The Pain Ontology
type: Ontology
version IRI: pain.owl
contributor: Mattew Diller
contributor: Bill Duncan
contributor: Alexander D. Diehl
contributor: Daniel W. McNeil
contributor: Finn Wilson
contributor: Ava E. Cunningham
contributor: Gopikrishnan M Chandrasekharan
created: 2022-08-23
description: The Pain Ontology contains terms for representing pain as defined by the International Association For the Study of Pain (IASP), meaning that pain is both an unpleasant physical sensation and unpleasant emotional experience. It includes terms and axioms to represent the multidimensional aspect of pain, such as temporality (e.g., acute, chronic), qualitative (e.g., sharp, throbbing), extent (e.g., local, widespread), biological mechanism (e.g., nociceptive, neuropathic), and specific anatomical locations (e.g., back, knee).
license: http://creativecommons.org/licenses/by/4.0/
version info: 2026-06-05

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example of usage
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).

definition source
type: AnnotationProperty
editor preferred term: definition source
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred term: curator note
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588
definition: A URL for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.
range: anyURI

ontology term requester
type: AnnotationProperty
editor preferred term: ontology term requester
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

is denotator type
type: AnnotationProperty
editor preferred term: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred term: imported from
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: 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)"
definition: 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
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred term: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred term: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred term: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred term: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred term: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred term: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: 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

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.

preferred label for community
type: AnnotationProperty
example of usage: The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
definition: A provenance property that denotes a synonym to be the preferred one for a specific community.
created: 2025-06-02

abbreviation
type: AnnotationProperty
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initialisms
created: 2023-03-03
sub property of: SynonymTypeProperty

ambiguous synonym
type: AnnotationProperty
definition: A synonym type for describing ambiguous synonyms
created: 2023-03-03
sub property of: SynonymTypeProperty

dubious synonym
type: AnnotationProperty
definition: A synonym type for describing dubious synonyms
created: 2023-03-03
sub property of: SynonymTypeProperty

layperson synonym
type: AnnotationProperty
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
definition: A synonym type for describing layperson or colloquial synonyms
created: 2023-03-03
sub property of: SynonymTypeProperty

plural form
type: AnnotationProperty
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
created: 2023-03-03
sub property of: SynonymTypeProperty

UK spelling synonym
type: AnnotationProperty
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
definition: A synonym type for describing UK spelling variants
created: 2023-03-03
sub property of: SynonymTypeProperty

misspelling
type: AnnotationProperty
definition: A synonym type for common misspellings
created: 2023-03-03
sub property of: SynonymTypeProperty

misnomer
type: AnnotationProperty
definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
created: 2023-03-03
sub property of: SynonymTypeProperty

previous name
type: AnnotationProperty
example of usage: MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
definition: A synonym type for names that have been used as primary labels in the past.
created: 2023-07-25
sub property of: SynonymTypeProperty

legal name
type: AnnotationProperty
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
definition: A synonym type for the legal entity name
created: 2023-07-27
sub property of: SynonymTypeProperty

International Nonproprietary Name
type: AnnotationProperty
example of usage: CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
definition: The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
created: 2023-09-30
has exact synonym: INN
sub property of: SynonymTypeProperty

latin term
type: AnnotationProperty
example of usage: nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
definition: A synonym type for describing Latin term synonyms.
created: 2023-10-12
sub property of: SynonymTypeProperty

acronym
type: AnnotationProperty
example of usage: NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
definition: A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
created: 2023-11-01
sub property of: SynonymTypeProperty

has ontology hierarchical property
type: AnnotationProperty
example of usage: The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.
definition: Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.
created: 2025-09-17

has symbol
type: AnnotationProperty
example of usage: A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
created: 2024-03-25

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

has cross-reference
type: AnnotationProperty
example of usage: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
created: 2024-03-18

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

experienced as
type: ObjectProperty
domain: nervous system process
range: cognition
example of usage: Concomitant continuous pain (CCP) in trigeminal neuralgia is often experienced as burning or throbbing.
definition: A relation between a nervous system process and a cognitive process in which the nervous system process is gives rise to an experiential mental process.
contributor: Bill Duncan
created: 2024-06-13T22:09:02Z

experienced in
type: ObjectProperty
example of usage: Brain freeze is a brief, intense pain experienced in the forehead.
definition: A relation between a physical sensation and an anatomical entity or site where an anatomical entity is usually located in which the sensation is subjectively experienced as occurring in the anatomical entity or site.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-04-28T16:36:53Z

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
alternative label: part_of
RO_0001900: RO_0001901
has cross-reference: BFO:0000050
has OBO namespace: external
has OBO namespace: quality
id: part_of
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam
shorthand: part_of
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
alternative label: has_part
RO_0001900: RO_0001901
has cross-reference: BFO:0000051
has OBO namespace: external
has OBO namespace: quality
id: has_part
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_part
label: has_part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
property chain axiom: part of
editor preferred term: preceded by
definition: 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.
alternative label: is preceded by
alternative label: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: part of
editor preferred term: precedes
definition: 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.
in subset: ro-eco

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
alternative label: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

has participant
type: ObjectProperty
property chain axiom: has part
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
definition: x overlaps y iff they have some part in common.
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
has cross-reference: RO:0002131
id: overlaps
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco
shorthand: overlaps
comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []

Axiom
annotated source: overlaps
annotated property: definition
annotated target: x overlaps y iff they have some part in common.
has cross-reference: BSPO:cjm

capable of
type: ObjectProperty
sub property of: capable of part of
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
has cross-reference: RO:0002215
id: capable_of
in subset: ro-eco
shorthand: capable_of

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in
has cross-reference: RO:0002216
id: capable_of_part_of
shorthand: capable_of_part_of

temporally related to
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: consumes
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: produces
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165
RO_0001900: RO_0001901

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165
has cross-reference: RO:0002328
id: functionally_related_to
shorthand: functionally_related_to

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
term editor: https://orcid.org/0000-0002-6601-2165
in subset: valid for gocam

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
term editor: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259
in subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
term editor: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259
in subset: ro-eco

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
definition: inverse of upstream of
term editor: https://orcid.org/0000-0002-6601-2165

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
term editor: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has cross-reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
term editor: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: part of
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
in subset: RO_0002259

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

throbbing pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: throbbing sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: throbbing sensation quality
definition: Pain that is experienced as a rhythmic, pulsating, or beating sensation in which the pain's intensity waxes and wanes in periodic bursts. Throbbing pain is typically synchronized with the cardiac cycle.
contributor: Bill Duncan
created: 2026-04-08T19:58:42Z

chronic high impact pain
type: Class
subclass of: chronic pain
definition: Chronic pain that significantly impacts a person's ability to function.
contributor: Bill Duncan
created: 2026-05-01T20:50:40Z

emotion process
type: Class
subclass of: behavior
definition: A behavioral response that includes overt action, cognitive response, verbal response, or physiological reaction in response to a situation or event, or internal process which evokes positive feelings, negative feelings, or surprise (i.e., emotional experiences).
contributor: Bill Duncan
contributor: Alexander D. Diehl
contributor: Daniel W. McNeil
created: 2025-11-24T20:50:19Z

phenomenal cognitive experience
type: Class
subclass of: cognition
definition: A cognitive process during which an organism is aware of something either internal or external to itself.
contributor: Bill Duncan
contributor: Alexander D. Diehl
contributor: Daniel W. McNeil
created: 2025-11-24T20:52:17Z

Axiom
annotated source: phenomenal cognitive experience
annotated property: definition
annotated target: A cognitive process during which an organism is aware of something either internal or external to itself.
definition source: https://dictionary.apa.org/consciousness

emotional experience (feeling)
type: Class
equivalent class: Class
  intersection of: phenomenal cognitive experience
  intersection of: Restriction
    on property: part of
    some values from: emotion process
subclass of: phenomenal cognitive experience
subclass of: Restriction
  on property: part of
  some values from: emotion process
definition: A phenomenal cognitive experience evaluated as pleasant or unpleasant.
contributor: Bill Duncan
contributor: Alexander D. Diehl
contributor: Daniel W. McNeil
created: 2025-11-24T20:52:39Z

Axiom
annotated source: emotional experience (feeling)
annotated property: definition
annotated target: A phenomenal cognitive experience evaluated as pleasant or unpleasant.
definition source: https://dictionary.apa.org/feeling

sensory experience
type: Class
subclass of: phenomenal cognitive experience
definition: A phenomenal cognitive experience produced by the parts of the nervous sysem involved in awareness of the external world (i.e., external stimulus) or changes to internal organs. A sensory experience does not necessarily entail the existence phenomenon experiences (e.g., hallucinations).
contributor: Bill Duncan
contributor: Alexander D. Diehl
contributor: Daniel W. McNeil
created: 2025-11-24T20:59:47Z

Axiom
annotated source: sensory experience
annotated property: definition
annotated target: A phenomenal cognitive experience produced by the parts of the nervous sysem involved in awareness of the external world (i.e., external stimulus) or changes to internal organs. A sensory experience does not necessarily entail the existence phenomenon experiences (e.g., hallucinations).
definition source: https://dictionary.apa.org/sensation

temporomandibular joint pain
type: Class
equivalent class: Class
  intersection of: orofacial pain
  intersection of: Restriction
    on property: experienced in
    some values from: temporomandibular joint
subclass of: orofacial pain
subclass of: Restriction
  on property: experienced in
  some values from: temporomandibular joint
definition: Pain that is experienced in the temporomandibular joint.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2026-03-17T13:10:32Z
has exact synonym: TMJ pain

concomitant continuous pain
type: Class
subclass of: chronic pain
definition: Chronic pain that is persistently occuring in the background.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2026-04-08T16:42:44Z

Axiom
annotated source: concomitant continuous pain
annotated property: definition
annotated target: Chronic pain that is persistently occuring in the background.
definition source: PMID:32791919

somatic pain
type: Class
subclass of: localized pain
definition: Pain that is experienced in the skin, muscles, joints, and bones.
contributor: Bill Duncan
created: 2026-04-08T18:15:23Z

Axiom
annotated source: somatic pain
annotated property: definition
annotated target: Pain that is experienced in the skin, muscles, joints, and bones.
definition source: https://www.verywellhealth.com/what-is-somatic-pain-2564619

obsolete pain testing procedure
type: Class
subclass of: obsolete class
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temperature pain testing procedure
type: Class
subclass of: obsolete pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete heat pain testing procedure
type: Class
subclass of: obsolete temperature pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete cold pain testing procedure
type: Class
subclass of: obsolete temperature pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temporal summation pain testing procedure
type: Class
subclass of: obsolete pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temporal summation of heat pain testing procedure
type: Class
subclass of: obsolete heat pain testing procedure
subclass of: obsolete temporal summation of temperature pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temporal summation of cold pain testing procedure
type: Class
subclass of: obsolete cold pain testing procedure
subclass of: obsolete temporal summation of temperature pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete pressure pain testing procedure
type: Class
subclass of: obsolete pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete punctate pain testing procedure
type: Class
subclass of: obsolete pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temporal summation of punctate pain testing procedure
type: Class
subclass of: obsolete temporal summation pain testing procedure
subclass of: obsolete punctate pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete temporal summation of temperature pain testing procedure
type: Class
subclass of: obsolete temperature pain testing procedure
subclass of: obsolete temporal summation pain testing procedure
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete pain sensitivity
type: Class
subclass of: obsolete class
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete pain questionnaire
type: Class
subclass of: obsolete class
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete In Vivo Coping Questionnaire
type: Class
subclass of: obsolete pain questionnaire
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete Pain Vigilance and Awareness Questionnaire
type: Class
subclass of: obsolete pain questionnaire
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete pain scale score
type: Class
subclass of: obsolete class
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete Kohn Reactivity Scale
type: Class
subclass of: obsolete pain scale score
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete Graded Chronic Pain Scale
type: Class
subclass of: obsolete pain scale score
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete Likert Scale
type: Class
subclass of: obsolete pain scale score
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete Western Ontario and McMaster Universities Osteoarthritis Index
type: Class
subclass of: obsolete pain scale score
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

obsolete widespread condition questionnaire
type: Class
subclass of: obsolete pain questionnaire
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
deprecated: true

pain
type: Class
subclass of: emotional experience (feeling)
subclass of: sensory experience
subclass of: Restriction
  on property: causally downstream of
  some values from: sensory perception of pain
definition: An unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage.
contributor: Bill Duncan
created: 2024-06-13T18:46:52Z
comment: Six key notes and etymology: - Pain is always a personal experience that is influenced to varying degrees by biological, psychological, and social factors. - Pain and nociception are different phenomena. Pain cannot be inferred solely from activity in sensory neurons. - Through their life experiences, individuals learn the concept of pain. - A person’s report of an experience as pain should be respected. - Although pain usually serves an adaptive role, it may have adverse effects on function and social and psychological well-being. - Verbal description is only one of several behaviors to express pain; inability to communicate does not negate the possibility that a human or a nonhuman animal experiences pain.
comment: The "emotional" part of pain captures the affective (i.e., unpleasant) dimension of experiencing pain.
see also: - The Revised IASP definition of pain: concepts, challenges, and compromises. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7680716/ - Merskey H, Albe-Fessard DG, Bonica JJ, et al: Pain terms: A list with definitions and notes on usage. Recommended by the IASP Subcommittee on Taxonomy. Pain 1979; 6:249-252. http://www.iasp-pain.org/source/eforums.

Axiom
annotated source: pain
annotated property: definition
annotated target: An unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage.
definition source: https://www.iasp-pain.org/resources/terminology/

idiopathic pain
type: Class
subclass of: pain
definition: Pain without known cause or of spontaneous origin.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2026-04-08T17:09:41Z

Axiom
annotated source: idiopathic pain
annotated property: definition
annotated target: Pain without known cause or of spontaneous origin.
definition source: https://dictionary.apa.org/idiopathic

episodic pain
type: Class
subclass of: pain
definition: Acute transient pain that is severe and has an intensity that flares over baseline.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2026-04-08T17:10:12Z
has related synonym: breakthrough pain
related match: NCIT C9203

Axiom
annotated source: episodic pain
annotated property: definition
annotated target: Acute transient pain that is severe and has an intensity that flares over baseline.
definition source: PMID:16675817

chronic pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: chronic
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: chronic
definition: Pain that persists for three months or longer.
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
comment: In many cases, the pain is initially caused by tissue damage or disease. The continuation of the pain is often the result of pathological changes in the central nervous system.

Axiom
annotated source: chronic pain
annotated property: definition
annotated target: Pain that persists for three months or longer.
definition source: https://www.iasp-pain.org/advocacy/definitions-of-chronic-pain-syndromes/

nociceptive pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: enabled by
    some values from: pain receptor cell
  intersection of: Restriction
    on property: causally downstream of
    some values from: response to pain
subclass of: pain
subclass of: Restriction
  on property: enabled by
  some values from: pain receptor cell
subclass of: Restriction
  on property: causally downstream of
  some values from: response to pain
definition: Pain that arises from actual or threatened damage to non-neural tissue and is due to the activation of nociceptors.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2024-06-13T18:47:03Z
note: The term is used to describe pain occurring with a normally functioning somatosensory nervous system to contrast with the abnormal function seen in neuropathic or nociplasitic pain.

Axiom
annotated source: nociceptive pain
annotated property: definition
annotated target: Pain that arises from actual or threatened damage to non-neural tissue and is due to the activation of nociceptors.
definition source: https://www.iasp-pain.org/resources/terminology/

sensation quality
type: Class
subclass of: process quality
subclass of: Restriction
  on property: characteristic of
  some values from: sensory experience
definition: A process quality that is the characteristic of a sensory experience.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:02:29Z

nociplastic pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has part
    some values from: sensitization
subclass of: pain
subclass of: Restriction
  on property: has part
  some values from: sensitization
definition: Pain that arises from altered nociception despite no clear evidence of actual or threatened tissue damage causing the activation of peripheral nociceptors or evidence for disease or lesion of the somatosensory system causing the pain.
contributor: Bill Duncan
created: 2024-06-13T18:47:11Z

Axiom
annotated source: nociplastic pain
annotated property: definition
annotated target: Pain that arises from altered nociception despite no clear evidence of actual or threatened tissue damage causing the activation of peripheral nociceptors or evidence for disease or lesion of the somatosensory system causing the pain.
definition source: https://www.iasp-pain.org/resources/terminology/

neuropathic pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: causally related to
    some values from: damaged neural tissue
subclass of: pain
subclass of: Restriction
  on property: causally related to
  some values from: damaged neural tissue
definition: Pain caused by a lesion or disease of the somatosensory nervous system.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2024-06-13T18:47:32Z
note: Neuropathic pain is a clinical description (and not a diagnosis) which requires a demonstrable lesion or a disease that satisfies established neurological diagnostic criteria. The term lesion is commonly used when diagnostic investigations (e.g. imaging, neurophysiology, biopsies, lab tests) reveal an abnormality or when there was obvious trauma.
note: Somatosensory refers to information about the body per se including visceral organs, rather than information about the external world (e.g., vision, hearing, or olfaction). The presence of symptoms or signs (e.g., touch-evoked pain) alone does not justify the use of the term neuropathic. Some disease entities, such as trigeminal neuralgia, are currently defined by their clinical presentation rather than by objective diagnostic testing. Other diagnoses such as postherpetic neuralgia are normally based upon the history. It is common when investigating neuropathic pain that diagnostic testing may yield inconclusive or even inconsistent data. In such instances, clinical judgment is required to reduce the totality of findings in a patient into one putative diagnosis or concise group of diagnoses.

Axiom
annotated source: neuropathic pain
annotated property: definition
annotated target: Pain caused by a lesion or disease of the somatosensory nervous system.
definition source: https://www.iasp-pain.org/resources/terminology/

damaged neural tissue
type: Class
equivalent class: Class
  intersection of: neural tissue
  intersection of: Restriction
    on property: has characteristic
    some values from: damaged
subclass of: neural tissue
subclass of: Restriction
  on property: has characteristic
  some values from: damaged
contributor: Bill Duncan
created: 2024-06-13T20:45:30Z

central nervous system neuropathic pain
type: Class
subclass of: neuropathic pain
definition: Pain caused by a lesion or disease of the central somatosensory nervous system.
contributor: Bill Duncan
created: 2024-06-13T21:22:21Z

Axiom
annotated source: central nervous system neuropathic pain
annotated property: definition
annotated target: Pain caused by a lesion or disease of the central somatosensory nervous system.
definition source: https://www.iasp-pain.org/resources/terminology/

dull sensation quality
type: Class
subclass of: sensation quality
definition: A sensation quality that characterizes a sensation as being persistent, deep, or nagging rather than a sharp or stabbing.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:02:36Z

Axiom
annotated source: dull sensation quality
annotated property: definition
annotated target: A sensation quality that characterizes a sensation as being persistent, deep, or nagging rather than a sharp or stabbing.
definition source: https://www.healthline.com/health/dull-pain
definition source: https://www.merriam-webster.com/dictionary/dull

generalized pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: distributed
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: distributed
definition: Pain that is experienced throughout the body rather than in a specific area.
contributor: Bill Duncan
created: 2026-04-12T22:16:38Z
has exact synonym: widespread pain

peripheral nervous system neuropathic pain
type: Class
subclass of: neuropathic pain
definition: Pain caused by a lesion or disease of the peripheral somatosensory nervous system.
contributor: Bill Duncan
created: 2024-06-13T21:22:44Z

Axiom
annotated source: peripheral nervous system neuropathic pain
annotated property: definition
annotated target: Pain caused by a lesion or disease of the peripheral somatosensory nervous system.
definition source: https://www.iasp-pain.org/resources/terminology/

acute pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: acute
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: acute
definition: Pain that happens suddenly, starts out sharp or intense, and serves as a warning sign of disease or threat to the body.
contributor: Bill Duncan
creation date: 2022-11-24T06:02:26Z
comment: Acute pain is caused by injury, surgery, illness, trauma, or painful medical procedures and generally lasts from a few minutes to less than six months. Acute pain usually disappears whenever the underlying cause is treated or healed.

