2022-08-23 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). http://creativecommons.org/licenses/by/4.0/ The Pain Ontology 2026-06-05 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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). alternative label definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for 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" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to 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. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct 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). A provenance property that denotes a synonym to be the preferred one for a specific community. 2025-06-02 preferred label for community CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initialisms 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants 2023-03-03 UK spelling synonym A synonym type for common misspellings 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name 2023-07-27 legal name 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 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. 2023-09-30 INN International Nonproprietary Name nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. 2023-10-12 latin term 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. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. 2023-11-01 acronym 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`. 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. 2025-09-17 has ontology hierarchical property A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 2024-03-25 has symbol An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. 2024-03-18 has cross-reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 Concomitant continuous pain (CCP) in trigeminal neuralgia is often experienced as burning or throbbing. 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. 2024-06-13T22:09:02Z experienced as Brain freeze is a brief, intense pain experienced in the forehead. 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. 2025-04-28T16:36:53Z experienced in is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole part_of BFO:0000050 external quality part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part has_part BFO:0000051 external quality has_part has_part has part has part has_part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps x overlaps y iff they have some part in common. BSPO:cjm mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in RO:0002215 capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in RO:0002216 capable_of_part_of capable_of_part_of capable of part of capable of part of https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to 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. consumes has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output https://wiki.geneontology.org/Has_output 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. inheres in part of characteristic of part of A mereological relationship or a topological relationship mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. RO:0002328 functionally_related_to functionally_related_to functionally related to functionally related to inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of has input input of inverse of has output output of inverse of upstream of causally downstream of 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. causally related to 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. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is '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. influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. causal relation between processes depends on A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process 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. 2026-04-08T19:58:42Z throbbing pain Chronic pain that significantly impacts a person's ability to function. 2026-05-01T20:50:40Z chronic high impact pain 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). 2025-11-24T20:50:19Z emotion process A cognitive process during which an organism is aware of something either internal or external to itself. 2025-11-24T20:52:17Z phenomenal cognitive experience A cognitive process during which an organism is aware of something either internal or external to itself. https://dictionary.apa.org/consciousness A phenomenal cognitive experience evaluated as pleasant or unpleasant. 2025-11-24T20:52:39Z emotional experience (feeling) A phenomenal cognitive experience evaluated as pleasant or unpleasant. https://dictionary.apa.org/feeling 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). 2025-11-24T20:59:47Z sensory experience 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). https://dictionary.apa.org/sensation Pain that is experienced in the temporomandibular joint. 2026-03-17T13:10:32Z TMJ pain temporomandibular joint pain Chronic pain that is persistently occuring in the background. 2026-04-08T16:42:44Z concomitant continuous pain Chronic pain that is persistently occuring in the background. PMID:32791919 Pain that is experienced in the skin, muscles, joints, and bones. 