:AT1320
https://www.worldwildlife.org/ecoregions/at1320
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:13:00Z
WWF:AT1319
https://www.worldwildlife.org/ecoregions/at1319
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:15:07Z
Islands east of the Horn of Africa and south of Yemen Ecoregion
WWF:AT1318
https://www.worldwildlife.org/ecoregions/at1318
Socotran Archipelago Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:18:55Z
WWF:AT1317
https://www.worldwildlife.org/ecoregions/at1317
Red Sea Coastal Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:20:56Z
WWF:AT1316
https://www.worldwildlife.org/ecoregions/at1316
Namibian Savanna Woodland Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:24:28Z
Africa: Namibia Ecoregion
WWF:AT1315
https://www.worldwildlife.org/ecoregions/at1315
Namib Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:26:15Z
WWF:AT1314
https://www.worldwildlife.org/ecoregions/at1314
Nama Karoo Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:28:43Z
WWF:AT1313
https://www.worldwildlife.org/ecoregions/at1313
Masai Xeric Grasslands and Shrublands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:30:23Z
WWF:AT1312
https://www.worldwildlife.org/ecoregions/at1312
Madagascar Succulent Woodlands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:31:29Z
WWF:AT1311
https://www.worldwildlife.org/ecoregions/at1311
Madagascar spiny desert ecoregion
Madagascar Spiny Thickets Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:39:32Z
WWF:AT1310
https://www.worldwildlife.org/ecoregions/at1310
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:42:47Z
WWF:AT1309
https://www.worldwildlife.org/ecoregions/at1309
Kalahari Xeric Savanna Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:44:54Z
WWF:AT1308
https://www.worldwildlife.org/ecoregions/at1308
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:46:58Z
Eastern Africa: Somalia
WWF:AT1307
https://www.worldwildlife.org/ecoregions/at1307
Hobyo Grassland and Shrubland Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-06T22:54:57Z
WWF:AT1306
https://www.worldwildlife.org/ecoregions/at1306
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-07T00:08:06Z
WWF:AT1305
https://www.worldwildlife.org/ecoregions/at1305
Ethiopian Xeric Grasslands and Shrublands Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-07T00:11:29Z
WWF:AT1304
https://www.worldwildlife.org/ecoregions/at1304
Eritrean Coastal Desert Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-07T00:13:33Z
WWF:AT1303
https://www.worldwildlife.org/ecoregions/at1303
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-07T00:16:12Z
WWF:AT1302
https://www.worldwildlife.org/ecoregions/at1302
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
http://orcid.org/0000-0002-4366-3088
2019-03-07T00:18:09Z
WWF:AT1301
https://www.worldwildlife.org/ecoregions/at1301
Aldabra Island Xeric Scrub Ecoregion
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
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.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
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."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
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.
pending final vetting
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
other
true
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
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.
Alan Ruttenberg
group:OBI
requires discussion
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
third planet from the Sun in the Solar System
Earth
third planet from the Sun in the Solar System
https://www.wikidata.org/wiki/Q2
"Suni, or Jalca, is one of the eight Natural Regions of Peru. It is located in the Andes at an altitude between 3,500 and 4,000 metres above sea level. Suni has a dry and cold weather and there are many glacial valleys. The flora includes gramineous plants and shrubs such as the taya-taya (Caesalpinia spinosa), the quishuar (Buddleja coriacea), and the cantuta (Cantua buxifolia) which was considered sacred by the Incas. Even though it is hard for plants to grow because of the weather, people are able to cultivate such crops as quinoa, qañiwa, broad beans and ulluku (Ullucus tuberosus). The main fauna is the guinea pig and, among numerous other highland birds, the Chiguanco thrush."
Jalca
Suni
"Suni, or Jalca, is one of the eight Natural Regions of Peru. It is located in the Andes at an altitude between 3,500 and 4,000 metres above sea level. Suni has a dry and cold weather and there are many glacial valleys. The flora includes gramineous plants and shrubs such as the taya-taya (Caesalpinia spinosa), the quishuar (Buddleja coriacea), and the cantuta (Cantua buxifolia) which was considered sacred by the Incas. Even though it is hard for plants to grow because of the weather, people are able to cultivate such crops as quinoa, qañiwa, broad beans and ulluku (Ullucus tuberosus). The main fauna is the guinea pig and, among numerous other highland birds, the Chiguanco thrush."
https://en.wikipedia.org/wiki/Suni_(geography)
Earth's interconnected water system
World Ocean
Earth's interconnected water system
https://www.wikidata.org/wiki/Q715269
2
2
1
2
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
From ligand activity to has_ligand
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
From has_ligand to ligand activity
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).