Axiom
annotated source: acute pain
annotated property: definition
annotated target: Pain that happens suddenly, starts out sharp or intense, and serves as a warning sign of disease or threat to the body.
definition source: https://www.iasp-pain.org/resources/topics/acute-pain/

referred pain
type: Class
subclass of: pain
definition: Pain that is experienced in an area different from the area stimulated.
contributor: Bill Duncan
created: 2024-06-13T21:22:52Z

Axiom
annotated source: referred pain
annotated property: definition
annotated target: Pain that is experienced in an area different from the area stimulated.
definition source: PMID:37448749
definition source: https://dictionary.apa.org/referred-sensation

phantom limb pain
type: Class
subclass of: pain
subclass of: Restriction
  on property: experienced as
  some values from: localized pain
definition: Pain that is experienced in an area where a limb no longer exists.
contributor: Bill Duncan
created: 2024-06-13T21:23:11Z

localized pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: localized
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: localized
definition: Pain that is confined or restricted to a particular anatomical area (or zone) of the body.
contributor: Bill Duncan
created: 2024-06-13T21:27:59Z

Axiom
annotated source: localized pain
annotated property: definition
annotated target: Pain that is confined or restricted to a particular anatomical area (or zone) of the body.
definition source: PMID:18077092
definition source: https://ospinamedical.com/orthopedic-blog/localized-vs-radicular-pain-decoding-your-discomfort

knee osteoarthritis pain
type: Class
subclass of: knee pain
definition: knee pain resulting from knee osteoarthritis.
contributor: Bill Duncan
created: 2024-06-13T21:33:51Z

throbbing sensation quality
type: Class
subclass of: sensation quality
definition: A rhythmic, pulsating, or beating sensation quality in which the intensity waxes and wanes in periodic bursts.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:06:15Z

burning sensation quality
type: Class
subclass of: sensation quality
definition: A intense, searing, or hot sensation quality.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:06:31Z

lower back pain
type: Class
equivalent class: Class
  intersection of: back pain
  intersection of: Restriction
    on property: experienced in
    some values from: lower back
subclass of: back pain
subclass of: Restriction
  on property: experienced in
  some values from: lower back
definition: Pain that is experienced in the lower back.
contributor: Bill Duncan
created: 2026-03-17T03:22:33Z

stump pain
type: Class
subclass of: localized pain
definition: Pain that is experienced in the area proximal to an amputation site.
contributor: Bill Duncan
created: 2025-04-28T16:45:26Z
has exact synonym: residual limb pain

freezing sensation quality
type: Class
subclass of: sensation quality
definition: A sensation quality that characterizes a sensation as being intensely cold, typically accompanied by qualities of stillness, heaviness, numbness, and in extreme cases a paradoxical burning or painful character.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:06:51Z

shooting sensation quality
type: Class
subclass of: sensation quality
definition: A sudden, intense, and sharp sensation quality.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:07:06Z

sharp sensation quality
type: Class
subclass of: sensation quality
definition: A piercing, stabbling, cutting, or prickling sensation quality.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:08:02Z

intense sensation quality
type: Class
subclass of: sensation quality
definition: A great or extreme sensation quality.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:08:30Z
related match: ExO_0000065
related match: FBcv_0000169
related match: SIO_001212

Axiom
annotated source: intense sensation quality
annotated property: definition
annotated target: A great or extreme sensation quality.
definition source: https://www.merriam-webster.com/dictionary/intense

aching sensation quality
type: Class
subclass of: sensation quality
definition: A diffuse, sustained, low-to-moderate intensity, dull, deep, pressure-like sensation quality that lacks sharp localization.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:08:36Z

stabbing sensation quality
type: Class
subclass of: sensation quality
definition: An intense, sudden, and sharp sensation, often described as a knife-like or shooting, sensation quality that pierces a specific area.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:09:02Z

stabbing pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: stabbing sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: stabbing sensation quality
definition: Pain experienced as an intense, sudden, and sharp sensation, often described as a knife-like or shooting pain that pierces a specific body area.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:09:33Z

sharp pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: sharp sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: sharp sensation quality
definition: Pain that is experienced as piercing, stabbling, cutting, or prickling.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:09:47Z

dull pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: dull sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: dull sensation quality
definition: Pain that is experienced as a deep ache, pressure, or heaviness rather than a sharp, stabbing sensation.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:09:53Z

Axiom
annotated source: dull pain
annotated property: definition
annotated target: Pain that is experienced as a deep ache, pressure, or heaviness rather than a sharp, stabbing sensation.
definition source: https://www.healthline.com/health/dull-pain

burning pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: burning sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: burning sensation quality
definition: Pain that is experienced as an intense, searing, or hot sensation.
contributor: Bill Duncan
created: 2025-05-12T17:10:00Z

freezing pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: freezing sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: freezing sensation quality
definition: Pain that is experienced as a burning or aching sensation and is the result of cold stimuli.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:10:18Z

shooting pain
type: Class
equivalent class: Class
  intersection of: pain
  intersection of: Restriction
    on property: has characteristic
    some values from: shooting sensation quality
subclass of: pain
subclass of: Restriction
  on property: has characteristic
  some values from: shooting sensation quality
definition: Pain that is experienced as a sudden, intense, and sharp sensation that moves or radiates through the body, often from one point to another.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-05-12T17:10:35Z

limb pain
type: Class
equivalent class: Class
  intersection of: localized pain
  intersection of: Restriction
    on property: experienced in
    some values from: limb segment
subclass of: localized pain
subclass of: Restriction
  on property: experienced in
  some values from: limb segment
definition: Pain that is experienced in a limb, such as an arm or leg.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-06-23T16:57:24Z

finger pain
type: Class
equivalent class: Class
  intersection of: hand pain
  intersection of: Restriction
    on property: experienced in
    some values from: manual digit
subclass of: hand pain
subclass of: Restriction
  on property: experienced in
  some values from: manual digit
definition: Pain that is experienced in the finger.
contributor: Bill Duncan
created: 2025-06-23T16:57:32Z

lower limb pain
type: Class
equivalent class: Class
  intersection of: limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: lower limb segment
subclass of: limb pain
subclass of: Restriction
  on property: experienced in
  some values from: lower limb segment
definition: Pain that is experienced in a lower limb.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-06-23T16:57:36Z

axial pain
type: Class
equivalent class: Class
  intersection of: localized pain
  intersection of: Restriction
    on property: experienced in
    some values from: main body axis
subclass of: localized pain
subclass of: Restriction
  on property: experienced in
  some values from: main body axis
definition: Pain that is experienced in the main axis of the body.
contributor: Bill Duncan
created: 2025-06-23T16:58:46Z

back pain
type: Class
equivalent class: Class
  intersection of: axial pain
  intersection of: Restriction
    on property: experienced in
    some values from: dorsum
subclass of: axial pain
subclass of: Restriction
  on property: experienced in
  some values from: dorsum
definition: Pain that is experienced in the back.
contributor: Bill Duncan
created: 2025-06-23T16:59:01Z

neck pain
type: Class
equivalent class: Class
  intersection of: axial pain
  intersection of: Restriction
    on property: experienced in
    some values from: neck
subclass of: axial pain
subclass of: Restriction
  on property: experienced in
  some values from: neck
contributor: Bill Duncan
created: 2025-06-23T16:59:08Z

upper limb pain
type: Class
equivalent class: Class
  intersection of: limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: upper limb segment
subclass of: limb pain
subclass of: Restriction
  on property: experienced in
  some values from: upper limb segment
definition: Pain that is experienced in an upper limb.
contributor: Bill Duncan
created: 2025-06-23T16:59:31Z

hand pain
type: Class
equivalent class: Class
  intersection of: upper limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: manus
subclass of: upper limb pain
subclass of: Restriction
  on property: experienced in
  some values from: manus
definition: Pain that is experienced in the hand.
contributor: Bill Duncan
created: 2025-06-23T17:01:00Z

elbow pain
type: Class
equivalent class: Class
  intersection of: upper limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: elbow
subclass of: upper limb pain
subclass of: Restriction
  on property: experienced in
  some values from: elbow
definition: Pain that is experienced in the elbow.
contributor: Bill Duncan
created: 2025-06-23T17:01:20Z

shoulder pain
type: Class
equivalent class: Class
  intersection of: upper limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: shoulder
subclass of: upper limb pain
subclass of: Restriction
  on property: experienced in
  some values from: shoulder
definition: Pain that is experienced in the shoulder.
contributor: Bill Duncan
created: 2025-06-23T17:01:25Z

foot pain
type: Class
equivalent class: Class
  intersection of: lower limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: pes
subclass of: lower limb pain
subclass of: Restriction
  on property: experienced in
  some values from: pes
definition: Pain that is experienced in the foot.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-06-23T17:01:49Z

toe pain
type: Class
equivalent class: Class
  intersection of: foot pain
  intersection of: Restriction
    on property: experienced in
    some values from: pedal digit
subclass of: foot pain
subclass of: Restriction
  on property: experienced in
  some values from: pedal digit
definition: Pain that is experienced in the toe.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2025-06-23T17:01:54Z

head pain
type: Class
equivalent class: Class
  intersection of: localized pain
  intersection of: Restriction
    on property: experienced in
    some values from: skull
subclass of: localized pain
subclass of: Restriction
  on property: experienced in
  some values from: skull
definition: Pain that is experienced in the head.
contributor: Bill Duncan
created: 2025-06-23T17:02:29Z

orofacial pain
type: Class
equivalent class: Class
  intersection of: head pain
  intersection of: Class
    union of: Restriction
      on property: experienced in
      some values from: mouth
    union of: Restriction
      on property: experienced in
      some values from: face
subclass of: head pain
definition: Pain that is experienced in the orofacial region, which includes the mouth and face.
contributor: Bill Duncan
contributor: Ava E. Cunningham
created: 2025-06-23T17:02:39Z

visceral pain
type: Class
subclass of: localized pain
definition: Pain that is experienced in the internal organs.
contributor: Bill Duncan
created: 2025-06-23T17:05:02Z

Axiom
annotated source: visceral pain
annotated property: definition
annotated target: Pain that is experienced in the internal organs.
definition source: https://www.ncbi.nlm.nih.gov/books/NBK12991/
source: PMID:26516492

chronic widespread pain
type: Class
equivalent class: Class
  intersection of: chronic pain
  intersection of: Restriction
    on property: has characteristic
    some values from: distributed
subclass of: chronic pain
subclass of: generalized pain
definition: Chronic pain that is diffuse and experienced in body regions and in at least 3 or more body quadrants (as defined by upper-lower/left-right side of the body) and axial skeleton (neck, back, chest, and abdomen).
contributor: Bill Duncan
created: 2025-06-23T17:11:58Z
comment: Chronic widespread pain (CWP) is associated with significant emotional distress (anxiety, anger/frustration or depressed mood) or functional disability (interference in daily life activities and reduced participation in social roles). CWP is multifactorial: biological, psychological and social factors contribute to the pain syndrome. The diagnosis is appropriate when the pain is not directly attributable to a nociceptive process in these regions and there are features consistent with nociplastic pain and identified psychological and social contributors.
note: Additional criteria to consider: - Include quantrants/regions of body in the definition. - E.g., >= 3 quadrants & axial - >= 4 body regions - Use the notion of functional region instead of regions divided by joints. define as chronic & multi-localized.

Axiom
annotated source: chronic widespread pain
annotated property: definition
annotated target: Chronic pain that is diffuse and experienced in body regions and in at least 3 or more body quadrants (as defined by upper-lower/left-right side of the body) and axial skeleton (neck, back, chest, and abdomen).
definition source: PMID:39445928
definition source: https://www.findacode.com/icd-11/code-849253504.html

Axiom
annotated source: chronic widespread pain
annotated property: comment
annotated target: Chronic widespread pain (CWP) is associated with significant emotional distress (anxiety, anger/frustration or depressed mood) or functional disability (interference in daily life activities and reduced participation in social roles). CWP is multifactorial: biological, psychological and social factors contribute to the pain syndrome. The diagnosis is appropriate when the pain is not directly attributable to a nociceptive process in these regions and there are features consistent with nociplastic pain and identified psychological and social contributors.
source: https://www.findacode.com/icd-11/code-849253504.html

upper back pain
type: Class
equivalent class: Class
  intersection of: back pain
  intersection of: Restriction
    on property: experienced in
    some values from: thoracic region of vertebral column
subclass of: back pain
subclass of: Restriction
  on property: experienced in
  some values from: thoracic region of vertebral column
definition: Pain that is experienced in the upper back.
contributor: Bill Duncan
created: 2026-03-17T03:22:41Z

knee pain
type: Class
equivalent class: Class
  intersection of: lower limb pain
  intersection of: Restriction
    on property: experienced in
    some values from: knee
subclass of: lower limb pain
subclass of: Restriction
  on property: experienced in
  some values from: knee
definition: Pain that is experienced in the knee.
contributor: http://orcid.org/0000-0001-9625-1899
created: 2026-03-17T03:25:24Z

process
type: Class
BFO_0000179: process
BFO_0000180: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: 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])
has associated axiom(fol): (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]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity

realizable entity
type: Class
subclass of: characteristic

material entity
type: Class
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being

cell
type: Class
subclass of: anatomical structure
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has cross-reference: CALOHA:TS-2035
has cross-reference: FBbt:00007002
has cross-reference: FMA:68646
has cross-reference: GO:0005623
has cross-reference: KUPO:0000002
has cross-reference: MESH:D002477
has cross-reference: VHOG:0001533
has cross-reference: WBbt:0004017
has cross-reference: XAO:0003012
has cross-reference: ZFA:0009000
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset
in subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: definition
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has cross-reference: CARO:mah

Axiom
annotated source: cell
annotated property: has cross-reference
annotated target: FBbt:00007002
mapping justification: ManualMappingCuration

Axiom
annotated source: cell
annotated property: has cross-reference
annotated target: ZFA:0009000
mapping justification: UnspecifiedMatching

neuronal receptor cell
type: Class
subclass of: sensory neuron
subclass of: sensory receptor cell
definition: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
has cross-reference: ZFA:0009001
has exact synonym: neuronal receptor cell (sensu Animalia)
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset

Axiom
annotated source: neuronal receptor cell
annotated property: definition
annotated target: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
has cross-reference: FBC:Autogenerated

Axiom
annotated source: neuronal receptor cell
annotated property: has cross-reference
annotated target: ZFA:0009001
mapping justification: UnspecifiedMatching

neuron associated cell
type: Class
subclass of: neural cell
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset

sensory neuron
type: Class
subclass of: afferent neuron
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
RO_0002175: NCBITaxon 9606
has cross-reference: BTO:0001037
has cross-reference: FBbt:00005124
has cross-reference: FMA:84649
has cross-reference: MESH:D011984
has cross-reference: WBbt:0005759
has cross-reference: ZFA:0009053
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset
in subset: human reference atlas

Axiom
annotated source: sensory neuron
annotated property: definition
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
has cross-reference: ISBN:0721662544

Axiom
annotated source: sensory neuron
annotated property: has cross-reference
annotated target: FBbt:00005124
mapping justification: ManualMappingCuration

Axiom
annotated source: sensory neuron
annotated property: has cross-reference
annotated target: ZFA:0009053
mapping justification: UnspecifiedMatching

glial cell
type: Class
subclass of: neuron associated cell
definition: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
RO_0002175: NCBITaxon 9606
description: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
has cross-reference: BTO:0002606
has cross-reference: CALOHA:TS-0415
has cross-reference: FBbt:00005144
has cross-reference: FMA:54536
has cross-reference: ZFA:0009073
has exact synonym: neuroglial cell
has related synonym: neuroglia
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset
in subset: human reference atlas
comment: Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571

Axiom
annotated source: glial cell
annotated property: definition
annotated target: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
has cross-reference: MESH:D009457

Axiom
annotated source: glial cell
annotated property: description
annotated target: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
has cross-reference: DOI:10.1002/glia.24343
has cross-reference: DOI:10.1038/nn1988
has cross-reference: DOI:10.1101/cshperspect.a020602
has cross-reference: DOI:10.1126/science.aat0473
has cross-reference: DOI:10.3389/fncel.2017.00024

Axiom
annotated source: glial cell
annotated property: has cross-reference
annotated target: FBbt:00005144
mapping justification: ManualMappingCuration

Axiom
annotated source: glial cell
annotated property: has cross-reference
annotated target: ZFA:0009073
mapping justification: UnspecifiedMatching

glial cell on CELLxGENE CellGuide
type: Axiom
annotated source: glial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000125

sensory receptor cell
type: Class
subclass of: eukaryotic cell
definition: A cell that is capable of detection of a stimulus involved in sensory perception.
has cross-reference: MESH:D011984
has exact synonym: receptor cell
in subset: human subset
in subset: mouse subset

pain receptor cell
type: Class
subclass of: neuronal receptor cell
definition: The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.
has cross-reference: ZFA:0009119
has exact synonym: nociceptor
has exact synonym: nocireceptor
in subset: human subset
in subset: mouse subset
comment: Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship

Axiom
annotated source: pain receptor cell
annotated property: definition
annotated target: The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.
has cross-reference: MESH:D009619

Axiom
annotated source: pain receptor cell
annotated property: has cross-reference
annotated target: ZFA:0009119
mapping justification: UnspecifiedMatching

Axiom
annotated source: pain receptor cell
annotated property: has exact synonym
annotated target: nociceptor

Axiom
annotated source: pain receptor cell
annotated property: has exact synonym
annotated target: nocireceptor

electrically active cell
type: Class
subclass of: cell
definition: A cell whose function is determined by the generation or the reception of an electric signal.
has cross-reference: ZFA:0009128
in subset: human subset
in subset: mouse subset

Axiom
annotated source: electrically active cell
annotated property: definition
annotated target: A cell whose function is determined by the generation or the reception of an electric signal.
has cross-reference: FB:ma

Axiom
annotated source: electrically active cell
annotated property: has cross-reference
annotated target: ZFA:0009128
mapping justification: UnspecifiedMatching

eukaryotic cell
type: Class
subclass of: cell
definition: Any cell that in taxon some Eukaryota.
has cross-reference: MESH:D005057
in subset: human subset
in subset: mouse subset

Axiom
annotated source: eukaryotic cell
annotated property: definition
annotated target: Any cell that in taxon some Eukaryota.
has cross-reference: FBC:Autogenerated

electrically responsive cell
type: Class
subclass of: electrically active cell
definition: A cell whose function is determined by its response to an electric signal.
has cross-reference: ZFA:0009190
in subset: human subset
in subset: mouse subset

Axiom
annotated source: electrically responsive cell
annotated property: definition
annotated target: A cell whose function is determined by its response to an electric signal.
has cross-reference: FB:ma

Axiom
annotated source: electrically responsive cell
annotated property: has cross-reference
annotated target: ZFA:0009190
mapping justification: UnspecifiedMatching

electrically signaling cell
type: Class
subclass of: electrically active cell
definition: A cell that initiates an electrical signal and passes that signal to another cell.
has cross-reference: ZFA:0009193
in subset: human subset
in subset: mouse subset

Axiom
annotated source: electrically signaling cell
annotated property: definition
annotated target: A cell that initiates an electrical signal and passes that signal to another cell.
has cross-reference: FB:ma

Axiom
annotated source: electrically signaling cell
annotated property: has cross-reference
annotated target: ZFA:0009193
mapping justification: UnspecifiedMatching

afferent neuron
type: Class
subclass of: neuron
definition: A neuron which conveys sensory information centrally from the periphery.
RO_0002175: NCBITaxon 9606
has cross-reference: FMA:87653
has cross-reference: ZFA:0009238
has exact synonym: input neuron
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset
in subset: human reference atlas

Axiom
annotated source: afferent neuron
annotated property: definition
annotated target: A neuron which conveys sensory information centrally from the periphery.
has cross-reference: GOC:tfm
has cross-reference: MESH:D009475

Axiom
annotated source: afferent neuron
annotated property: has cross-reference
annotated target: ZFA:0009238
mapping justification: UnspecifiedMatching

neuron
type: Class
subclass of: electrically responsive cell
subclass of: electrically signaling cell
subclass of: neural cell
subclass of: Restriction
  on property: capable of
  some values from: transmission of nerve impulse
definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
RO_0002175: NCBITaxon 9606
has cross-reference: BTO:0000938
has cross-reference: CALOHA:TS-0683
has cross-reference: FBbt:00005106
has cross-reference: FMA:54527
has cross-reference: VHOG:0001483
has cross-reference: WBbt:0003679
has cross-reference: ZFA:0009248
has exact synonym: nerve cell
in subset: cellxgene subset
in subset: human subset
in subset: mouse subset
in subset: human reference atlas
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

Axiom
annotated source: neuron
annotated property: definition
annotated target: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
has cross-reference: MESH:D009474
has cross-reference: http://en.wikipedia.org/wiki/Neuron

Axiom
annotated source: neuron
annotated property: has cross-reference
annotated target: FBbt:00005106
mapping justification: ManualMappingCuration

Axiom
annotated source: neuron
annotated property: has cross-reference
annotated target: ZFA:0009248
mapping justification: UnspecifiedMatching

unimodal nocireceptor
type: Class
subclass of: pain receptor cell
in subset: human subset
in subset: mouse subset

polymodal nocireceptor
type: Class
subclass of: pain receptor cell
in subset: human subset
in subset: mouse subset

neural cell
type: Class
subclass of: eukaryotic cell
definition: A cell that is part of the nervous system.
contributor: https://orcid.org/0000-0003-1980-3228
creation date: 2010-09-15T01:34:57Z
has cross-reference: CALOHA:TS-2040
has cross-reference: FMA:70333
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human subset
in subset: mouse subset

Axiom
annotated source: neural cell
annotated property: definition
annotated target: A cell that is part of the nervous system.
has cross-reference: GOC:tfm
has cross-reference: ISBN:0618947256

characteristic
type: Class

action potential
type: Class
subclass of: regulation of membrane potential
definition: A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
has OBO namespace: biological_process
id: GO:0001508
comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.