2026-04-08T18:15:23Z somatic pain Pain that is experienced in the skin, muscles, joints, and bones. https://www.verywellhealth.com/what-is-somatic-pain-2564619 https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temperature pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete heat pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete cold pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temporal summation pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temporal summation of heat pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temporal summation of cold pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete pressure pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete punctate pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temporal summation of punctate pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete temporal summation of temperature pain testing procedure true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete pain sensitivity true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete pain questionnaire true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete In Vivo Coping Questionnaire true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete Pain Vigilance and Awareness Questionnaire true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete pain scale score true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete Kohn Reactivity Scale true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete Graded Chronic Pain Scale true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete Likert Scale true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete Western Ontario and McMaster Universities Osteoarthritis Index true https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z obsolete widespread condition questionnaire true An unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage. 2024-06-13T18:46:52Z 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. The "emotional" part of pain captures the affective (i.e., unpleasant) dimension of experiencing pain. pain - 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. An unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage. https://www.iasp-pain.org/resources/terminology/ Pain without known cause or of spontaneous origin. 2026-04-08T17:09:41Z idiopathic pain Pain without known cause or of spontaneous origin. https://dictionary.apa.org/idiopathic Acute transient pain that is severe and has an intensity that flares over baseline. 2026-04-08T17:10:12Z breakthrough pain episodic pain Acute transient pain that is severe and has an intensity that flares over baseline. PMID:16675817 Pain that persists for three months or longer. https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z 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. chronic pain Pain that persists for three months or longer. https://www.iasp-pain.org/advocacy/definitions-of-chronic-pain-syndromes/ Pain that arises from actual or threatened damage to non-neural tissue and is due to the activation of nociceptors. 2024-06-13T18:47:03Z nociceptive pain 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. Pain that arises from actual or threatened damage to non-neural tissue and is due to the activation of nociceptors. https://www.iasp-pain.org/resources/terminology/ A process quality that is the characteristic of a sensory experience. 2025-05-12T17:02:29Z sensation quality 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. 2024-06-13T18:47:11Z nociplastic pain 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. https://www.iasp-pain.org/resources/terminology/ Pain caused by a lesion or disease of the somatosensory nervous system. 2024-06-13T18:47:32Z neuropathic pain 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. 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. Pain caused by a lesion or disease of the somatosensory nervous system. https://www.iasp-pain.org/resources/terminology/ 2024-06-13T20:45:30Z damaged neural tissue Pain caused by a lesion or disease of the central somatosensory nervous system. 2024-06-13T21:22:21Z central nervous system neuropathic pain Pain caused by a lesion or disease of the central somatosensory nervous system. https://www.iasp-pain.org/resources/terminology/ A sensation quality that characterizes a sensation as being persistent, deep, or nagging rather than a sharp or stabbing. 2025-05-12T17:02:36Z dull sensation quality A sensation quality that characterizes a sensation as being persistent, deep, or nagging rather than a sharp or stabbing. https://www.healthline.com/health/dull-pain https://www.merriam-webster.com/dictionary/dull Pain that is experienced throughout the body rather than in a specific area. 2026-04-12T22:16:38Z widespread pain generalized pain http://snomed.info/id/82991003 Pain caused by a lesion or disease of the peripheral somatosensory nervous system. 2024-06-13T21:22:44Z peripheral nervous system neuropathic pain Pain caused by a lesion or disease of the peripheral somatosensory nervous system. https://www.iasp-pain.org/resources/terminology/ Pain that happens suddenly, starts out sharp or intense, and serves as a warning sign of disease or threat to the body. https://orcid.org/0000-0001-9625-1899 2022-11-24T06:02:26Z 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. acute pain Pain that happens suddenly, starts out sharp or intense, and serves as a warning sign of disease or threat to the body. https://www.iasp-pain.org/resources/topics/acute-pain/ Pain that is experienced in an area different from the area stimulated. 2024-06-13T21:22:52Z referred pain Pain that is experienced in an area different from the area stimulated. PMID:37448749 https://dictionary.apa.org/referred-sensation Pain that is experienced in an area where a limb no longer exists. 2024-06-13T21:23:11Z phantom limb pain Pain that is confined or restricted to a particular anatomical area (or zone) of the body. 2024-06-13T21:27:59Z localized pain Pain that is confined or restricted to a particular anatomical area (or zone) of the body. PMID:18077092 https://ospinamedical.com/orthopedic-blog/localized-vs-radicular-pain-decoding-your-discomfort knee pain resulting from knee osteoarthritis. 2024-06-13T21:33:51Z knee osteoarthritis pain A rhythmic, pulsating, or beating sensation quality in which the intensity waxes and wanes in periodic bursts. 2025-05-12T17:06:15Z throbbing sensation quality A intense, searing, or hot sensation quality. 