Axiom
annotated source: action potential
annotated property: definition
annotated target: A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
has cross-reference: GOC:dph
has cross-reference: GOC:go_curators
has cross-reference: GOC:tb
has cross-reference: ISBN:978-0-07-139011-8

system process
type: Class
subclass of: multicellular organismal process
definition: A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
RO_0002161: NCBITaxon 2
RO_0002161: NCBITaxon 2157
RO_0002161: NCBITaxon 4896
RO_0002161: NCBITaxon 4932
has exact synonym: organ system process
has OBO namespace: biological_process
id: GO:0003008

Axiom
annotated source: system process
annotated property: definition
annotated target: A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
has cross-reference: GOC:mtg_cardio

response to stress
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
term tracker item: https://github.com/geneontology/go-ontology/issues/26810
has OBO namespace: biological_process
has related synonym: response to abiotic stress
has related synonym: response to biotic stress
id: GO:0006950
in subset: goslim candida
in subset: goslim chembl
in subset: goslim drosophila
in subset: goslim metagenomics
in subset: goslim plant
in subset: goslim plant ribbon

Axiom
annotated source: response to stress
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
has cross-reference: GOC:mah

sensory perception
type: Class
subclass of: nervous system process
definition: The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has cross-reference: Reactome:R-HSA-9709957
has cross-reference: Wikipedia:Perception
has OBO namespace: biological_process
id: GO:0007600
in subset: goslim drosophila

Axiom
annotated source: sensory perception
annotated property: definition
annotated target: The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has cross-reference: GOC:ai
has cross-reference: GOC:dph

Sensory Perception
type: Axiom
annotated source: sensory perception
annotated property: has cross-reference
annotated target: Reactome:R-HSA-9709957

behavior
type: Class
subclass of: multicellular organismal process
definition: 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.
created by: jl
creation date: 2012-09-20T14:06:08Z
has alternative id: GO:0023032
has alternative id: GO:0044708
has alternative id: GO:0044709
has cross-reference: Wikipedia:Behavior
has exact synonym: behavioral response to stimulus
has exact synonym: behaviour
has exact synonym: behavioural response to stimulus
has OBO namespace: biological_process
has related synonym: single-organism behavior
id: GO:0007610
in subset: gocheck do not annotate
in subset: goslim agr
in subset: goslim flybase ribbon
comment: 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).
preferred label: behavioral response to stimulus

Axiom
annotated source: behavior
annotated property: definition
annotated target: 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.
has cross-reference: GOC:ems
has cross-reference: GOC:jl
has cross-reference: ISBN:0395448956
has cross-reference: PMID:20160973

learning or memory
type: Class
subclass of: behavior
subclass of: cognition
definition: The acquisition and processing of information and/or the storage and retrieval of this information over time.
has OBO namespace: biological_process
id: GO:0007611

Axiom
annotated source: learning or memory
annotated property: definition
annotated target: The acquisition and processing of information and/or the storage and retrieval of this information over time.
has cross-reference: GOC:jid
has cross-reference: PMID:8938125

learning
type: Class
subclass of: learning or memory
definition: Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
has cross-reference: Wikipedia:Learning
has OBO namespace: biological_process
id: GO:0007612

Axiom
annotated source: learning
annotated property: definition
annotated target: Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
has cross-reference: ISBN:0582227089
has cross-reference: ISBN:0721662544

biological_process
type: Class
subclass of: process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
created by: jl
creation date: 2012-09-19T15:05:24Z
has alternative id: GO:0000004
has alternative id: GO:0007582
has alternative id: GO:0044699
has cross-reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has OBO namespace: biological_process
has related synonym: single organism process
has related synonym: single-organism process
id: GO:0008150
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
has cross-reference: GOC:pdt

response to temperature stimulus
type: Class
subclass of: response to abiotic stimulus
definition: 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 temperature stimulus.
has exact synonym: response to thermal stimulus
has OBO namespace: biological_process
id: GO:0009266

Axiom
annotated source: response to temperature stimulus
annotated property: definition
annotated target: 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 temperature stimulus.
has cross-reference: GOC:hb

detection of external stimulus
type: Class
subclass of: response to external stimulus
subclass of: detection of stimulus
definition: The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
has OBO namespace: biological_process
has related synonym: perception of external stimulus
id: GO:0009581

Axiom
annotated source: detection of external stimulus
annotated property: definition
annotated target: The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
has cross-reference: GOC:hb

detection of abiotic stimulus
type: Class
subclass of: response to abiotic stimulus
subclass of: detection of stimulus
definition: The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
has OBO namespace: biological_process
has related synonym: perception of abiotic stimulus
id: GO:0009582

Axiom
annotated source: detection of abiotic stimulus
annotated property: definition
annotated target: The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
has cross-reference: GOC:hb

detection of chemical stimulus
type: Class
subclass of: detection of stimulus
definition: The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
has exact synonym: chemoperception
has exact synonym: detection of chemical substance
has OBO namespace: biological_process
has related synonym: chemoreception
has related synonym: perception of chemical stimulus
has related synonym: perception of chemical substance
id: GO:0009593

Axiom
annotated source: detection of chemical stimulus
annotated property: definition
annotated target: The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
has cross-reference: GOC:jl

response to external stimulus
type: Class
subclass of: response to stimulus
definition: 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.
has exact synonym: response to environmental stimulus
has OBO namespace: biological_process
id: GO:0009605
in subset: gocheck do not annotate
in subset: goslim drosophila
in subset: goslim plant
comment: 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.

Axiom
annotated source: response to external stimulus
annotated property: definition
annotated target: 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.
has cross-reference: GOC:hb

response to mechanical stimulus
type: Class
subclass of: response to external stimulus
subclass of: response to abiotic stimulus
definition: 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 mechanical stimulus.
has exact synonym: mechanical stimulus response
has OBO namespace: biological_process
has related synonym: chemi-mechanical coupling
id: GO:0009612

Axiom
annotated source: response to mechanical stimulus
annotated property: definition
annotated target: 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 mechanical stimulus.
has cross-reference: GOC:hb

response to abiotic stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
term tracker item: https://github.com/geneontology/go-ontology/issues/16572
has narrow synonym: response to abiotic stress
has OBO namespace: biological_process
id: GO:0009628
in subset: gocheck do not annotate
in subset: goslim metagenomics
in subset: goslim plant
comment: 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.

Axiom
annotated source: response to abiotic stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
has cross-reference: GOC:hb

detection of temperature stimulus
type: Class
subclass of: response to temperature stimulus
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus
definition: The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal.
has exact synonym: detection of temperature
has exact synonym: detection of thermal stimulus
has OBO namespace: biological_process
has related synonym: perception of temperature
id: GO:0016048

Axiom
annotated source: detection of temperature stimulus
annotated property: definition
annotated target: The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal.
has cross-reference: GOC:hb

transmission of nerve impulse
type: Class
subclass of: nervous system process
definition: The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
has exact synonym: conduction of nerve impulse
has exact synonym: signal transmission along a neuron
has OBO namespace: biological_process
id: GO:0019226

Axiom
annotated source: transmission of nerve impulse
annotated property: definition
annotated target: The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
has cross-reference: GOC:curators
has cross-reference: ISBN:0815316194

Axiom
annotated source: transmission of nerve impulse
annotated property: has exact synonym
annotated target: conduction of nerve impulse
has cross-reference: GOC:dph

neuronal action potential
type: Class
subclass of: action potential
definition: An action potential that occurs in a neuron.
has OBO namespace: biological_process
has related synonym: generation of action potential
id: GO:0019228

Axiom
annotated source: neuronal action potential
annotated property: definition
annotated target: An action potential that occurs in a neuron.
has cross-reference: GOC:dph
has cross-reference: GOC:isa_complete
has cross-reference: GOC:tb

Axiom
annotated source: neuronal action potential
annotated property: has related synonym
annotated target: generation of action potential
has cross-reference: GOC:dph
has cross-reference: GOC:tb

sensory perception of pain
type: Class
subclass of: sensory perception
definition: The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. A painful stimulus is any physical or chemical event that has the potential to cause tissue damage (actual or perceived) and activates the nociceptive system.
term tracker item: https://github.com/geneontology/go-ontology/issues/29807
has cross-reference: Wikipedia:Nociception
has narrow synonym: perception of physiological pain
has OBO namespace: biological_process
has related synonym: nociception
id: GO:0019233

Axiom
annotated source: sensory perception of pain
annotated property: definition
annotated target: The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. A painful stimulus is any physical or chemical event that has the potential to cause tissue damage (actual or perceived) and activates the nociceptive system.
has cross-reference: GOC:curators

sensory perception of fast pain
type: Class
subclass of: sensory perception of pain
definition: The series of events required for an organism to receive a fast pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Fast pain is often subjectively described as a sharp or stabbing pain; in humans, the signals from a fast pain stimulus are perceived and relayed along myelinated A-delta fibers to the central nervous system, reaching their target in about 0.1 seconds.
has OBO namespace: biological_process
id: GO:0019234

Axiom
annotated source: sensory perception of fast pain
annotated property: definition
annotated target: The series of events required for an organism to receive a fast pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Fast pain is often subjectively described as a sharp or stabbing pain; in humans, the signals from a fast pain stimulus are perceived and relayed along myelinated A-delta fibers to the central nervous system, reaching their target in about 0.1 seconds.
has cross-reference: PMID:38704307

sensory perception of slow pain
type: Class
subclass of: sensory perception of pain
definition: The series of events required for an organism to receive a slow pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Slow pain is often subjectively described as an aching or throbbing pain; in humans, the signals from a slow pain stimulus are perceived and relayed along unmyelinated C fibers to the central nervous system, reaching their target in about 1 second. Slow pain is often associated with tissue destruction.
has OBO namespace: biological_process
id: GO:0019235

Axiom
annotated source: sensory perception of slow pain
annotated property: definition
annotated target: The series of events required for an organism to receive a slow pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Slow pain is often subjectively described as an aching or throbbing pain; in humans, the signals from a slow pain stimulus are perceived and relayed along unmyelinated C fibers to the central nervous system, reaching their target in about 1 second. Slow pain is often associated with tissue destruction.
has cross-reference: PMID:38704307
has cross-reference: http://www.people.vcu.edu/~mikuleck/ssspain/

multicellular organismal process
type: Class
subclass of: biological_process
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
RO_0002161: NCBITaxon 2
RO_0002161: NCBITaxon 2157
RO_0002161: NCBITaxon 4896
RO_0002161: NCBITaxon 4932
created by: jl
creation date: 2012-09-19T16:07:47Z
has alternative id: GO:0044707
has alternative id: GO:0050874
has exact synonym: organismal physiological process
has OBO namespace: biological_process
has related synonym: single-multicellular organism process
id: GO:0032501
in subset: gocheck do not annotate
in subset: goslim pir
comment: 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.

Axiom
annotated source: multicellular organismal process
annotated property: definition
annotated target: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
has cross-reference: GOC:curators
has cross-reference: GOC:dph
has cross-reference: GOC:isa_complete
has cross-reference: GOC:tb

multicellular organismal response to stress
type: Class
subclass of: response to stress
subclass of: multicellular organismal process
definition: Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
has OBO namespace: biological_process
id: GO:0033555

Axiom
annotated source: multicellular organismal response to stress
annotated property: definition
annotated target: Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
has cross-reference: GOC:mah

regulation of membrane potential
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
has OBO namespace: biological_process
id: GO:0042391

Axiom
annotated source: regulation of membrane potential
annotated property: definition
annotated target: Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
has cross-reference: GOC:jl
has cross-reference: GOC:mtg_cardio
has cross-reference: GOC:tb
has cross-reference: ISBN:0198506732

nonassociative learning
type: Class
subclass of: learning
definition: A simple form of learning whereby the repeated presence of a stimulus leads to a change in the probability or strength of the response to that stimulus. There is no association of one type of stimulus with another, rather it is a generalized response to the environment.
has exact synonym: unconditional response
has OBO namespace: biological_process
id: GO:0046958

Axiom
annotated source: nonassociative learning
annotated property: definition
annotated target: A simple form of learning whereby the repeated presence of a stimulus leads to a change in the probability or strength of the response to that stimulus. There is no association of one type of stimulus with another, rather it is a generalized response to the environment.
has cross-reference: ISBN:0582227089

sensitization
type: Class
subclass of: nonassociative learning
definition: An increased in a behavioral response to a repeated stimulus. For example, a shock to the tail of the marine snail Aplysia, to which the snail responds by withdrawing its gill, will result in increased gill withdrawal the next time the skin is touched.
has cross-reference: Wikipedia:Sensitization
has OBO namespace: biological_process
id: GO:0046960

Axiom
annotated source: sensitization
annotated property: definition
annotated target: An increased in a behavioral response to a repeated stimulus. For example, a shock to the tail of the marine snail Aplysia, to which the snail responds by withdrawing its gill, will result in increased gill withdrawal the next time the skin is touched.
has cross-reference: ISBN:0582227089

response to pain
type: Class
subclass of: multicellular organismal response to stress
definition: 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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
has alternative id: GO:0048267
has exact synonym: physiological response to pain
has OBO namespace: biological_process
id: GO:0048265

Axiom
annotated source: response to pain
annotated property: definition
annotated target: 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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
has cross-reference: GOC:jid
has cross-reference: PMID:10203867
has cross-reference: PMID:12723742
has cross-reference: PMID:12843304
has cross-reference: Wikipedia:Pain

behavioral response to pain
type: Class
subclass of: behavior
subclass of: Restriction
  on property: part of
  some values from: response to pain
definition: Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
has exact synonym: behavioural response to pain
has OBO namespace: biological_process
id: GO:0048266

Axiom
annotated source: behavioral response to pain
annotated property: definition
annotated target: Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
has cross-reference: GOC:jid

nervous system process
type: Class
subclass of: system process
definition: An organ system process carried out by any of the organs or tissues of the neurological system.
term tracker item: https://github.com/geneontology/go-ontology/issues/13824
has exact synonym: neurological system process
has exact synonym: neurophysiological process
has OBO namespace: biological_process
has related synonym: pan-neural process
id: GO:0050877
in subset: goslim agr
in subset: goslim chembl
in subset: goslim flybase ribbon
in subset: goslim generic
in subset: goslim pir

Axiom
annotated source: nervous system process
annotated property: definition
annotated target: An organ system process carried out by any of the organs or tissues of the neurological system.
has cross-reference: GOC:ai
has cross-reference: GOC:mtg_cardio

cognition
type: Class
subclass of: nervous system process
definition: The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
has cross-reference: Wikipedia:Cognition
has OBO namespace: biological_process
id: GO:0050890
in subset: goslim drosophila
preferred label: cognitive process

Axiom
annotated source: cognition
annotated property: definition
annotated target: The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
has cross-reference: ISBN:0721619908

sensory processing
type: Class
subclass of: cognition
subclass of: Restriction
  on property: part of
  some values from: sensory perception
definition: Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect.
has OBO namespace: biological_process
id: GO:0050893

Axiom
annotated source: sensory processing
annotated property: definition
annotated target: Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect.
has cross-reference: GOC:dph
has cross-reference: ISBN:0721662544

determination of affect
type: Class
subclass of: sensory processing
definition: Any process in which an emotional response is associated with a particular sensory stimulation.
has OBO namespace: biological_process
id: GO:0050894

Axiom
annotated source: determination of affect
annotated property: definition
annotated target: Any process in which an emotional response is associated with a particular sensory stimulation.
has cross-reference: GOC:ai
has cross-reference: GOC:dph
has cross-reference: ISBN:0721662544

response to stimulus
type: Class
subclass of: biological_process
definition: 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.
has alternative id: GO:0051869
has exact synonym: physiological response to stimulus
has OBO namespace: biological_process
id: GO:0050896
in subset: gocheck do not annotate
in subset: goslim agr
in subset: goslim flybase ribbon
in subset: goslim mouse
in subset: goslim pir
in subset: goslim prokaryote
in subset: goslim prokaryote ribbon
comment: 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.

Axiom
annotated source: response to stimulus
annotated property: definition
annotated target: 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.
has cross-reference: GOC:ai
has cross-reference: GOC:bf

detection of stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of stimulus
subclass of: Restriction
  on property: part of
  some values from: sensory perception
definition: The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
has cross-reference: Wikipedia:Transduction_(physiology)
has exact synonym: sensory detection of stimulus
has exact synonym: sensory perception, sensory transduction of stimulus
has exact synonym: sensory perception, stimulus detection
has exact synonym: sensory transduction
has OBO namespace: biological_process
id: GO:0050906

Axiom
annotated source: detection of stimulus involved in sensory perception
annotated property: definition
annotated target: The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai
has cross-reference: GOC:dos
has cross-reference: GOC:dph

detection of chemical stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of chemical stimulus
subclass of: detection of stimulus involved in sensory perception
definition: The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception.
has exact synonym: sensory detection of chemical stimulus
has exact synonym: sensory detection of chemical stimulus during sensory perception
has exact synonym: sensory perception, sensory detection of chemical stimulus
has exact synonym: sensory perception, sensory transduction of chemical stimulus
has exact synonym: sensory transduction of chemical stimulus
has exact synonym: sensory transduction of chemical stimulus during sensory perception
has OBO namespace: biological_process
id: GO:0050907

Axiom
annotated source: detection of chemical stimulus involved in sensory perception
annotated property: definition
annotated target: The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

detection of temperature stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of temperature stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of temperature stimulus
subclass of: detection of stimulus involved in sensory perception
definition: The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception.
has exact synonym: sensory detection of temperature stimulus
has exact synonym: sensory detection of temperature stimulus during sensory perception
has exact synonym: sensory detection of thermal stimulus during sensory perception
has exact synonym: sensory perception, sensory detection of temperature stimulus
has exact synonym: sensory perception, sensory detection of thermal stimulus
has exact synonym: sensory perception, sensory transduction of temperature stimulus
has exact synonym: sensory perception, sensory transduction of thermal stimulus
has exact synonym: sensory transduction of temperature stimulus
has exact synonym: sensory transduction of temperature stimulus during sensory perception
has exact synonym: sensory transduction of thermal stimulus during sensory perception
has narrow synonym: sensory detection of heat stimulus during sensory perception
has narrow synonym: sensory perception, sensory detection of heat stimulus
has narrow synonym: sensory perception, sensory transduction of heat stimulus
has narrow synonym: sensory transduction of heat stimulus during sensory perception
has OBO namespace: biological_process
id: GO:0050961

Axiom
annotated source: detection of temperature stimulus involved in sensory perception
annotated property: definition
annotated target: The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

detection of temperature stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of temperature stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of temperature stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of pain
definition: The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal.
has exact synonym: perception of pain, detection of temperature stimulus
has exact synonym: perception of pain, sensory detection of temperature stimulus
has exact synonym: perception of pain, sensory transduction of temperature stimulus
has exact synonym: sensory detection of temperature stimulus during perception of pain
has exact synonym: sensory detection of thermal stimulus during sensory perception of pain
has exact synonym: sensory perception of pain, sensory detection of thermal stimulus
has exact synonym: sensory perception of pain, sensory transduction of thermal stimulus
has exact synonym: sensory transduction of temperature stimulus during perception of pain
has exact synonym: sensory transduction of thermal stimulus during sensory perception of pain
has OBO namespace: biological_process
has related synonym: thermal nociception
id: GO:0050965

Axiom
annotated source: detection of temperature stimulus involved in sensory perception of pain
annotated property: definition
annotated target: The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

Axiom
annotated source: detection of temperature stimulus involved in sensory perception of pain
annotated property: has related synonym
annotated target: thermal nociception
has cross-reference: GOC:pr

detection of mechanical stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of mechanical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of pain
definition: The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal.
has exact synonym: perception of pain, detection of mechanical stimulus
has exact synonym: perception of pain, sensory detection of mechanical stimulus
has exact synonym: perception of pain, sensory transduction of mechanical stimulus
has exact synonym: sensory detection of mechanical stimulus during perception of pain
has exact synonym: sensory transduction of mechanical stimulus during perception of pain
has OBO namespace: biological_process
has related synonym: mechanical nociception
id: GO:0050966

Axiom
annotated source: detection of mechanical stimulus involved in sensory perception of pain
annotated property: definition
annotated target: The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

Axiom
annotated source: detection of mechanical stimulus involved in sensory perception of pain
annotated property: has related synonym
annotated target: mechanical nociception
has cross-reference: GOC:pr

obsolete detection of electrical stimulus involved in sensory perception of pain
type: Class
subclass of: obsolete detection of stimulus involved in sensory perception of pain
definition: OBSOLETE. The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal.
term tracker item: https://github.com/geneontology/go-ontology/issues/31306
has exact synonym: perception of pain, detection of electrical stimulus
has exact synonym: perception of pain, sensory detection of electrical stimulus
has exact synonym: perception of pain, sensory transduction of electrical stimulus
has OBO namespace: biological_process
has related synonym: detection of electrical stimulus during sensory perception of pain
has related synonym: sensory detection of electrical stimulus during perception of pain
has related synonym: sensory transduction of electrical stimulus during perception of pain
id: GO:0050967
comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
deprecated: true

Axiom
annotated source: obsolete detection of electrical stimulus involved in sensory perception of pain
annotated property: definition
annotated target: OBSOLETE. The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai
has cross-reference: GOC:dos
has cross-reference: GOC:dph
has cross-reference: GOC:tb

Axiom
annotated source: obsolete detection of electrical stimulus involved in sensory perception of pain
annotated property: has related synonym
annotated target: detection of electrical stimulus during sensory perception of pain
has cross-reference: GOC:dph
has cross-reference: GOC:tb

detection of chemical stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of chemical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of pain
definition: The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal.
has exact synonym: perception of pain, detection of chemical stimulus
has exact synonym: perception of pain, sensory detection of chemical stimulus
has exact synonym: perception of pain, sensory transduction of chemical stimulus
has exact synonym: sensory detection of chemical stimulus during perception of pain
has exact synonym: sensory transduction of chemical stimulus during perception of pain
has OBO namespace: biological_process
has related synonym: chemical nociception
id: GO:0050968

Axiom
annotated source: detection of chemical stimulus involved in sensory perception of pain
annotated property: definition
annotated target: The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai

Axiom
annotated source: detection of chemical stimulus involved in sensory perception of pain
annotated property: has related synonym
annotated target: chemical nociception
has cross-reference: GOC:pr

detection of mechanical stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of stimulus involved in sensory perception
subclass of: detection of mechanical stimulus
definition: The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception.
has exact synonym: sensory detection of mechanical stimulus
has exact synonym: sensory detection of mechanical stimulus during sensory perception
has exact synonym: sensory perception, sensory detection of mechanical stimulus
has exact synonym: sensory perception, sensory transduction of mechanical stimulus
has exact synonym: sensory transduction of mechanical stimulus
has exact synonym: sensory transduction of mechanical stimulus during sensory perception
has OBO namespace: biological_process
id: GO:0050974

Axiom
annotated source: detection of mechanical stimulus involved in sensory perception
annotated property: definition
annotated target: The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

detection of mechanical stimulus
type: Class
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus
subclass of: response to mechanical stimulus
definition: The series of events by which a mechanical stimulus is received and converted into a molecular signal.
has OBO namespace: biological_process
id: GO:0050982

Axiom
annotated source: detection of mechanical stimulus
annotated property: definition
annotated target: The series of events by which a mechanical stimulus is received and converted into a molecular signal.
has cross-reference: GOC:ai
has cross-reference: GOC:dos

detection of stimulus
type: Class
subclass of: response to stimulus
definition: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
has exact synonym: stimulus detection
has OBO namespace: biological_process
has related synonym: perception of stimulus
has related synonym: stimulus sensing
id: GO:0051606
in subset: goslim pir

Axiom
annotated source: detection of stimulus
annotated property: definition
annotated target: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
has cross-reference: GOC:add
has cross-reference: GOC:ai
has cross-reference: GOC:dph
has cross-reference: GOC:mah

obsolete detection of stimulus involved in sensory perception of pain
type: Class
subclass of: obsolete class
definition: OBSOLETE. The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal.
term tracker item: https://github.com/geneontology/go-ontology/issues/31330
created by: dph
creation date: 2019-09-13T13:48:47Z
has OBO namespace: biological_process
id: GO:0062149
comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
deprecated: true

Axiom
annotated source: obsolete detection of stimulus involved in sensory perception of pain
annotated property: definition
annotated target: OBSOLETE. The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal.
has cross-reference: PMID:19837031

biological regulation
type: Class
subclass of: biological_process
definition: Any process that modulates a measurable attribute of any biological process, quality or function.
has broad synonym: regulation
has OBO namespace: biological_process
id: GO:0065007
in subset: gocheck do not annotate
in subset: goslim pir

Axiom
annotated source: biological regulation
annotated property: definition
annotated target: Any process that modulates a measurable attribute of any biological process, quality or function.
has cross-reference: GOC:dph
has cross-reference: GOC:isa_complete
has cross-reference: GOC:mah
has cross-reference: GOC:pr
has cross-reference: GOC:vw

regulation of biological quality
type: Class
subclass of: biological regulation
definition: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
term tracker item: https://github.com/geneontology/go-ontology/issues/30599
has exact synonym: regulation of biological attribute
has exact synonym: regulation of biological characteristic
has OBO namespace: biological_process
id: GO:0065008
in subset: gocheck do not annotate
in subset: goslim pir

Axiom
annotated source: regulation of biological quality
annotated property: definition
annotated target: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
has cross-reference: GOC:dph
has cross-reference: GOC:isa_complete
has cross-reference: GOC:mah
has cross-reference: GOC:pr
has cross-reference: GOC:vw

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has OBO namespace: quality
id: PATO:0000051
in subset: attribute slim

Axiom
annotated source: morphology
annotated property: definition
annotated target: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has cross-reference: PATOC:GVG

spatial pattern
type: Class
subclass of: morphology
definition: A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
has alternative id: PATO:0000132
has alternative id: PATO:0001565
has exact synonym: distribution
has OBO namespace: quality
has related synonym: pattern
id: PATO:0000060
in subset: attribute slim
in subset: hpo slim

Axiom
annotated source: spatial pattern
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
has cross-reference: PATOC:GVG

structure
type: Class
subclass of: morphology
definition: 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.
has alternative id: PATO:0001452
has broad synonym: conformation
has exact synonym: relational structural quality
has OBO namespace: quality
id: PATO:0000141
in subset: attribute slim

Axiom
annotated source: structure
annotated property: definition
annotated target: 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.
has cross-reference: PATOC:GVG

Axiom
annotated source: structure
annotated property: has broad synonym
annotated target: conformation
has cross-reference: VT:1000738

acute
type: Class
subclass of: duration
definition: A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
RO_0002604: chronic
has OBO namespace: quality
id: PATO:0000389
in subset: hpo slim
in subset: mpath slim
in subset: value slim

Axiom
annotated source: acute
annotated property: definition
annotated target: A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
has cross-reference: dictionary:reference

localized
type: Class
subclass of: spatial pattern
definition: A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location.
has exact synonym: focal
has exact synonym: localised
has OBO namespace: quality
id: PATO:0000627
in subset: hpo slim
in subset: mpath slim
in subset: value slim

Axiom
annotated source: localized
annotated property: definition
annotated target: A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location.
has cross-reference: WordNet:WordNet

damage
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled.
has OBO namespace: quality
id: PATO:0001020
in subset: attribute slim

Axiom
annotated source: damage
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled.
has cross-reference: WordNet:WordNet

damaged
type: Class
subclass of: damage
definition: A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
RO_0002604: PATO_0001168
has OBO namespace: quality
id: PATO:0001167
in subset: value slim

Axiom
annotated source: damaged
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
has cross-reference: WordNet:WordNet

process quality
type: Class
subclass of: characteristic
disjoint with: physical object quality
definition: A quality which inheres in an process.
has alternative id: PATO:0001239
has alternative id: PATO:0001240
has exact synonym: quality of a process
has exact synonym: quality of occurrent
has exact synonym: quality of process
has exact synonym: relational quality of occurrent
has OBO namespace: quality
id: PATO:0001236
comment: See comments of relational quality of a physical entity.

Axiom
annotated source: process quality
annotated property: definition
annotated target: A quality which inheres in an process.
has cross-reference: PATOC:GVG

physical object quality
type: Class
subclass of: characteristic
definition: A quality which inheres in a continuant.
has alternative id: PATO:0001237
has alternative id: PATO:0001238
has cross-reference: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has OBO namespace: quality
id: PATO:0001241
comment: 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.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has cross-reference: PATOC:GVG

duration
type: Class
subclass of: physical quality of a process
definition: A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
has alternative id: PATO:0000081
has exact synonym: period
has OBO namespace: quality
has related synonym: time
id: PATO:0001309
in subset: attribute slim
in subset: hpo slim

Axiom
annotated source: duration
annotated property: definition
annotated target: A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
has cross-reference: PATOC:mellybelly

distributed
type: Class
subclass of: spatial pattern
definition: A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up.
RO_0002604: PATO_0001567
has alternative id: PATO:0001513
has exact synonym: diffuse
has exact synonym: scattered
has OBO namespace: quality
id: PATO:0001566
in subset: mpath slim
in subset: value slim

Axiom
annotated source: distributed
annotated property: definition
annotated target: A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up.
has cross-reference: WordNet:WordNet

multi-localised
type: Class
subclass of: spatial pattern
definition: A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations.
has exact synonym: multi-focal
has OBO namespace: quality
id: PATO:0001791
in subset: mpath slim
in subset: value slim

Axiom
annotated source: multi-localised
annotated property: definition
annotated target: A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations.
has cross-reference: PATOC:GVG

chronic
type: Class
subclass of: duration
definition: A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
RO_0002604: acute
has OBO namespace: quality
id: PATO:0001863
in subset: hpo slim
in subset: mpath slim
in subset: value slim

Axiom
annotated source: chronic
annotated property: definition
annotated target: A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
has cross-reference: PATOC:cjm

physical quality of a process
type: Class
subclass of: process quality
contributor: 0000-0002-2061-091X
creation date: 2009-06-05T09:16:46Z
has OBO namespace: quality
id: PATO:0002062
in subset: attribute slim

peracute
type: Class
subclass of: acute
definition: Extremely acute and aggressive onset of a pathological process.
contributor: 0000-0002-2061-091X
creation date: 2012-09-15T02:57:46Z
has exact synonym: per-acute
has OBO namespace: quality
id: PATO:0002387
in subset: mpath slim
in subset: value slim

Axiom
annotated source: peracute
annotated property: definition
annotated target: Extremely acute and aggressive onset of a pathological process.
has cross-reference: PATOC:PNS

chronic-active
type: Class
subclass of: chronic
definition: A quality of duration having progressive course of indefinite duration with active, acute-like elements.
contributor: 0000-0002-2061-091X
creation date: 2012-12-17T10:59:58Z
has OBO namespace: quality
id: PATO:0002414
in subset: mpath slim
in subset: value slim

Axiom
annotated source: chronic-active
annotated property: definition
annotated target: A quality of duration having progressive course of indefinite duration with active, acute-like elements.
has cross-reference: PATOC:MPATH

spatial distribution of a process
type: Class
subclass of: physical quality of a process
definition: A physical quality of a process that is its spatial distribution. For example, bone mineralization follows stereotypical spatial distribution patterns during development, which may be altered in some phenotypes.
contributor: https://orcid.org/0000-0002-7073-9172
creation date: 2019-07-18T18:49:08Z
has OBO namespace: quality
id: PATO:0010005
in subset: attribute slim

Axiom
annotated source: spatial distribution of a process
annotated property: definition
annotated target: A physical quality of a process that is its spatial distribution. For example, bone mineralization follows stereotypical spatial distribution patterns during development, which may be altered in some phenotypes.
has cross-reference: https://orcid.org/0000-0002-7073-9172

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
RO_0002175: NCBITaxon 9606
has cross-reference: AAO:0010825
has cross-reference: AEO:0000003
has cross-reference: BILA:0000003
has cross-reference: CARO:0000003
has cross-reference: EHDAA2:0003003
has cross-reference: EMAPA:0
has cross-reference: FAO:0000001
has cross-reference: FBbt:00007001
has cross-reference: FMA:305751
has cross-reference: FMA:67135
has cross-reference: GAID:781
has cross-reference: HAO:0000003
has cross-reference: MA:0003000
has cross-reference: MESH:D000825
has cross-reference: SCTID:362889002
has cross-reference: TAO:0000037
has cross-reference: TGMA:0001823
has cross-reference: VHOG:0001759
has cross-reference: XAO:0003000
has cross-reference: ZFA:0000037
has cross-reference: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
id: UBERON:0000061
in subset: common anatomy
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has cross-reference: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: has cross-reference
annotated target: FBbt:00007001
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical structure
annotated property: has exact synonym
annotated target: connected biological structure
has cross-reference: CARO:0000003

organ
type: Class
subclass of: multicellular anatomical structure
disjoint with: multi organ part structure
definition: Anatomical structure that performs a specific function or group of functions [WP].
RO_0002161: NCBITaxon_110815
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000001: 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.
UBPROP_0000012: 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
has cross-reference: BIRNLEX:4
has cross-reference: CARO:0020004
has cross-reference: EFO:0000634
has cross-reference: EMAPA:35949
has cross-reference: ENVO:01000162
has cross-reference: FMA:67498
has cross-reference: MA:0003001
has cross-reference: NCIT:C13018
has cross-reference: SCTID:272625005
has cross-reference: UMLS:C0178784
has cross-reference: WBbt:0003760
has cross-reference: Wikipedia:Organ_(anatomy)
has related synonym: anatomical unit
has related synonym: body organ
has related synonym: element
id: UBERON:0000062
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: organ
annotated property: definition
annotated target: Anatomical structure that performs a specific function or group of functions [WP].
has cross-reference: Wikipedia:Organ_(anatomy)

Axiom
annotated source: organ
annotated property: RO_0002161
annotated target: NCBITaxon_110815
source: Wikipedia

Axiom
annotated source: organ
annotated property: UBPROP_0000001
annotated target: 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.
source: GO:0048513

Axiom
annotated source: organ
annotated property: has cross-reference
annotated target: UMLS:C0178784
source: ncithesaurus:Organ

Axiom
annotated source: organ
annotated property: has related synonym
annotated target: element
has cross-reference: http://orcid.org/0000-0002-6601-2165

organ part
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: organ
definition: A multicellular structure that is a part of an organ.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: AAO:0011124
has cross-reference: BIRNLEX:16
has cross-reference: EFO:0000635
has cross-reference: FMA:82472
has cross-reference: SCTID:113343008
has cross-reference: SCTID:91717005
has exact synonym: cardinal organ part
has related synonym: regional part of organ
id: UBERON:0000064
in subset: common anatomy
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: non informative
in subset: upper level

Axiom
annotated source: organ part
annotated property: definition
annotated target: A multicellular structure that is a part of an organ.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: organ part
annotated property: has exact synonym
annotated target: cardinal organ part
has cross-reference: FMA:82472

Axiom
annotated source: organ part
annotated property: has related synonym
annotated target: regional part of organ
has cross-reference: BIRNLEX:16

subdivision of skeletal system
type: Class
subclass of: organ system subdivision
definition: Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
has alternative id: UBERON:0010322
has cross-reference: FMA:85544
has cross-reference: NCIT:C34076
has cross-reference: SCTID:118966000
has cross-reference: UMLS:C1519343
has cross-reference: galen:ComplexSkeletalStructure
has exact synonym: skeletal system subdivision
has related synonym: skeletal system part
id: UBERON:0000075
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: subdivision of skeletal system
annotated property: definition
annotated target: Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
has cross-reference: UBERONREF:0000003
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of skeletal system
annotated property: has cross-reference
annotated target: UMLS:C1519343
source: ncithesaurus:Skeletal_System_Part

Axiom
annotated source: subdivision of skeletal system
annotated property: has exact synonym
annotated target: skeletal system subdivision
has cross-reference: FMA:85544

mouth
type: Class
subclass of: subdivision of digestive tract
definition: 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).
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
UBPROP_0000003: 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]
UBPROP_0000007: oral
UBPROP_0000011: some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
UBPROP_0000012: 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
has cross-reference: AAO:0010355
has cross-reference: BTO:0001090
has cross-reference: BTO:0004698
has cross-reference: CALOHA:TS-1315
has cross-reference: EFO:0000825
has cross-reference: EHDAA2:0001326
has cross-reference: EHDAA:542
has cross-reference: EMAPA:16262
has cross-reference: FBbt:00003126
has cross-reference: FMA:49184
has cross-reference: GAID:75
has cross-reference: MA:0000341
has cross-reference: MA:0002474
has cross-reference: MAT:0000038
has cross-reference: MESH:D009055
has cross-reference: MIAA:0000038
has cross-reference: SCTID:21082005
has cross-reference: TADS:0000040
has cross-reference: TAO:0000547
has cross-reference: TAO:0000590
has cross-reference: TGMA:0000131
has cross-reference: VHOG:0000280
has cross-reference: VHOG:0000812
has cross-reference: Wikipedia:Mouth
has cross-reference: XAO:0003029
has cross-reference: ZFA:0000547
has cross-reference: ZFA:0000590
has cross-reference: galen:Mouth
has exact synonym: regio oralis
has narrow synonym: adult mouth
has related synonym: cavital oralis
has related synonym: cavitas oris
has related synonym: cavum oris
has related synonym: mouth cavity
has related synonym: oral region
has related synonym: oral vestibule
has related synonym: rima oris
has related synonym: stoma
has related synonym: stomatodaeum
has related synonym: trophic apparatus
has related synonym: vestibule of mouth
has related synonym: vestibulum oris
id: UBERON:0000165
in subset: efo slim
in subset: human reference atlas
in subset: human subset
in subset: major organ
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: mouth
annotated property: definition
annotated target: 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).
has cross-reference: Wikipedia:Mouth
has cross-reference: https://github.com/obophenotype/uberon/wiki/The-digestive-tract

Axiom
annotated source: mouth
annotated property: UBPROP_0000001
annotated target: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010355
ontology: AAO
source: AAO:BJB

Axiom
annotated source: mouth
annotated property: UBPROP_0000003
annotated target: 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]
date retrieved: 2012-09-17
external class: VHOG:0000812
ontology: VHOG
source: DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
source: http://bgee.unil.ch/

Axiom
annotated source: mouth
annotated property: UBPROP_0000012
annotated target: 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
external ontology: FMA

Axiom
annotated source: mouth
annotated property: has cross-reference
annotated target: FBbt:00003126
mapping justification: ManualMappingCuration

Axiom
annotated source: mouth
annotated property: has exact synonym
annotated target: regio oralis
has cross-reference: BTO:0004698
has cross-reference: FMA:49184
has cross-reference: FMA:TA
has synonym type: latin term

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: cavital oralis
has cross-reference: Wikipedia:Mouth
has synonym type: latin term

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: cavitas oris
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: cavum oris
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: mouth cavity
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: oral region
has cross-reference: EHDAA2:0001326

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: oral vestibule
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: rima oris
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: stomatodaeum
has cross-reference: VHOG:0000812

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: trophic apparatus
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: vestibule of mouth
has cross-reference: BTO:0001090

Axiom
annotated source: mouth
annotated property: has related synonym
annotated target: vestibulum oris
has cross-reference: BTO:0001090