2025-05-12T17:06:31Z burning sensation quality Pain that is experienced in the lower back. 2026-03-17T03:22:33Z lower back pain Pain that is experienced in the area proximal to an amputation site. 2025-04-28T16:45:26Z residual limb pain stump pain 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. 2025-05-12T17:06:51Z freezing sensation quality A sudden, intense, and sharp sensation quality. 2025-05-12T17:07:06Z shooting sensation quality A piercing, stabbling, cutting, or prickling sensation quality. 2025-05-12T17:08:02Z sharp sensation quality A great or extreme sensation quality. 2025-05-12T17:08:30Z intense sensation quality A great or extreme sensation quality. https://www.merriam-webster.com/dictionary/intense A diffuse, sustained, low-to-moderate intensity, dull, deep, pressure-like sensation quality that lacks sharp localization. 2025-05-12T17:08:36Z aching sensation quality An intense, sudden, and sharp sensation, often described as a knife-like or shooting, sensation quality that pierces a specific area. 2025-05-12T17:09:02Z stabbing sensation quality Pain experienced as an intense, sudden, and sharp sensation, often described as a knife-like or shooting pain that pierces a specific body area. 2025-05-12T17:09:33Z stabbing pain Pain that is experienced as piercing, stabbling, cutting, or prickling. 2025-05-12T17:09:47Z sharp pain Pain that is experienced as a deep ache, pressure, or heaviness rather than a sharp, stabbing sensation. 2025-05-12T17:09:53Z dull pain Pain that is experienced as a deep ache, pressure, or heaviness rather than a sharp, stabbing sensation. https://www.healthline.com/health/dull-pain Pain that is experienced as an intense, searing, or hot sensation. 2025-05-12T17:10:00Z burning pain Pain that is experienced as a burning or aching sensation and is the result of cold stimuli. 2025-05-12T17:10:18Z freezing pain Pain that is experienced as a sudden, intense, and sharp sensation that moves or radiates through the body, often from one point to another. 2025-05-12T17:10:35Z shooting pain Pain that is experienced in a limb, such as an arm or leg. 2025-06-23T16:57:24Z limb pain Pain that is experienced in the finger. 2025-06-23T16:57:32Z finger pain Pain that is experienced in a lower limb. 2025-06-23T16:57:36Z lower limb pain Pain that is experienced in the main axis of the body. 2025-06-23T16:58:46Z axial pain Pain that is experienced in the back. 2025-06-23T16:59:01Z back pain 2025-06-23T16:59:08Z neck pain Pain that is experienced in an upper limb. 2025-06-23T16:59:31Z upper limb pain Pain that is experienced in the hand. 2025-06-23T17:01:00Z hand pain Pain that is experienced in the elbow. 2025-06-23T17:01:20Z elbow pain Pain that is experienced in the shoulder. 2025-06-23T17:01:25Z shoulder pain Pain that is experienced in the foot. 2025-06-23T17:01:49Z foot pain Pain that is experienced in the toe. 2025-06-23T17:01:54Z toe pain Pain that is experienced in the head. 2025-06-23T17:02:29Z head pain Pain that is experienced in the orofacial region, which includes the mouth and face. 2025-06-23T17:02:39Z orofacial pain Pain that is experienced in the internal organs. 2025-06-23T17:05:02Z visceral pain Pain that is experienced in the internal organs. https://www.ncbi.nlm.nih.gov/books/NBK12991/ PMID:26516492 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). 2025-06-23T17:11:58Z 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. chronic widespread pain 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. 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). PMID:39445928 https://www.findacode.com/icd-11/code-849253504.html 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. https://www.findacode.com/icd-11/code-849253504.html Pain that is experienced in the upper back. 2026-03-17T03:22:41Z upper back pain Pain that is experienced in the knee. 2026-03-17T03:25:24Z knee pain process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition realizable entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being material entity 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. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 ZFA:0009000 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell 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. CARO:mah FBbt:00007002 ZFA:0009000 Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. ZFA:0009001 neuronal receptor cell (sensu Animalia) neuronal receptor cell neuronal receptor cell Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. FBC:Autogenerated ZFA:0009001 neuron associated cell neuron associated cell Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 MESH:D011984 WBbt:0005759 ZFA:0009053 sensory neuron sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 FBbt:00005124 ZFA:0009053 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. 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 and multiple sclerosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 neuroglial cell neuroglia Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell https://cellxgene.cziscience.com/cellguide/CL_0000125 glial cell 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. MESH:D009457 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 and multiple sclerosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) DOI:10.1002/glia.24343 DOI:10.1038/nn1988 DOI:10.1101/cshperspect.a020602 DOI:10.1126/science.aat0473 DOI:10.3389/fncel.2017.00024 FBbt:00005144 ZFA:0009073 https://cellxgene.cziscience.com/cellguide/CL_0000125 glial cell on CELLxGENE CellGuide A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell sensory receptor cell sensory receptor cell 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. ZFA:0009119 nociceptor nocireceptor Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship pain receptor cell 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. MESH:D009619 ZFA:0009119 nociceptor https://meshb.nlm.nih.gov/record/ui?ui=D009619 nocireceptor https://www.thefreedictionary.com/nocireceptor