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: Anatomical entity that has mass.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: AAO:0010264
has cross-reference: AEO:0000006
has cross-reference: BILA:0000006
has cross-reference: CARO:0000006
has cross-reference: EHDAA2:0003006
has cross-reference: FBbt:00007016
has cross-reference: FMA:67165
has cross-reference: HAO:0000006
has cross-reference: TAO:0001836
has cross-reference: TGMA:0001826
has cross-reference: VHOG:0001721
id: UBERON:0000465
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
has cross-reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: material anatomical entity
annotated property: has cross-reference
annotated target: FBbt:00007016
mapping justification: ManualMappingCuration

organism subdivision
type: Class
subclass of: multicellular anatomical structure
definition: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: AAO:0010053
has cross-reference: AEO:0000032
has cross-reference: BILA:0000032
has cross-reference: BIRNLEX:7
has cross-reference: CALOHA:TS-2084
has cross-reference: CARO:0000032
has cross-reference: EFO:0000808
has cross-reference: EHDAA2:0003032
has cross-reference: EMAPA:36031
has cross-reference: FBbt:00007009
has cross-reference: FMA:7153
has cross-reference: HAO:0000032
has cross-reference: MA:0002433
has cross-reference: MAT:0000293
has cross-reference: MESH:D001829
has cross-reference: MIAA:0000293
has cross-reference: NCIT:C32221
has cross-reference: TAO:0001308
has cross-reference: TGMA:0001840
has cross-reference: UMLS:C0229962
has cross-reference: VHOG:0001758
has cross-reference: Wikipedia:Body_part
has cross-reference: XAO:0003013
has cross-reference: ZFA:0001308
has cross-reference: galen:BodyPart
has exact synonym: anatomic region
has related synonym: body part
has related synonym: body region
has related synonym: cardinal body part
id: UBERON:0000475
in subset: common anatomy
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim
in subset: upper level

Axiom
annotated source: organism subdivision
annotated property: definition
annotated target: 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.
has cross-reference: CARO:0000032
has cross-reference: CARO:DOS
has cross-reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: organism subdivision
annotated property: has cross-reference
annotated target: FBbt:00007009
mapping justification: ManualMappingCuration

Axiom
annotated source: organism subdivision
annotated property: has cross-reference
annotated target: UMLS:C0229962
source: ncithesaurus:Body_Part

Axiom
annotated source: organism subdivision
annotated property: has exact synonym
annotated target: anatomic region
has cross-reference: MA:0002433

Axiom
annotated source: organism subdivision
annotated property: has related synonym
annotated target: body region
has cross-reference: FMA:7153

Axiom
annotated source: organism subdivision
annotated property: has related synonym
annotated target: cardinal body part
has cross-reference: FMA:7153

tissue
type: Class
subclass of: multicellular anatomical structure
definition: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: AAO:0000607
has cross-reference: AAO:0010054
has cross-reference: AEO:0000043
has cross-reference: BILA:0000043
has cross-reference: BIRNLEX:19
has cross-reference: CALOHA:TS-2090
has cross-reference: CARO:0000043
has cross-reference: EHDAA2:0003043
has cross-reference: EMAPA:35868
has cross-reference: FBbt:00007003
has cross-reference: FMA:9637
has cross-reference: HAO:0000043
has cross-reference: MA:0003002
has cross-reference: MESH:D014024
has cross-reference: NCIT:C12801
has cross-reference: TAO:0001477
has cross-reference: TGMA:0001844
has cross-reference: UMLS:C0040300
has cross-reference: VHOG:0001757
has cross-reference: WBbt:0005729
has cross-reference: XAO:0003040
has cross-reference: ZFA:0001477
has cross-reference: galen:Tissue
has exact synonym: portion of tissue
has exact synonym: tissue portion
has narrow synonym: simple tissue
id: UBERON:0000479
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: upper level

Axiom
annotated source: tissue
annotated property: definition
annotated target: 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.
has cross-reference: CARO:0000043

Axiom
annotated source: tissue
annotated property: has cross-reference
annotated target: FBbt:00007003
mapping justification: ManualMappingCuration

Axiom
annotated source: tissue
annotated property: has cross-reference
annotated target: UMLS:C0040300
source: ncithesaurus:Tissue

Axiom
annotated source: tissue
annotated property: has exact synonym
annotated target: portion of tissue
has cross-reference: CARO:0000043

Axiom
annotated source: tissue
annotated property: has narrow synonym
annotated target: simple tissue
has cross-reference: AEO:0000043

neck
type: Class
subclass of: organism subdivision
definition: An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
RO_0002174: NCBITaxon_32443
UBPROP_0000007: cervical
has cross-reference: AEO:0000108
has cross-reference: BTO:0000420
has cross-reference: CALOHA:TS-2045
has cross-reference: EFO:0000967
has cross-reference: EHDAA2:0003108
has cross-reference: EMAPA:35587
has cross-reference: FMA:7155
has cross-reference: GAID:86
has cross-reference: MA:0000024
has cross-reference: MAT:0000297
has cross-reference: MESH:D009333
has cross-reference: MIAA:0000297
has cross-reference: NCIT:C13063
has cross-reference: SCTID:302550007
has cross-reference: UMLS:C0027530
has cross-reference: Wikipedia:Neck
has cross-reference: galen:Neck
has related synonym: collum
has related synonym: neck (volume)
id: UBERON:0000974
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: neck
annotated property: definition
annotated target: An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: neck
annotated property: RO_0002174
annotated target: NCBITaxon_32443
source: ISBN:9780674021839

Axiom
annotated source: neck
annotated property: has cross-reference
annotated target: UMLS:C0027530
source: ncithesaurus:Neck

Axiom
annotated source: neck
annotated property: has related synonym
annotated target: collum
has cross-reference: Wikipedia:Neck
has synonym type: latin term

Axiom
annotated source: neck
annotated property: has related synonym
annotated target: neck (volume)
has cross-reference: FMA:7155

leg
type: Class
subclass of: multi-limb segment region
subclass of: lower limb segment
definition: The portion of the hindlimb that contains both the stylopod and zeugopod.
RO_0002175: NCBITaxon 9606
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
UBPROP_0000013: The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
has cross-reference: BTO:0000721
has cross-reference: CALOHA:TS-2206
has cross-reference: EFO:0001411
has cross-reference: EHDAA2:0000972
has cross-reference: EHDAA:5151
has cross-reference: EHDAA:6176
has cross-reference: EHDAA:8289
has cross-reference: EMAPA:17489
has cross-reference: GAID:49
has cross-reference: MA:0000047
has cross-reference: MESH:D035002
has cross-reference: VHOG:0000345
has cross-reference: Wikipedia:Leg#Limb
has exact synonym: tetrapod leg
has related synonym: lower extremity
id: UBERON:0000978
in subset: efo slim
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim
comment: we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot

Axiom
annotated source: leg
annotated property: definition
annotated target: The portion of the hindlimb that contains both the stylopod and zeugopod.
has cross-reference: Wikipedia:Leg#Limb

Axiom
annotated source: leg
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000345
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: leg
annotated property: UBPROP_0000013
annotated target: The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
source: 3

Axiom
annotated source: leg
annotated property: has related synonym
annotated target: lower extremity
has cross-reference: MESH:A01.378.610

skeletal joint
type: Class
subclass of: articulation
disjoint with: bone element
definition: Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
UBPROP_0000001: Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
UBPROP_0000001: Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
has broad synonym: articulation
has broad synonym: joint
has cross-reference: AEO:0000182
has cross-reference: BTO:0001686
has cross-reference: CALOHA:TS-2023
has cross-reference: EFO:0000948
has cross-reference: EMAPA:35456
has cross-reference: FMA:7490
has cross-reference: GAID:102
has cross-reference: MA:0000319
has cross-reference: MAT:0000188
has cross-reference: MESH:D007596
has cross-reference: MIAA:0000188
has cross-reference: NCIT:C13044
has cross-reference: RETIRED_EHDAA2:0003182
has cross-reference: SCTID:302536002
has cross-reference: TAO:0000367
has cross-reference: UMLS:C0022417
has cross-reference: VHOG:0001276
has cross-reference: VSAO:0000101
has cross-reference: Wikipedia:Joint
has cross-reference: XAO:0000171
has cross-reference: ZFA:0001596
has cross-reference: galen:Joint
has related synonym: articular joint
has related synonym: joints
id: UBERON:0000982
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: skeletal joint
annotated property: definition
annotated target: Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
has cross-reference: GO_REF:0000034
has cross-reference: VSAO:0000101
has cross-reference: Wikipedia:Joint
has cross-reference: http://dx.plos.org/10.1371/journal.pone.0051070

Axiom
annotated source: skeletal joint
annotated property: UBPROP_0000001
annotated target: Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000101
ontology: VSAO
source: PSPUB:0000170

Axiom
annotated source: skeletal joint
annotated property: UBPROP_0000001
annotated target: Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000367
ontology: TAO
source: TAO:pem

Axiom
annotated source: skeletal joint
annotated property: has broad synonym
annotated target: articulation
has cross-reference: VSAO:0000101

Axiom
annotated source: skeletal joint
annotated property: has broad synonym
annotated target: joint
has cross-reference: FMA:7490
has cross-reference: VSAO:0000101

Axiom
annotated source: skeletal joint
annotated property: has cross-reference
annotated target: UMLS:C0022417
source: ncithesaurus:Joint

Axiom
annotated source: skeletal joint
annotated property: has related synonym
annotated target: articular joint
has cross-reference: BTO:0001686

Axiom
annotated source: skeletal joint
annotated property: has related synonym
annotated target: joints
has cross-reference: ZFA:0001596
has synonym type: plural form

anatomical entity
type: Class
definition: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: AAO:0010841
has cross-reference: AEO:0000000
has cross-reference: BFO:0000004
has cross-reference: BILA:0000000
has cross-reference: BIRNLEX:6
has cross-reference: CARO:0000000
has cross-reference: EHDAA2:0002229
has cross-reference: FBbt:10000000
has cross-reference: FMA:62955
has cross-reference: HAO:0000000
has cross-reference: MA:0000001
has cross-reference: NCIT:C12219
has cross-reference: TAO:0100000
has cross-reference: TGMA:0001822
has cross-reference: UMLS:C1515976
has cross-reference: WBbt:0000100
has cross-reference: XAO:0000000
has cross-reference: ZFA:0100000
id: UBERON:0001062
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: 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.
has cross-reference: FMA:62955
has cross-reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: has cross-reference
annotated target: FBbt:10000000
mapping justification: ManualMappingCuration

Axiom
annotated source: anatomical entity
annotated property: has cross-reference
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

dorsum
type: Class
subclass of: organism subdivision
definition: 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..
UBPROP_0000007: dorsal
UBPROP_0000008: 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
has cross-reference: BTO:0001713
has cross-reference: CALOHA:TS-2223
has cross-reference: EFO:0001405
has cross-reference: FMA:14181
has cross-reference: GAID:30
has cross-reference: MESH:D001415
has cross-reference: NCIT:C13062
has cross-reference: SCTID:123961009
has cross-reference: UMLS:C0004600
has cross-reference: Wikipedia:Dorsum_(anatomy)
has cross-reference: galen:Back
has exact synonym: back
has exact synonym: back of body proper
has exact synonym: dorsal part of organism
id: UBERON:0001137
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: uberon slim

Axiom
annotated source: dorsum
annotated property: definition
annotated target: 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..
has cross-reference: BSPO:0000063
has cross-reference: UBERONREF:0000006
has cross-reference: Wikipedia:Dorsum_(anatomy)

Axiom
annotated source: dorsum
annotated property: has cross-reference
annotated target: UMLS:C0004600
source: ncithesaurus:Back

Axiom
annotated source: dorsum
annotated property: has exact synonym
annotated target: back
has cross-reference: FMA:14181

Axiom
annotated source: dorsum
annotated property: has exact synonym
annotated target: back of body proper
has cross-reference: FMA:14181

subdivision of head
type: Class
subclass of: organism subdivision
has cross-reference: FMA:24218
has cross-reference: SCTID:123852005
has cross-reference: XAO:0000040
has exact synonym: head subdivision
has related synonym: head region
has related synonym: region of head
id: UBERON:0001444
in subset: human subset
in subset: mouse subset
in subset: non informative

face
type: Class
subclass of: subdivision of head
definition: 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).
UBPROP_0000001: Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
UBPROP_0000001: The area that extends from the median ocellus to the oral foramen[HAO].
UBPROP_0000007: facial
UBPROP_0000011: 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)
has cross-reference: BTO:0003369
has cross-reference: CALOHA:TS-2216
has cross-reference: EMAPA:32763
has cross-reference: FMA:24728
has cross-reference: GAID:64
has cross-reference: HAO:0000316
has cross-reference: MA:0002473
has cross-reference: MESH:D005145
has cross-reference: NCIT:C13071
has cross-reference: SCTID:302549007
has cross-reference: UMLS:C0015450
has cross-reference: Wikipedia:Face
has cross-reference: galen:Face
has related synonym: facia/facies
has related synonym: visage
id: UBERON:0001456
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: face
annotated property: definition
annotated target: 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).
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: face
annotated property: UBPROP_0000001
annotated target: Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
source: FMA:24728

Axiom
annotated source: face
annotated property: UBPROP_0000001
annotated target: The area that extends from the median ocellus to the oral foramen[HAO].
source: HAO:0000316
source: http://api.hymao.org/api/ref/67791
taxon: NCBITaxon:7399

Axiom
annotated source: face
annotated property: UBPROP_0000011
annotated target: 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)
source: vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf

Axiom
annotated source: face
annotated property: has cross-reference
annotated target: UMLS:C0015450
source: ncithesaurus:Face

Axiom
annotated source: face
annotated property: has related synonym
annotated target: facia/facies
has cross-reference: Wikipedia:Face
has synonym type: latin term

Axiom
annotated source: face
annotated property: has related synonym
annotated target: visage
has cross-reference: BTO:0003369

arm
type: Class
subclass of: multi-limb segment region
subclass of: upper limb segment
definition: The part of the forelimb extending from the shoulder to the autopod[cjm].
UBPROP_0000003: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
has cross-reference: BTO:0001435
has cross-reference: CALOHA:TS-2204
has cross-reference: EFO:0001410
has cross-reference: EHDAA2:0000140
has cross-reference: EHDAA:4164
has cross-reference: EHDAA:6210
has cross-reference: EHDAA:8275
has cross-reference: EMAPA:17413
has cross-reference: GAID:52
has cross-reference: MA:0000033
has cross-reference: MESH:D001132
has cross-reference: VHOG:0000339
has cross-reference: Wikipedia:Arm
has related synonym: brachium
has related synonym: upper extremity
id: UBERON:0001460
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: arm
annotated property: definition
annotated target: The part of the forelimb extending from the shoulder to the autopod[cjm].
has cross-reference: Wikipedia:Arm

Axiom
annotated source: arm
annotated property: UBPROP_0000003
annotated target: Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000339
ontology: VHOG
source: ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
source: http://bgee.unil.ch/

Axiom
annotated source: arm
annotated property: has related synonym
annotated target: brachium
has cross-reference: Wikipedia:Arm
has synonym type: latin term

Axiom
annotated source: arm
annotated property: has related synonym
annotated target: upper extremity
has cross-reference: MESH:A01.378.800

elbow
type: Class
subclass of: upper limb segment
subclass of: Restriction
  on property: part of
  some values from: arm
definition: The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].
UBPROP_0000007: cubital
UBPROP_0000013: Naming conventions for pod terms under discussion within phenoscape group
has cross-reference: CALOHA:TS-2222
has cross-reference: EFO:0003069
has cross-reference: EHDAA2:0000429
has cross-reference: EHDAA:4166
has cross-reference: EHDAA:6212
has cross-reference: EMAPA:17414
has cross-reference: FMA:24901
has cross-reference: GAID:54
has cross-reference: MA:0000036
has cross-reference: MESH:D004550
has cross-reference: SCTID:76248009
has cross-reference: VHOG:0000340
has cross-reference: Wikipedia:Elbow
has cross-reference: galen:Elbow
has exact synonym: cubital region
has exact synonym: elbow limb segment
has exact synonym: elbow region
has related synonym: articulatio cubiti
id: UBERON:0001461
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: elbow
annotated property: definition
annotated target: The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].
has cross-reference: Wikipedia:Elbow

Axiom
annotated source: elbow
annotated property: has related synonym
annotated target: articulatio cubiti
has cross-reference: Wikipedia:Elbow
has synonym type: latin term

knee
type: Class
subclass of: lower limb segment
subclass of: Restriction
  on property: part of
  some values from: leg
definition: A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
RO_0002175: NCBITaxon 9606
has cross-reference: BTO:0003595
has cross-reference: CALOHA:TS-2220
has cross-reference: EHDAA2:0000895
has cross-reference: EHDAA:5159
has cross-reference: EHDAA:6184
has cross-reference: EMAPA:17493
has cross-reference: FMA:24974
has cross-reference: GAID:48
has cross-reference: MA:0000046
has cross-reference: MESH:D007717
has cross-reference: SCTID:361291001
has cross-reference: VHOG:0000347
has cross-reference: galen:Knee
has exact synonym: knee region
id: UBERON:0001465
in subset: efo slim
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: knee
annotated property: definition
annotated target: A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
has cross-reference: https://orcid.org/0000-0002-6601-2165

pedal digit
type: Class
equivalent class: Class
  intersection of: digit
  intersection of: Restriction
    on property: part of
    some values from: pes
subclass of: digit
subclass of: Restriction
  on property: part of
  some values from: pes
definition: A digit that is part of a pes (foot).
has alternative id: UBERON:0000027
has cross-reference: AAO:0000888
has cross-reference: BTO:0002348
has cross-reference: EMAPA:32649
has cross-reference: FMA:25046
has cross-reference: GAID:44
has cross-reference: MA:0000048
has cross-reference: NCIT:C33788
has cross-reference: SCTID:116667001
has cross-reference: UMLS:C0040357
has cross-reference: Wikipedia:Toe
has cross-reference: XAO:0003035
has cross-reference: galen:Toe
has exact synonym: digit of foot
has exact synonym: digit of terminal segment of lower limb
has exact synonym: digiti pedis
has exact synonym: digitus pedis
has exact synonym: foot digit
has exact synonym: hind digit
has exact synonym: hind_digit
has exact synonym: hindlimb digit
has exact synonym: pedal digit (phalangeal portion) plus soft tissue
has exact synonym: pes digit
has exact synonym: toe
has related synonym: digiti pedis
has related synonym: digitipedis
id: UBERON:0001466
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: pedal digit
annotated property: definition
annotated target: A digit that is part of a pes (foot).
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: pedal digit
annotated property: has cross-reference
annotated target: UMLS:C0040357
source: ncithesaurus:Toe

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: digit of terminal segment of lower limb
has cross-reference: OBOL:automatic

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: digiti pedis
has cross-reference: FMA:70664
has cross-reference: FMA:TA
has synonym type: plural form

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: foot digit
has cross-reference: MA:0000048

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: hind digit
has cross-reference: XAO:0003035

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: hind_digit
has cross-reference: AAO:0000888

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: pedal digit (phalangeal portion) plus soft tissue
has cross-reference: http://orcid.org/0000-0002-6601-2165
has synonym type: COMPARATIVE PREFERRED

Axiom
annotated source: pedal digit
annotated property: has exact synonym
annotated target: toe
has cross-reference: FMA:25046

Axiom
annotated source: pedal digit
annotated property: has related synonym
annotated target: digiti pedis
has cross-reference: Wikipedia:Toe
has synonym type: latin term

Axiom
annotated source: pedal digit
annotated property: has related synonym
annotated target: digitipedis
has cross-reference: BTO:0002348

shoulder
type: Class
subclass of: organism subdivision
definition: A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).
UBPROP_0000003: (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]
UBPROP_0000012: In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
has cross-reference: CALOHA:TS-2229
has cross-reference: EFO:0003068
has cross-reference: EHDAA2:0001834
has cross-reference: EHDAA:4180
has cross-reference: EHDAA:6228
has cross-reference: EMAPA:17421
has cross-reference: FMA:25202
has cross-reference: GAID:60
has cross-reference: MA:0000038
has cross-reference: MESH:D012782
has cross-reference: NCIT:C25203
has cross-reference: SCTID:361103004
has cross-reference: UMLS:C0037004
has cross-reference: VHOG:0000342
has cross-reference: Wikipedia:Shoulder
has cross-reference: galen:Shoulder
has exact synonym: shoulder region
has related synonym: articulatio humeri
id: UBERON:0001467
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: shoulder
annotated property: definition
annotated target: A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: shoulder
annotated property: UBPROP_0000003
annotated target: (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000342
ontology: VHOG
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332
source: http://bgee.unil.ch/

Axiom
annotated source: shoulder
annotated property: UBPROP_0000012
annotated target: In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
external ontology: FMA

Axiom
annotated source: shoulder
annotated property: has cross-reference
annotated target: UMLS:C0037004
source: ncithesaurus:Shoulder

Axiom
annotated source: shoulder
annotated property: has related synonym
annotated target: articulatio humeri
has cross-reference: Wikipedia:Shoulder
has synonym type: latin term

bone element
type: Class
subclass of: skeletal element
disjoint with: paired limb/fin segment
definition: Skeletal element that is composed of bone tissue.
RO_0002171: UBERON_0001015
RO_0002171: UBERON_0001630
RO_0002171: UBERON_0002385
UBPROP_0000001: Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
UBPROP_0000001: Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
UBPROP_0000001: Skeletal element that is composed of bone tissue.[VSAO]
UBPROP_0000002: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
UBPROP_0000003: The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
has cross-reference: AAO:0000047
has cross-reference: AEO:0000082
has cross-reference: BTO:0000140
has cross-reference: CALOHA:TS-0088
has cross-reference: EFO:0000298
has cross-reference: EHDAA2:0003082
has cross-reference: EMAPA:32782
has cross-reference: ENVO:00002039
has cross-reference: EV:0100140
has cross-reference: FMA:30317
has cross-reference: FMA:5018
has cross-reference: GAID:92
has cross-reference: MA:0001459
has cross-reference: MAT:0000299
has cross-reference: MIAA:0000299
has cross-reference: NCIT:C12366
has cross-reference: SCTID:90780006
has cross-reference: TAO:0001514
has cross-reference: UMLS:C0262950
has cross-reference: VHOG:0001190
has cross-reference: VSAO:0000057
has cross-reference: Wikipedia:Bone
has cross-reference: XAO:0000169
has cross-reference: ZFA:0001514
has cross-reference: galen:Bone
has exact synonym: bone organ
has related synonym: bone
has related synonym: bones
id: UBERON:0001474
in subset: efo slim
in subset: human subset
in subset: major organ
in subset: mouse subset
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: bone element
annotated property: definition
annotated target: Skeletal element that is composed of bone tissue.
has cross-reference: GO_REF:0000034
has cross-reference: PSPUB:0000170
has cross-reference: VSAO:0000057
has cross-reference: http://dx.plos.org/10.1371/journal.pone.0051070
has cross-reference: https://github.com/obophenotype/uberon/issues/277

Axiom
annotated source: bone element
annotated property: UBPROP_0000001
annotated target: Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000047
ontology: AAO
source: AAO:LAP

Axiom
annotated source: bone element
annotated property: UBPROP_0000001
annotated target: Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001514
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: bone element
annotated property: UBPROP_0000001
annotated target: Skeletal element that is composed of bone tissue.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000057
ontology: VSAO
source: PSPUB:0000170

Axiom
annotated source: bone element
annotated property: UBPROP_0000002
annotated target: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
date retrieved: 2012-06-20
external class: AAO:0000047
ontology: AAO

Axiom
annotated source: bone element
annotated property: UBPROP_0000003
annotated target: The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001190
ontology: VHOG
source: DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
source: http://bgee.unil.ch/

Axiom
annotated source: bone element
annotated property: has cross-reference
annotated target: UMLS:C0262950
source: ncithesaurus:Bone

Axiom
annotated source: bone element
annotated property: has exact synonym
annotated target: bone organ
has cross-reference: FMA:5018

Axiom
annotated source: bone element
annotated property: has related synonym
annotated target: bone
has cross-reference: AEO:0000082
has cross-reference: BTO:0000140
has cross-reference: MA:0001459
has cross-reference: VHOG:0001190

Axiom
annotated source: bone element
annotated property: has related synonym
annotated target: bones
has cross-reference: ZFA:0001514
has synonym type: plural form

mandible
type: Class
subclass of: intramembranous bone
subclass of: dentary
definition: A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
RO_0002175: NCBITaxon 9606
UBPROP_0000007: mandibular
UBPROP_0000012: Note in ZFA 'mandible' is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term 'mandibular symphysis' refers to the dentary
UBPROP_0000013: 'mandible' also refers to either the upper OR lower part of the beak in birds
has broad synonym: lower jaw
has broad synonym: lower jaw bone
has cross-reference: BTO:0001748
has cross-reference: CALOHA:TS-2225
has cross-reference: EFO:0001965
has cross-reference: EHDAA2:0001059
has cross-reference: EHDAA:8007
has cross-reference: EMAPA:18290
has cross-reference: FMA:52748
has cross-reference: GAID:68
has cross-reference: MA:0001487
has cross-reference: MESH:D008334
has cross-reference: NCIT:C12290
has cross-reference: SCTID:181812008
has cross-reference: UMLS:C0024687
has cross-reference: Wikipedia:Human_mandible
has cross-reference: galen:Mandible
has exact synonym: inferior maxillary bone
has exact synonym: mammaliam mandible
has exact synonym: mandibulla
has narrow synonym: lower mandibula
has related synonym: mandibula
has related synonym: mandibular series
id: UBERON:0001684
in subset: efo slim
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: mandible
annotated property: definition
annotated target: A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
has cross-reference: Wikipedia:Human_mandible
has cross-reference: Wikipedia:Mandible

Axiom
annotated source: mandible
annotated property: UBPROP_0000012
annotated target: Note in ZFA 'mandible' is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term 'mandibular symphysis' refers to the dentary
external ontology: ZFA

Axiom
annotated source: mandible
annotated property: has broad synonym
annotated target: lower jaw
has synonym type: SENSU

Axiom
annotated source: mandible
annotated property: has broad synonym
annotated target: lower jaw bone
has synonym type: SENSU

Axiom
annotated source: mandible
annotated property: has cross-reference
annotated target: UMLS:C0024687
source: ncithesaurus:Mandible

Axiom
annotated source: mandible
annotated property: has narrow synonym
annotated target: lower mandibula
has cross-reference: Wikipedia:Mandible
has synonym type: SENSU

Axiom
annotated source: mandible
annotated property: has related synonym
annotated target: mandibula
has cross-reference: BTO:0001748
has cross-reference: Wikipedia:Human_mandible
has synonym type: latin term

Axiom
annotated source: mandible
annotated property: has related synonym
annotated target: mandibular series
has cross-reference: ZFA:0001273

synovial joint
type: Class
subclass of: skeletal joint
definition: 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].
UBPROP_0000001: 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]
has cross-reference: AEO:0000183
has cross-reference: CALOHA:TS-2138
has cross-reference: EHDAA2:0003183
has cross-reference: FMA:7501
has cross-reference: MA:0000322
has cross-reference: NCIT:C32461
has cross-reference: SCTID:113234001
has cross-reference: TAO:0005153
has cross-reference: Wikipedia:Synovial_joint
has cross-reference: ZFA:0005153
has cross-reference: galen:SynovialJoint
has exact synonym: articulatio synoviale
has exact synonym: diarthroses
has exact synonym: diarthrosis
has exact synonym: diarthrosis joint
has related synonym: diarthrodial joints
id: UBERON:0002217
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: synovial joint
annotated property: definition
annotated target: 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].
has cross-reference: FMA:7501
has cross-reference: Wikipedia:Synovial_joint

Axiom
annotated source: synovial joint
annotated property: UBPROP_0000001
annotated target: 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]
date retrieved: 2012-08-14
external class: TAO:0005153
ontology: TAO
source: ZFIN:Curator

Axiom
annotated source: synovial joint
annotated property: has exact synonym
annotated target: diarthroses
has cross-reference: ZFA:0005153
has synonym type: plural form

Axiom
annotated source: synovial joint
annotated property: has related synonym
annotated target: diarthrodial joints
has cross-reference: ZFA:0005153
has synonym type: plural form

pes
type: Class
subclass of: autopod region
subclass of: lower limb segment
definition: Distal portion of the hind limb, including tarsal region, metatarsal region and digits.
UBPROP_0000007: pedal
has cross-reference: BTO:0000476
has cross-reference: CALOHA:TS-0377
has cross-reference: EFO:0003065
has cross-reference: EHDAA2:0000546
has cross-reference: EMAPA:17459
has cross-reference: FMA:9664
has cross-reference: GAID:40
has cross-reference: MA:0000044
has cross-reference: MESH:D005528
has cross-reference: NCIT:C32622
has cross-reference: SCTID:302545001
has cross-reference: UMLS:C0016504
has cross-reference: VHOG:0000350
has cross-reference: Wikipedia:Pes_(anatomy)
has cross-reference: galen:Foot
has exact synonym: foot
has exact synonym: hindlimb autopod
has exact synonym: hindlimb autopodium
has exact synonym: hindlimb distal free limb segment
has exact synonym: pes
has exact synonym: terminal segment of free lower limb
has narrow synonym: hind foot
has narrow synonym: hind paw
has narrow synonym: hind-paw
has narrow synonym: hindfeet
has narrow synonym: hindfoot
has narrow synonym: hindfoot of quadruped
has narrow synonym: hindpaw
has related synonym: hind limb autopodium
id: UBERON:0002387
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: pes
annotated property: definition
annotated target: Distal portion of the hind limb, including tarsal region, metatarsal region and digits.
has cross-reference: Wikipedia:Foot
has cross-reference: Wikipedia:Pes_(anatomy)

Axiom
annotated source: pes
annotated property: has cross-reference
annotated target: UMLS:C0016504
source: ncithesaurus:Foot

Axiom
annotated source: pes
annotated property: has exact synonym
annotated target: foot
has cross-reference: MA:0000044
has synonym type: HUMAN PREFERRED

Axiom
annotated source: pes
annotated property: has exact synonym
annotated target: hindlimb autopod
has cross-reference: OBOL:automatic

Axiom
annotated source: pes
annotated property: has exact synonym
annotated target: hindlimb autopodium
has cross-reference: OBOL:automatic

Axiom
annotated source: pes
annotated property: has exact synonym
annotated target: hindlimb distal free limb segment
has cross-reference: OBOL:automatic

Axiom
annotated source: pes
annotated property: has exact synonym
annotated target: pes
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: pes
annotated property: has narrow synonym
annotated target: hind paw
has cross-reference: EMAPA:17428
has cross-reference: OBOL:automatic
has synonym type: SENSU

Axiom
annotated source: pes
annotated property: has narrow synonym
annotated target: hind-paw
has cross-reference: EMAPA:17428
has synonym type: SENSU

Axiom
annotated source: pes
annotated property: has narrow synonym
annotated target: hindfeet
has synonym type: plural form

Axiom
annotated source: pes
annotated property: has narrow synonym
annotated target: hindpaw
has cross-reference: MA:0000044
has synonym type: SENSU

Axiom
annotated source: pes
annotated property: has related synonym
annotated target: hind limb autopodium
has cross-reference: VHOG:0000350

manual digit
type: Class
subclass of: digit
subclass of: Restriction
  on property: part of
  some values from: manus
definition: A digit that is part of a manus (hand).
UBPROP_0000001: One of the fingers of the manus.[AAO]
has alternative id: UBERON:0000028
has cross-reference: AAO:0000857
has cross-reference: BTO:0004669
has cross-reference: EHDAA2:0000404
has cross-reference: EMAPA:32642
has cross-reference: FMA:9666
has cross-reference: GAID:57
has cross-reference: MA:0000041
has cross-reference: MESH:D005385
has cross-reference: NCIT:C32608
has cross-reference: NLXANAT:20090602
has cross-reference: SCTID:283992002
has cross-reference: UMLS:C0016129
has cross-reference: Wikipedia:Finger
has cross-reference: XAO:0003036
has cross-reference: galen:Finger
has exact synonym: digit of hand
has exact synonym: digit of manus
has exact synonym: digitus manus
has exact synonym: finger
has exact synonym: fore digit
has exact synonym: forelimb digit
has exact synonym: hand digit
has exact synonym: manual digit (phalangeal portion) plus soft tissue
id: UBERON:0002389
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: manual digit
annotated property: definition
annotated target: A digit that is part of a manus (hand).
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: manual digit
annotated property: UBPROP_0000001
annotated target: One of the fingers of the manus.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000857
ontology: AAO
source: AAO:LAP

Axiom
annotated source: manual digit
annotated property: has cross-reference
annotated target: UMLS:C0016129
source: ncithesaurus:Finger

Axiom
annotated source: manual digit
annotated property: has exact synonym
annotated target: digit of hand
has cross-reference: FMA:9666

Axiom
annotated source: manual digit
annotated property: has exact synonym
annotated target: finger
has cross-reference: FMA:9666

Axiom
annotated source: manual digit
annotated property: has exact synonym
annotated target: fore digit
has cross-reference: AAO:0000857
has cross-reference: XAO:0003036

Axiom
annotated source: manual digit
annotated property: has exact synonym
annotated target: hand digit
has cross-reference: MA:0000041

Axiom
annotated source: manual digit
annotated property: has exact synonym
annotated target: manual digit (phalangeal portion) plus soft tissue
has cross-reference: http://orcid.org/0000-0002-6601-2165
has synonym type: COMPARATIVE PREFERRED

maxilla
type: Class
subclass of: intramembranous bone
subclass of: pneumatized bone
subclass of: dermal bone
subclass of: neural crest-derived structure
subclass of: bone of upper jaw
subclass of: lateral structure
definition: The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO]
UBPROP_0000001: Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO]
UBPROP_0000002: relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO]
UBPROP_0000002: relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO]
UBPROP_0000005: In some teleosts, the maxilla is located postero-ventral to the supramaxilla. Commonly, the articular process of the maxilla articulates with the autopalatine and ethmoidal region antero-medially. The maxilla is usually the largest bone in the upper jaw assemblage.[TAO]
UBPROP_0000007: maxillary
has broad synonym: upper jaw bone
has cross-reference: AAO:0000285
has cross-reference: CALOHA:TS-2217
has cross-reference: EHDAA2:0001068
has cross-reference: EHDAA:8043
has cross-reference: EMAPA:17639
has cross-reference: FMA:9711
has cross-reference: GAID:220
has cross-reference: MA:0001491
has cross-reference: MESH:D008437
has cross-reference: NCIT:C26470
has cross-reference: SCTID:181813003
has cross-reference: TAO:0000270
has cross-reference: UMLS:C0024947
has cross-reference: VHOG:0001021
has cross-reference: VSAO:0000207
has cross-reference: Wikipedia:Maxilla
has cross-reference: ZFA:0000270
has cross-reference: galen:Maxilla
has related synonym: maxillae
has related synonym: maxillary bone
id: UBERON:0002397
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Fusion of maxilla + premaxilla

Axiom
annotated source: maxilla
annotated property: definition
annotated target: The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods.
has cross-reference: Wikipedia:Maxilla
has cross-reference: http://palaeos.com/vertebrates/glossary/glossaryM.html

Axiom
annotated source: maxilla
annotated property: UBPROP_0000001
annotated target: Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000270
ontology: TAO
source: TAO:GA_TG

Axiom
annotated source: maxilla
annotated property: UBPROP_0000001
annotated target: Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000285
ontology: AAO
source: AAO:LAP

Axiom
annotated source: maxilla
annotated property: UBPROP_0000002
annotated target: relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000270
ontology: TAO

Axiom
annotated source: maxilla
annotated property: UBPROP_0000002
annotated target: relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000270
ontology: TAO

Axiom
annotated source: maxilla
annotated property: UBPROP_0000005
annotated target: In some teleosts, the maxilla is located postero-ventral to the supramaxilla. Commonly, the articular process of the maxilla articulates with the autopalatine and ethmoidal region antero-medially. The maxilla is usually the largest bone in the upper jaw assemblage.[TAO]
date retrieved: 2012-09-06
external class: TAO:0000270
ontology: TAO
source: Curator

Axiom
annotated source: maxilla
annotated property: has cross-reference
annotated target: UMLS:C0024947
source: ncithesaurus:Maxilla

Axiom
annotated source: maxilla
annotated property: has related synonym
annotated target: maxillae
has synonym type: plural form

Axiom
annotated source: maxilla
annotated property: has related synonym
annotated target: maxillary bone
has cross-reference: Wikipedia:Maxilla

manus
type: Class
subclass of: autopod region
subclass of: upper limb segment
definition: Distal segment of the fore limb, including carpal region, metacarpal region and digits.
UBPROP_0000007: manual
has cross-reference: AAO:0010803
has cross-reference: BTO:0004668
has cross-reference: CALOHA:TS-2213
has cross-reference: EHDAA2:0000728
has cross-reference: EMAPA:17428
has cross-reference: FMA:9712
has cross-reference: GAID:56
has cross-reference: MA:0000037
has cross-reference: MESH:D006225
has cross-reference: NCIT:C32712
has cross-reference: NLXANAT:20090603
has cross-reference: SCTID:302539009
has cross-reference: UMLS:C0018563
has cross-reference: VHOG:0000344
has cross-reference: Wikipedia:Manus_(anatomy)
has cross-reference: galen:Hand
has exact synonym: forelimb autopod
has exact synonym: forelimb autopodium
has exact synonym: hand
has exact synonym: hand region
has exact synonym: terminal segment of free upper limb
has narrow synonym: fore foot
has narrow synonym: fore paw
has narrow synonym: fore-paw
has narrow synonym: forefeet
has narrow synonym: forefoot
has narrow synonym: forefoot of quadruped
has narrow synonym: forepaw
id: UBERON:0002398
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: manus
annotated property: definition
annotated target: Distal segment of the fore limb, including carpal region, metacarpal region and digits.
has cross-reference: Wikipedia:Hand
has cross-reference: Wikipedia:Manus_(anatomy)

Axiom
annotated source: manus
annotated property: has cross-reference
annotated target: UMLS:C0018563
source: ncithesaurus:Hand

Axiom
annotated source: manus
annotated property: has exact synonym
annotated target: forelimb autopod
has cross-reference: OBOL:automatic

Axiom
annotated source: manus
annotated property: has exact synonym
annotated target: forelimb autopodium
has cross-reference: OBOL:automatic

Axiom
annotated source: manus
annotated property: has exact synonym
annotated target: hand
has cross-reference: MA:0000037
has synonym type: HUMAN PREFERRED

Axiom
annotated source: manus
annotated property: has exact synonym
annotated target: hand region
has cross-reference: EHDAA2:0000728

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: fore foot
has synonym type: INCONSISTENT

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: fore paw
has cross-reference: EMAPA:17428
has cross-reference: OBOL:automatic
has synonym type: SENSU

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: fore-paw
has cross-reference: EMAPA:17428
has synonym type: SENSU

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: forefeet
has synonym type: plural form

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: forefoot
has synonym type: INCONSISTENT

Axiom
annotated source: manus
annotated property: has narrow synonym
annotated target: forepaw
has cross-reference: MA:0000037
has synonym type: SENSU

autopod region
type: Class
subclass of: limb segment
definition: Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.
UBPROP_0000013: Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
has broad synonym: autopod
has cross-reference: BTO:0004359
has cross-reference: EFO:0000877
has cross-reference: EMAPA:32722
has cross-reference: FMA:83015
has cross-reference: MA:0002714
has cross-reference: MAT:0000091
has cross-reference: MIAA:0000091
has cross-reference: NCIT:C77660
has cross-reference: SCTID:95936004
has cross-reference: UMLS:C0687080
has exact synonym: autopodial limb segment
has exact synonym: autopodial segment
has exact synonym: autopodium
has exact synonym: autopodium region
has exact synonym: distal free limb segment
has exact synonym: distal segment of free limb
has related synonym: autopodial element
has related synonym: distal segment of limb
has related synonym: manus/pes
has related synonym: paw
has related synonym: paw/hand/foot/hoof
has related synonym: pod
id: UBERON:0002470
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: autopod region
annotated property: definition
annotated target: Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.
has cross-reference: https://github.com/obophenotype/uberon/issues/303
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: autopod region
annotated property: has broad synonym
annotated target: autopod
has cross-reference: MA:0002714

Axiom
annotated source: autopod region
annotated property: has cross-reference
annotated target: UMLS:C0687080
source: ncithesaurus:Paw

Axiom
annotated source: autopod region
annotated property: has exact synonym
annotated target: autopodial limb segment
has cross-reference: MA:th

Axiom
annotated source: autopod region
annotated property: has exact synonym
annotated target: distal free limb segment
has cross-reference: FMA:83015

Axiom
annotated source: autopod region
annotated property: has exact synonym
annotated target: distal segment of free limb
has cross-reference: FMA:83015

Axiom
annotated source: autopod region
annotated property: has related synonym
annotated target: distal segment of limb
has cross-reference: EMAPA:32722

intramembranous bone
type: Class
subclass of: bone element
definition: Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
UBPROP_0000001: Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
UBPROP_0000005: [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
has cross-reference: EMAPA:36615
has cross-reference: TAO:0001644
has cross-reference: Wikipedia:Intramembranous_ossification
has cross-reference: ZFA:0001635
has related synonym: intramembranous bones
has related synonym: membrane bone
id: UBERON:0002514
in subset: human subset
in subset: mouse subset

Axiom
annotated source: intramembranous bone
annotated property: definition
annotated target: Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
has cross-reference: GO:0001957
has cross-reference: Wikipedia:Intramembranous_ossification
has cross-reference: https://github.com/obophenotype/uberon/issues/267

Axiom
annotated source: intramembranous bone
annotated property: UBPROP_0000001
annotated target: Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001644
ontology: TAO
source: TAO:wd

Axiom
annotated source: intramembranous bone
annotated property: UBPROP_0000005
annotated target: [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
date retrieved: 2012-09-06
external class: TAO:0001644
ontology: TAO
source: Curator

Axiom
annotated source: intramembranous bone
annotated property: has related synonym
annotated target: intramembranous bones
has cross-reference: ZFA:0001635
has synonym type: plural form

Axiom
annotated source: intramembranous bone
annotated property: has related synonym
annotated target: membrane bone
has cross-reference: AEO:0000085

limb segment
type: Class
subclass of: paired limb/fin segment
definition: A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
UBPROP_0000012: FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
has cross-reference: FMA:241863
has cross-reference: MA:0002889
has cross-reference: NCIT:C38630
has cross-reference: UMLS:C1268195
has exact synonym: free limb segment
has exact synonym: segment of limb
has exact synonym: subdivision of limb
has related synonym: extremity part
has related synonym: limb region
has related synonym: region of limb
id: UBERON:0002529
in subset: human subset
in subset: mouse subset

Axiom
annotated source: limb segment
annotated property: definition
annotated target: A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: limb segment
annotated property: UBPROP_0000012
annotated target: FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
external ontology: FMA

Axiom
annotated source: limb segment
annotated property: has cross-reference
annotated target: UMLS:C1268195
source: ncithesaurus:Extremity_Part

Axiom
annotated source: limb segment
annotated property: has exact synonym
annotated target: free limb segment
has cross-reference: FMA:241863

digit
type: Class
subclass of: autopodial extension
definition: A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
RO_0002171: UBERON_0009877
UBPROP_0000003: Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
UBPROP_0000007: digital
contributor: https://orcid.org/0000-0001-7972-3866
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-8688-6599
contributor: https://orcid.org/0000-0003-3162-7490
has cross-reference: AAO:0011126
has cross-reference: EFO:0000881
has cross-reference: EMAPA:32725
has cross-reference: FMA:85518
has cross-reference: MA:0000690
has cross-reference: MAT:0000285
has cross-reference: MIAA:0000285
has cross-reference: NCIT:C40186
has cross-reference: SCTID:361367007
has cross-reference: UMLS:C0582802
has cross-reference: VHOG:0000944
has cross-reference: Wikipedia:Digit_(anatomy)
has cross-reference: XAO:0003032
has cross-reference: galen:Digit
has exact synonym: acropodial unit
has exact synonym: digit (phalangeal portion) plus soft tissue
has exact synonym: limb digit
id: UBERON:0002544
in subset: efo slim
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: digit
annotated property: definition
annotated target: A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
has cross-reference: http://orcid.org/0000-0002-6601-2165
has cross-reference: https://github.com/obophenotype/uberon/issues/420

Axiom
annotated source: digit
annotated property: UBPROP_0000003
annotated target: Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000944
ontology: VHOG
source: DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)
source: http://bgee.unil.ch/

Axiom
annotated source: digit
annotated property: has cross-reference
annotated target: FMA:85518
notes: GAT

Axiom
annotated source: digit
annotated property: has cross-reference
annotated target: UMLS:C0582802
source: ncithesaurus:Digit

Axiom
annotated source: digit
annotated property: has exact synonym
annotated target: digit (phalangeal portion) plus soft tissue
has cross-reference: http://orcid.org/0000-0002-6601-2165
has synonym type: COMPARATIVE PREFERRED

Axiom
annotated source: digit
annotated property: has exact synonym
annotated target: limb digit
has cross-reference: MA:0000690

skull
type: Class
subclass of: subdivision of skeletal system
definition: Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
UBPROP_0000012: 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.
UBPROP_0000012: in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
UBPROP_0000013: 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
has cross-reference: BTO:0001295
has cross-reference: CALOHA:TS-2344
has cross-reference: EHDAA2:0000325
has cross-reference: EMAPA:17680
has cross-reference: FMA:46565
has cross-reference: GAID:82
has cross-reference: MESH:D012886
has cross-reference: NCIT:C12789
has cross-reference: SCTID:110530005
has cross-reference: UMLS:C0037303
has cross-reference: Wikipedia:Skull
has cross-reference: WikipediaCategory:Skull
has cross-reference: galen:Skull
has related synonym: cranial skeleton
has related synonym: skeletal system of head
id: UBERON:0003129
in subset: human subset
in subset: mouse subset
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: skull
annotated property: definition
annotated target: Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
has cross-reference: PMID:11523816
has cross-reference: Wikipedia:Skull
has cross-reference: http://sourceforge.net/tracker/

Axiom
annotated source: skull
annotated property: UBPROP_0000012
annotated target: 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.
external ontology: FMA

Axiom
annotated source: skull
annotated property: UBPROP_0000013
annotated target: 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
source: WP

Axiom
annotated source: skull
annotated property: has cross-reference
annotated target: UMLS:C0037303
source: ncithesaurus:Skull

head bone
type: Class
subclass of: bone of craniocervical region
definition: A bone that is part of a head [Automatically generated definition].
has cross-reference: EMAPA:35996
has cross-reference: MA:0000576
has cross-reference: SCTID:118646007
has exact synonym: adult head bone
has exact synonym: adult head bone organ
has exact synonym: bone of adult head
has exact synonym: bone of head
has exact synonym: bone organ of adult head
has exact synonym: bone organ of head
has exact synonym: head bone organ
has related synonym: craniofacial bone
id: UBERON:0003457
in subset: human subset
in subset: mouse subset
in subset: pheno slim
comment: Different sources vary regarding which bones are craniofacial; e.g. hyoid bone

Axiom
annotated source: head bone
annotated property: definition
annotated target: A bone that is part of a head [Automatically generated definition].
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: adult head bone
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: adult head bone organ
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: bone of adult head
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: bone of head
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: bone organ of adult head
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: bone organ of head
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has exact synonym
annotated target: head bone organ
has cross-reference: OBOL:automatic

Axiom
annotated source: head bone
annotated property: has related synonym
annotated target: craniofacial bone
has cross-reference: http://orcid.org/0000-0002-6601-2165

facial bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part of
    some values from: facial skeleton
subclass of: head bone
subclass of: Restriction
  on property: part of
  some values from: facial skeleton
definition: A bone that is part of a facial skeleton [Automatically generated definition].
has cross-reference: EMAPA:19019
has cross-reference: EMAPA:35924
has cross-reference: MA:0001482
has cross-reference: MA:0003159
has cross-reference: MESH:D005147
has cross-reference: NCIT:C63706
has cross-reference: SCTID:181799005
has cross-reference: UMLS:C0015455
has exact synonym: bone of facial skeleton
has exact synonym: facial bone
has exact synonym: facial skeleton bone
has related synonym: bone of viscerocranium
has related synonym: viscerocranium bone
id: UBERON:0003462
in subset: human subset
in subset: mouse subset
in subset: pheno slim

Axiom
annotated source: facial bone
annotated property: definition
annotated target: A bone that is part of a facial skeleton [Automatically generated definition].
has cross-reference: OBOL:automatic

Axiom
annotated source: facial bone
annotated property: has cross-reference
annotated target: MESH:D005147
authored by: https://orcid.org/0000-0001-9439-5346
mapping justification: ManualMappingCuration

Axiom
annotated source: facial bone
annotated property: has cross-reference
annotated target: UMLS:C0015455
source: ncithesaurus:Facial_Bone

Axiom
annotated source: facial bone
annotated property: has exact synonym
annotated target: bone of facial skeleton
has cross-reference: OBOL:automatic

Axiom
annotated source: facial bone
annotated property: has exact synonym
annotated target: facial bone
has cross-reference: EMAPA:19019

Axiom
annotated source: facial bone
annotated property: has exact synonym
annotated target: facial skeleton bone
has cross-reference: OBOL:automatic

Axiom
annotated source: facial bone
annotated property: has related synonym
annotated target: bone of viscerocranium
has cross-reference: OBOL:automatic

Axiom
annotated source: facial bone
annotated property: has related synonym
annotated target: viscerocranium bone
has cross-reference: OBOL:automatic

temporomandibular joint
type: Class
subclass of: joint connecting upper and lower jaws
subclass of: lateral structure
subclass of: Restriction
  on property: part of
  some values from: mouth
definition: A synovial joint of the jaw that connects the mandible to the temporal bone.
has cross-reference: BTO:0003674
has cross-reference: EMAPA:19196
has cross-reference: FMA:54832
has cross-reference: GAID:272
has cross-reference: MA:0002899
has cross-reference: MESH:D013704
has cross-reference: NCIT:C32888
has cross-reference: SCTID:181814009
has cross-reference: UMLS:C0039493
has cross-reference: Wikipedia:Temporomandibular_joint
has exact synonym: TMJ
has exact synonym: temperomandibular joint
has related synonym: articulatio temporomandibularis
has related synonym: dentary-squamosal joint
has related synonym: squamosal-dentary joint
has related synonym: tempero-mandibular joint
has related synonym: temporalmandibular joint
has related synonym: temporomandibular
has related synonym: temporomandibular articulation
has related synonym: temporomandibular joint
id: UBERON:0003700
in subset: human subset
in subset: mouse subset
in subset: pheno slim
comment: There are two TMJs, one on either side, working in unison. The unique feature of the TMJs is the articular disc. The disc is composed of fibrocartilagenous tissue (like the firm and flexible elastic cartilage of the ear) which is positioned between the two bones that form the joint. The TMJs are one of the only synovial joints in the human body with an articular disc, another being the sternoclavicular joint. The disc divides each joint into two. The lower joint compartment formed by the mandible and the articular disc is involved in rotational movement -- this is the initial movement of the jaw when the mouth opens. The upper joint compartment formed by the articular disk and the temporal bone is involved in translational movement -- this is the secondary gliding motion of the jaw as it is opened widely. The part of the mandible which mates to the under-surface of the disc is the condyle and the part of the temporal bone which mates to the upper surface of the disk is the glenoid (or mandibular) fossa[WP].

Axiom
annotated source: temporomandibular joint
annotated property: definition
annotated target: A synovial joint of the jaw that connects the mandible to the temporal bone.
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has cross-reference
annotated target: UMLS:C0039493
source: ncithesaurus:Jaw_Joint

Axiom
annotated source: temporomandibular joint
annotated property: has exact synonym
annotated target: TMJ
has cross-reference: BTO:0003674
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has exact synonym
annotated target: temperomandibular joint
has cross-reference: HP:0010754

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: articulatio temporomandibularis
has cross-reference: Wikipedia:Temporomandibular_joint
has synonym type: latin term

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: dentary-squamosal joint
has cross-reference: http://palaeos.com/vertebrates/glossary/glossaryT.html

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: squamosal-dentary joint
has cross-reference: http://palaeos.com/vertebrates/glossary/glossaryT.html

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: tempero-mandibular joint
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: temporalmandibular joint
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: temporomandibular
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: temporomandibular articulation
has cross-reference: Wikipedia:Temporomandibular_joint

Axiom
annotated source: temporomandibular joint
annotated property: has related synonym
annotated target: temporomandibular joint
has cross-reference: Wikipedia:Temporomandibular_joint

neural tissue
type: Class
subclass of: tissue
definition: Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
UBPROP_0000001: One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
UBPROP_0000012: FMA definition includes vasculature
has cross-reference: AAO:0000325
has cross-reference: AEO:0000123
has cross-reference: EHDAA2:0003123
has cross-reference: FMA:9642
has cross-reference: GAID:609
has cross-reference: MESH:D009417
has cross-reference: NCIT:C13052
has cross-reference: SCTID:91728009
has cross-reference: UMLS:C0027757
has exact synonym: nerve tissue
has exact synonym: nervous tissue
has exact synonym: portion of neural tissue
id: UBERON:0003714
in subset: human subset
in subset: mouse subset

Axiom
annotated source: neural tissue
annotated property: definition
annotated target: Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
has cross-reference: FMA:9642

Axiom
annotated source: neural tissue
annotated property: UBPROP_0000001
annotated target: One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000325
ontology: AAO
source: AAO:LAP

Axiom
annotated source: neural tissue
annotated property: UBPROP_0000012
annotated target: FMA definition includes vasculature
external ontology: FMA

Axiom
annotated source: neural tissue
annotated property: has cross-reference
annotated target: UMLS:C0027757
source: ncithesaurus:Nervous_Tissue

Axiom
annotated source: neural tissue
annotated property: has exact synonym
annotated target: nerve tissue
has cross-reference: FMA:9642

Axiom
annotated source: neural tissue
annotated property: has exact synonym
annotated target: nervous tissue
has cross-reference: FMA:9642

Axiom
annotated source: neural tissue
annotated property: has exact synonym
annotated target: portion of neural tissue
has cross-reference: FMA:9642

ectoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the ectoderm.
has exact synonym: ectodermal deriviative
id: UBERON:0004121
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: ectoderm-derived structure
annotated property: definition
annotated target: An anatomical structure that develops (entirely or partially) from the ectoderm.
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ectoderm-derived structure
annotated property: has exact synonym
annotated target: ectodermal deriviative
has cross-reference: FBbt:00025990

dentary
type: Class
subclass of: bone of lower jaw
subclass of: dermal bone
subclass of: lateral structure
definition: The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
UBPROP_0000001: Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
UBPROP_0000001: Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
UBPROP_0000001: The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
UBPROP_0000002: relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
UBPROP_0000003: Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
UBPROP_0000008: In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
has cross-reference: AAO:0000124
has cross-reference: EFO:0003508
has cross-reference: TAO:0000191
has cross-reference: VHOG:0001022
has cross-reference: ZFA:0000191
has exact synonym: dentaries
has exact synonym: dentary bone
has related synonym: dentale
has related synonym: os dentale
has related synonym: sur-angulaire
id: UBERON:0004742
in subset: efo slim
in subset: human subset
in subset: mouse subset

Axiom
annotated source: dentary
annotated property: definition
annotated target: The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
has cross-reference: VHOG:0001022

Axiom
annotated source: dentary
annotated property: UBPROP_0000001
annotated target: Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000191
ontology: TAO
source: TAO:GA_TG

Axiom
annotated source: dentary
annotated property: UBPROP_0000001
annotated target: Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000124
ontology: AAO
source: AAO:LAP

Axiom
annotated source: dentary
annotated property: UBPROP_0000001
annotated target: The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001022
ontology: VHOG
source: http://bgee.unil.ch/

Axiom
annotated source: dentary
annotated property: UBPROP_0000002
annotated target: relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000191
ontology: TAO

Axiom
annotated source: dentary
annotated property: UBPROP_0000003
annotated target: Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001022
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248
source: http://bgee.unil.ch/

Axiom
annotated source: dentary
annotated property: has exact synonym
annotated target: dentaries
has cross-reference: TAO:0000191
has synonym type: plural form

Axiom
annotated source: dentary
annotated property: has exact synonym
annotated target: dentary bone
has cross-reference: ZFA:0000191

Axiom
annotated source: dentary
annotated property: has related synonym
annotated target: dentale
has cross-reference: AAO:0000124

Axiom
annotated source: dentary
annotated property: has related synonym
annotated target: os dentale
has cross-reference: AAO:0000124

Axiom
annotated source: dentary
annotated property: has related synonym
annotated target: sur-angulaire
has cross-reference: AAO:0000124

dermal skeletal element
type: Class
subclass of: skeletal element
definition: Dermis-derived entity that is made of skeletal tissue.
has exact synonym: dermal element
id: UBERON:0004756
in subset: human subset
in subset: mouse subset

Axiom
annotated source: dermal skeletal element
annotated property: definition
annotated target: Dermis-derived entity that is made of skeletal tissue.
has cross-reference: http://orcid.org/0000-0002-6601-2165
has cross-reference: https://github.com/obophenotype/uberon/issues/206

Axiom
annotated source: dermal skeletal element
annotated property: has exact synonym
annotated target: dermal element
has cross-reference: VSAO:curator

skeletal element
type: Class
subclass of: organ
definition: Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
UBPROP_0000001: Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
UBPROP_0000001: Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
has cross-reference: AAO:0011129
has cross-reference: TAO:0001890
has cross-reference: VSAO:0000128
has cross-reference: XAO:0004012
has cross-reference: ZFA:0005494
has cross-reference: galen:SkeletalStructure
id: UBERON:0004765
in subset: human subset
in subset: mouse subset
in subset: organ slim
in subset: uberon slim

Axiom
annotated source: skeletal element
annotated property: definition
annotated target: Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: skeletal element
annotated property: UBPROP_0000001
annotated target: Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000128
ontology: VSAO
source: PSPUB:0000170

Axiom
annotated source: skeletal element
annotated property: UBPROP_0000001
annotated target: Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001890
ontology: TAO
source: TAO:VSAO_workshop

bone of lower jaw
type: Class
subclass of: neural crest-derived structure
subclass of: bone of jaw
definition: Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
has exact synonym: lower jaw bone
id: UBERON:0004768
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: bone of lower jaw
annotated property: definition
annotated target: Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
has cross-reference: https://orcid.org/0000-0002-6601-2165

articulation
type: Class
subclass of: multi organ part structure
definition: Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
has cross-reference: FBbt:00005811
has narrow synonym: joint
id: UBERON:0004905
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: articulation
annotated property: definition
annotated target: Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: articulation
annotated property: has cross-reference
annotated target: FBbt:00005811
mapping justification: ManualMappingCuration

subdivision of digestive tract
type: Class
subclass of: subdivision of tube
definition: A proximal-distal subdivision of the digestive tract.
RO_0002175: NCBITaxon 9606
has cross-reference: FBbt:00100315
has cross-reference: FMA:71131
has related synonym: alimentary system subdivision
has related synonym: gut section
has related synonym: intestinal tract
has related synonym: segment of intestinal tract
has related synonym: subdivision of alimentary system
id: UBERON:0004921
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: subdivision of digestive tract
annotated property: definition
annotated target: A proximal-distal subdivision of the digestive tract.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of digestive tract
annotated property: has cross-reference
annotated target: FBbt:00100315
mapping justification: ManualMappingCuration

Axiom
annotated source: subdivision of digestive tract
annotated property: has related synonym
annotated target: alimentary system subdivision
has cross-reference: FMA:71131

Axiom
annotated source: subdivision of digestive tract
annotated property: has related synonym
annotated target: gut section
has cross-reference: FBbt:00100315

Axiom
annotated source: subdivision of digestive tract
annotated property: has related synonym
annotated target: subdivision of alimentary system
has cross-reference: FMA:71131

lower back
type: Class
subclass of: subdivision of trunk
subclass of: Restriction
  on property: part of
  some values from: dorsum
definition: Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA].
UBPROP_0000007: lumbar
has broad synonym: lumbar region
has cross-reference: BTO:0001505
has cross-reference: EMAPA:36623
has cross-reference: FMA:61681
has cross-reference: MA:0000027
has cross-reference: NCIT:C34004
has cross-reference: SCTID:182343007
has cross-reference: UMLS:C0024090
has exact synonym: abdominal back
has exact synonym: back of abdomen
has exact synonym: dorsum of abdomen
has exact synonym: lower back
has exact synonym: lumbar part of back
has exact synonym: lumbar region of back
has exact synonym: posterior part of abdomen
has exact synonym: regio lumbalis
has related synonym: loin
has related synonym: lombus
has related synonym: lumbos
id: UBERON:0005462
in subset: human subset
in subset: mouse subset
comment: overlaps with region sometimes called 'loin'

Axiom
annotated source: lower back
annotated property: definition
annotated target: Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA].
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has broad synonym
annotated target: lumbar region
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has cross-reference
annotated target: UMLS:C0024090
source: ncithesaurus:Lumbar_Region

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: abdominal back
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: back of abdomen
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: dorsum of abdomen
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: lower back
has cross-reference: MA:0000027

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: lumbar part of back
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: lumbar region of back
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: posterior part of abdomen
has cross-reference: FMA:61681

Axiom
annotated source: lower back
annotated property: has exact synonym
annotated target: regio lumbalis
has cross-reference: FMA:61681
has cross-reference: FMA:TA
has synonym type: latin term

Axiom
annotated source: lower back
annotated property: has related synonym
annotated target: loin
has cross-reference: BTO:0001505
has cross-reference: Wikipedia:Loin

autopodial extension
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part of
  some values from: autopod region
definition: A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
has related synonym: digit or predigit
has related synonym: limb outgrowth
id: UBERON:0005881
in subset: human subset
in subset: mouse subset
comment: encompasses digits and prepollex. requires review

Axiom
annotated source: autopodial extension
annotated property: definition
annotated target: A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
has cross-reference: http://orcid.org/0000-0002-6601-2165

multi-limb segment region
type: Class
subclass of: subdivision of organism along appendicular axis
subclass of: Restriction
  on property: has part
  some values from: limb segment
definition: A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
id: UBERON:0006058
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: multi-limb segment region
annotated property: definition
annotated target: A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
has cross-reference: https://orcid.org/0000-0002-6601-2165

thoracic region of vertebral column
type: Class
subclass of: subdivision of vertebral column
definition: That part of the spine comprising the thoracic vertebrae.
UBPROP_0000001: Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
has cross-reference: BTO:0004150
has cross-reference: EHDAA:5063
has cross-reference: EMAPA:17396
has cross-reference: FMA:9140
has cross-reference: MA:0003155
has cross-reference: NCIT:C69315
has cross-reference: SCTID:243931006
has cross-reference: UMLS:C0581269
has exact synonym: axial skeleton thoracic region
has exact synonym: columna vertebralis thoracicus
has exact synonym: thoracic spine
has exact synonym: thoracic vertebrae series
has exact synonym: thoracic vertebral column
id: UBERON:0006073
in subset: human subset
in subset: mouse subset
in subset: pheno slim

Axiom
annotated source: thoracic region of vertebral column
annotated property: definition
annotated target: That part of the spine comprising the thoracic vertebrae.
has cross-reference: http://medical-dictionary.thefreedictionary.com/

Axiom
annotated source: thoracic region of vertebral column
annotated property: UBPROP_0000001
annotated target: Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000612
ontology: AAO
source: AAO:Duellman_and_Trueb_1994

Axiom
annotated source: thoracic region of vertebral column
annotated property: has cross-reference
annotated target: UMLS:C0581269
source: ncithesaurus:Thoracic_Spine

Axiom
annotated source: thoracic region of vertebral column
annotated property: has exact synonym
annotated target: axial skeleton thoracic region
has cross-reference: MA:0003155

Axiom
annotated source: thoracic region of vertebral column
annotated property: has exact synonym
annotated target: columna vertebralis thoracicus
has cross-reference: FMA:9140

Axiom
annotated source: thoracic region of vertebral column
annotated property: has exact synonym
annotated target: thoracic spine
has cross-reference: FMA:9140

Axiom
annotated source: thoracic region of vertebral column
annotated property: has exact synonym
annotated target: thoracic vertebral column
has cross-reference: FMA:9140

subdivision of vertebral column
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: part of
  some values from: dorsum
definition: A collection of all skeletal elements in some subdivision of the vertebral column.
has cross-reference: FMA:16201
has exact synonym: subdivision of vertebral skeleton
has exact synonym: vertebrae series
has exact synonym: vertebral column subdivision
has exact synonym: vertebral series
has related synonym: vertebral region
has related synonym: vertebral subdivision
id: UBERON:0006077
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: subdivision of vertebral column
annotated property: definition
annotated target: A collection of all skeletal elements in some subdivision of the vertebral column.
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of vertebral column
annotated property: has exact synonym
annotated target: subdivision of vertebral skeleton
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of vertebral column
annotated property: has exact synonym
annotated target: vertebral column subdivision
has cross-reference: FMA:16201

membrane bone
type: Class
subclass of: bone element
definition: Bone element that arises as a result of intramembranous ossification.
UBPROP_0000001: Bone element that arises as a result of intramembranous ossification.[VSAO]
UBPROP_0000001: Intramembranous bone that forms deep in the organism.[TAO]
has cross-reference: AEO:0000085
has cross-reference: EHDAA2:0003085
has cross-reference: TAO:0001645
has cross-reference: VSAO:0000023
has cross-reference: XAO:0004014
has cross-reference: ZFA:0001636
has related synonym: membrane bones
id: UBERON:0007842
in subset: human subset
in subset: mouse subset

Axiom
annotated source: membrane bone
annotated property: definition
annotated target: Bone element that arises as a result of intramembranous ossification.
has cross-reference: GO_REF:0000034
has cross-reference: VSAO:0000023
has cross-reference: http://dx.plos.org/10.1371/journal.pone.0051070
has cross-reference: https://github.com/obophenotype/uberon/issues/267

Axiom
annotated source: membrane bone
annotated property: UBPROP_0000001
annotated target: Bone element that arises as a result of intramembranous ossification.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000023
ontology: VSAO
source: GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
source: PSPUB:0000170

Axiom
annotated source: membrane bone
annotated property: UBPROP_0000001
annotated target: Intramembranous bone that forms deep in the organism.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001645
ontology: TAO
source: TAO:wd

Axiom
annotated source: membrane bone
annotated property: has related synonym
annotated target: membrane bones
has cross-reference: ZFA:0001636
has synonym type: plural form

bone of craniocervical region
type: Class
subclass of: bone element
definition: A bone that is part of a craniocervical region.
has cross-reference: EMAPA:37245
has cross-reference: MA:0000569
has exact synonym: head or neck bone
has related synonym: cranial bone
id: UBERON:0007914
in subset: human subset
in subset: mouse subset

Axiom
annotated source: bone of craniocervical region
annotated property: definition
annotated target: A bone that is part of a craniocervical region.
has cross-reference: OBOL:automatic

Axiom
annotated source: bone of craniocervical region
annotated property: has cross-reference
annotated target: EMAPA:37245
source: MA:th

Axiom
annotated source: bone of craniocervical region
annotated property: has exact synonym
annotated target: head or neck bone
has cross-reference: MA:0000569

pneumatized bone
type: Class
subclass of: bone element
definition: A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
UBPROP_0000008: Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
has cross-reference: FMA:7478
has cross-reference: SCTID:333008005
has cross-reference: Wikipedia:Skeletal_pneumaticity
has cross-reference: galen:PneumaticBone
has exact synonym: os pneumaticum
has exact synonym: pneumatic bone
has related synonym: hollow bone
id: UBERON:0008193
in subset: human subset
in subset: mouse subset

Axiom
annotated source: pneumatized bone
annotated property: definition
annotated target: A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
has cross-reference: http://www.medilexicon.com/medicaldictionary.php

Axiom
annotated source: pneumatized bone
annotated property: has exact synonym
annotated target: os pneumaticum
has cross-reference: FMA:7478

Axiom
annotated source: pneumatized bone
annotated property: has exact synonym
annotated target: pneumatic bone
has cross-reference: FMA:7478

lower limb segment
type: Class
subclass of: limb segment
definition: A limb segment that is part of a hindlimb.
has cross-reference: FMA:24877
has exact synonym: free lower limb segment
has exact synonym: free lower limb subdivision
has exact synonym: segment of free lower limb
has exact synonym: subdivision of free lower limb
id: UBERON:0008784
in subset: human subset
in subset: mouse subset

Axiom
annotated source: lower limb segment
annotated property: definition
annotated target: A limb segment that is part of a hindlimb.
has cross-reference: OBOL:automatic

Axiom
annotated source: lower limb segment
annotated property: has exact synonym
annotated target: free lower limb segment
has cross-reference: FMA:24877

Axiom
annotated source: lower limb segment
annotated property: has exact synonym
annotated target: free lower limb subdivision
has cross-reference: FMA:24877

Axiom
annotated source: lower limb segment
annotated property: has exact synonym
annotated target: segment of free lower limb
has cross-reference: FMA:24877

Axiom
annotated source: lower limb segment
annotated property: has exact synonym
annotated target: subdivision of free lower limb
has cross-reference: FMA:24877

upper limb segment
type: Class
subclass of: limb segment
definition: A limb segment that is part of a forelimb.
has cross-reference: FMA:24876
has exact synonym: free upper limb segment
has exact synonym: free upper limb subdivision
has exact synonym: segment of free upper limb
has exact synonym: subdivision of free upper limb
id: UBERON:0008785
in subset: human subset
in subset: mouse subset

Axiom
annotated source: upper limb segment
annotated property: definition
annotated target: A limb segment that is part of a forelimb.
has cross-reference: OBOL:automatic

Axiom
annotated source: upper limb segment
annotated property: has exact synonym
annotated target: free upper limb segment
has cross-reference: FMA:24876

Axiom
annotated source: upper limb segment
annotated property: has exact synonym
annotated target: free upper limb subdivision
has cross-reference: FMA:24876

Axiom
annotated source: upper limb segment
annotated property: has exact synonym
annotated target: segment of free upper limb
has cross-reference: FMA:24876

Axiom
annotated source: upper limb segment
annotated property: has exact synonym
annotated target: subdivision of free upper limb
has cross-reference: FMA:24876

dermal bone
type: Class
subclass of: dermal skeletal element
subclass of: membrane bone
definition: Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
UBPROP_0000001: Intramembranous bone that forms superficially in the organism.[TAO]
UBPROP_0000012: other AOs are not yet in sync with this classification
has cross-reference: AAO:0010769
has cross-reference: TAO:0001590
has cross-reference: VSAO:0000130
has cross-reference: Wikipedia:Dermal_bone
has cross-reference: XAO:0004015
has cross-reference: ZFA:0001590
has related synonym: dermal bones
id: UBERON:0008907
in subset: human subset
in subset: mouse subset

Axiom
annotated source: dermal bone
annotated property: definition
annotated target: Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
has cross-reference: GO_REF:0000034
has cross-reference: VSAO:0000130
has cross-reference: http://dx.plos.org/10.1371/journal.pone.0051070
has cross-reference: https://github.com/obophenotype/uberon/issues/267

Axiom
annotated source: dermal bone
annotated property: UBPROP_0000001
annotated target: Intramembranous bone that forms superficially in the organism.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001590
ontology: TAO
source: TAO:wd

Axiom
annotated source: dermal bone
annotated property: has related synonym
annotated target: dermal bones
has cross-reference: ZFA:0001590
has synonym type: plural form

subdivision of trunk
type: Class
subclass of: organism subdivision
has cross-reference: FMA:25054
has cross-reference: SCTID:22943007
has exact synonym: region of trunk
has exact synonym: trunk subdivision
id: UBERON:0009569
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: subdivision of trunk
annotated property: has exact synonym
annotated target: region of trunk
has cross-reference: FMA:25054

Axiom
annotated source: subdivision of trunk
annotated property: has exact synonym
annotated target: trunk subdivision
has cross-reference: FMA:25054

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: CARO:0010000
has cross-reference: FBbt:00100313
has exact synonym: multicellular structure
id: UBERON:0010000
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: multicellular anatomical structure
annotated property: definition
annotated target: An anatomical structure that has more than one cell as a part.
has cross-reference: CARO:0010000

Axiom
annotated source: multicellular anatomical structure
annotated property: has cross-reference
annotated target: FBbt:00100313
mapping justification: ManualMappingCuration

Axiom
annotated source: multicellular anatomical structure
annotated property: has exact synonym
annotated target: multicellular structure
has cross-reference: FBbt:00100313

neural crest-derived structure
type: Class
subclass of: ectoderm-derived structure
subclass of: structure with developmental contribution from neural crest
definition: An anatomical structure that develops from the neural crest.
id: UBERON:0010313
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: neural crest-derived structure
annotated property: definition
annotated target: An anatomical structure that develops from the neural crest.
has cross-reference: https://orcid.org/0000-0002-6601-2165

structure with developmental contribution from neural crest
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has some part that develops from the neural crest.
id: UBERON:0010314
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: structure with developmental contribution from neural crest
annotated property: definition
annotated target: An anatomical structure that has some part that develops from the neural crest.
has cross-reference: https://orcid.org/0000-0002-6601-2165

paired limb/fin segment
type: Class
subclass of: subdivision of organism along appendicular axis
definition: An appendage segment that is part of a limb/fin.
has exact synonym: limb/fin segment
id: UBERON:0010538
in subset: homology grouping
in subset: human subset
in subset: mouse subset

Axiom
annotated source: paired limb/fin segment
annotated property: definition
annotated target: An appendage segment that is part of a limb/fin.
has cross-reference: OBOL:automatic

subdivision of organism along appendicular axis
type: Class
subclass of: organism subdivision
definition: A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
has cross-reference: FBbt:00007018
has exact synonym: appendage segment
has exact synonym: appendicular segment
id: UBERON:0010758
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: subdivision of organism along appendicular axis
annotated property: definition
annotated target: A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of organism along appendicular axis
annotated property: has cross-reference
annotated target: FBbt:00007018
mapping justification: ManualMappingCuration

Axiom
annotated source: subdivision of organism along appendicular axis
annotated property: has exact synonym
annotated target: appendage segment
has cross-reference: FBbt:00007018

facial skeleton
type: Class
subclass of: neural crest-derived structure
subclass of: primary subdivision of skull
subclass of: Restriction
  on property: part of
  some values from: face
definition: Subdivision of skull that consists of the facial bones.
has cross-reference: EHDAA2:0002206
has cross-reference: EHDAA:8361
has cross-reference: EMAPA:18022
has cross-reference: FMA:53673
has cross-reference: MA:0000318
has cross-reference: Wikipedia:Facial_skeleton
has exact synonym: facial skeleton
has related synonym: facial bone
has related synonym: ossa facialia
has related synonym: ossa faciei
has related synonym: viscerocranium
id: UBERON:0011156
in subset: human subset
in subset: mouse subset
in subset: pheno slim

Axiom
annotated source: facial skeleton
annotated property: definition
annotated target: Subdivision of skull that consists of the facial bones.
has cross-reference: MP:0005274
has cross-reference: Wikipedia:Facial_skeleton
has cross-reference: http://www.bartleby.com/107/37.html
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: facial skeleton
annotated property: has exact synonym
annotated target: facial skeleton
has cross-reference: FMA:53673

Axiom
annotated source: facial skeleton
annotated property: has related synonym
annotated target: facial bone
has cross-reference: MA:0000318

Axiom
annotated source: facial skeleton
annotated property: has related synonym
annotated target: ossa facialia
has cross-reference: Wikipedia:Facial_skeleton
has synonym type: latin term

Axiom
annotated source: facial skeleton
annotated property: has related synonym
annotated target: ossa faciei
has cross-reference: Wikipedia:Facial_skeleton
has synonym type: latin term

Axiom
annotated source: facial skeleton
annotated property: has related synonym
annotated target: viscerocranium
has cross-reference: MA:0000318
has synonym type: INCONSISTENT

primary subdivision of skull
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: part of
  some values from: skull
definition: The skull can be divided into two: the neurocranium and the facial skeleton.
has cross-reference: FMA:54964
has exact synonym: skull subdivision
has exact synonym: subdivision of skull
id: UBERON:0011158
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: primary subdivision of skull
annotated property: definition
annotated target: The skull can be divided into two: the neurocranium and the facial skeleton.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: primary subdivision of skull
annotated property: has exact synonym
annotated target: skull subdivision
has cross-reference: FMA:54964

Axiom
annotated source: primary subdivision of skull
annotated property: has exact synonym
annotated target: subdivision of skull
has cross-reference: FMA:54964

joint connecting upper and lower jaws
type: Class
subclass of: synovial joint
definition: Synovial joint that articulates bones of upper and lower jaw.
UBPROP_0000008: Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
has broad synonym: jaw joint
has narrow synonym: craniomandibular joint
id: UBERON:0011171
in subset: human subset
in subset: mouse subset

Axiom
annotated source: joint connecting upper and lower jaws
annotated property: definition
annotated target: Synovial joint that articulates bones of upper and lower jaw.
has cross-reference: http://evolution.berkeley.edu/evolibrary/article/evograms_05
has cross-reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: joint connecting upper and lower jaws
annotated property: UBPROP_0000008
annotated target: Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
source: http://evolution.berkeley.edu

organ system subdivision
type: Class
subclass of: multicellular anatomical structure
definition: A subdivision of an anatomical system.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
RO_0002175: NCBITaxon 9606
has cross-reference: FBbt:00007330
has cross-reference: FMA:67509
has cross-reference: SCTID:91690000
id: UBERON:0011216
in subset: common anatomy
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: organ system subdivision
annotated property: definition
annotated target: A subdivision of an anatomical system.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: organ system subdivision
annotated property: has cross-reference
annotated target: FBbt:00007330
mapping justification: ManualMappingCuration

bone of upper jaw
type: Class
subclass of: bone of jaw
definition: Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
has exact synonym: upper jaw bone
id: UBERON:0011597
in subset: grouping class
in subset: human subset
in subset: mouse subset

Axiom
annotated source: bone of upper jaw
annotated property: definition
annotated target: Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
has cross-reference: https://orcid.org/0000-0002-6601-2165

bone of jaw
type: Class
subclass of: facial bone
subclass of: digestive system element
definition: A bone element that is part of a jaw region.
has cross-reference: EMAPA:35453
has cross-reference: MA:0003130
has cross-reference: SCTID:369003004
has exact synonym: jaw bone
id: UBERON:0012360
in subset: human subset
in subset: mouse subset

Axiom
annotated source: bone of jaw
annotated property: definition
annotated target: A bone element that is part of a jaw region.
has cross-reference: OBOL:automatic

subdivision of tube
type: Class
subclass of: organ part
id: UBERON:0013522
in subset: human subset
in subset: mouse subset

main body axis
type: Class
subclass of: organism subdivision
definition: 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.
id: UBERON:0013701
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: main body axis
annotated property: definition
annotated target: 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.
has cross-reference: https://orcid.org/0000-0002-6601-2165

digestive system element
type: Class
subclass of: organ
definition: Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
has cross-reference: EMAPA:37843
has cross-reference: SCTID:272627002
has exact synonym: digestive organ
has exact synonym: digestive system organ
id: UBERON:0013765
in subset: grouping class
in subset: human subset
in subset: mouse subset
in subset: pheno slim

Axiom
annotated source: digestive system element
annotated property: definition
annotated target: Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
has cross-reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: digestive system element
annotated property: has cross-reference
annotated target: EMAPA:37843
source: MA:th

lateral structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: material anatomical entity
definition: Any structure that is placed on one side of the left-right axis of a bilaterian.
id: UBERON:0015212
in subset: grouping class
in subset: human subset
in subset: mouse subset
in subset: non informative

Axiom
annotated source: lateral structure
annotated property: definition
annotated target: Any structure that is placed on one side of the left-right axis of a bilaterian.
has cross-reference: http://orcid.org/0000-0002-6601-2165

multi organ part structure
type: Class
subclass of: multicellular anatomical structure
definition: An multicellular anatomical structure that has subparts of multiple organs as a part.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has cross-reference: CARO:0020001
has related synonym: anatomical cluster
id: UBERON:0034921
in subset: common anatomy
in subset: human subset
in subset: mouse subset

Axiom
annotated source: multi organ part structure
annotated property: definition
annotated target: An multicellular anatomical structure that has subparts of multiple organs as a part.
has cross-reference: CARO:0020001

Axiom
annotated source: multi organ part structure
annotated property: has related synonym
annotated target: anatomical cluster
has cross-reference: CARO:0020001

obsolete class
type: Class

Mattew Diller
type: NamedIndividual

Bill Duncan
type: NamedIndividual

Alexander D. Diehl
type: NamedIndividual

Daniel W. McNeil
type: NamedIndividual

John Beverley
type: NamedIndividual

Finn Wilson
type: NamedIndividual

Ava E. Cunningham
type: NamedIndividual

Gopikrishnan M Chandrasekharan
type: NamedIndividual

Jisoo Seo
type: NamedIndividual