A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 electrically active cell electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. FB:ma ZFA:0009128 Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell eukaryotic cell Any cell that in taxon some Eukaryota. FBC:Autogenerated A cell whose function is determined by its response to an electric signal. ZFA:0009190 electrically responsive cell electrically responsive cell A cell whose function is determined by its response to an electric signal. FB:ma ZFA:0009190 A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 electrically signaling cell electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. FB:ma ZFA:0009193 A neuron which conveys sensory information centrally from the periphery. FMA:87653 ZFA:0009238 input neuron afferent neuron afferent neuron A neuron which conveys sensory information centrally from the periphery. GOC:tfm MESH:D009475 ZFA:0009238 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. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 ZFA:0009248 nerve cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron neuron https://www.swissbiopics.org/api/image/Neuron_cells.svg 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. MESH:D009474 http://en.wikipedia.org/wiki/Neuron FBbt:00005106 ZFA:0009248 unimodal nocireceptor polymodal nocireceptor A cell that is part of the nervous system. 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 neural cell neural cell A cell that is part of the nervous system. GOC:tfm ISBN:0618947256 characteristic 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. biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential 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. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 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. organ system process biological_process GO:0003008 system process 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. GOC:mtg_cardio 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). https://github.com/geneontology/go-ontology/issues/26810 biological_process response to abiotic stress response to biotic stress GO:0006950 response to stress 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). GOC:mah 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. Reactome:R-HSA-9709957 Wikipedia:Perception biological_process GO:0007600 sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai GOC:dph Reactome:R-HSA-9709957 Sensory Perception 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. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior behavioral response to stimulus The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 The acquisition and processing of information and/or the storage and retrieval of this information over time. biological_process GO:0007611 learning or memory The acquisition and processing of information and/or the storage and retrieval of this information over time. GOC:jid PMID:8938125 Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. Wikipedia:Learning biological_process GO:0007612 learning Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. ISBN:0582227089 ISBN:0721662544 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. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process 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. GOC:pdt 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. response to thermal stimulus biological_process GO:0009266 response to temperature stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. GOC:hb The series of events in which an external stimulus is received by a cell and converted into a molecular signal. biological_process perception of external stimulus GO:0009581 detection of external stimulus The series of events in which an external stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. biological_process perception of abiotic stimulus GO:0009582 detection of abiotic stimulus The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. chemoperception detection of chemical substance biological_process chemoreception perception of chemical stimulus perception of chemical substance GO:0009593 detection of chemical stimulus The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. GOC:jl 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. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb 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. mechanical stimulus response biological_process chemi-mechanical coupling GO:0009612 response to mechanical stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. GOC:hb 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. https://github.com/geneontology/go-ontology/issues/16572 response to abiotic stress biological_process GO:0009628 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to abiotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus. GOC:hb The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal. detection of temperature detection of thermal stimulus biological_process perception of temperature GO:0016048 detection of temperature stimulus The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal. GOC:hb The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. conduction of nerve impulse signal transmission along a neuron biological_process GO:0019226 transmission of nerve impulse The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. GOC:curators ISBN:0815316194 conduction of nerve impulse GOC:dph An action potential that occurs in a neuron. biological_process generation of action potential GO:0019228 neuronal action potential An action potential that occurs in a neuron. GOC:dph GOC:isa_complete GOC:tb generation of action potential GOC:dph GOC:tb 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. https://github.com/geneontology/go-ontology/issues/29807 Wikipedia:Nociception perception of physiological pain biological_process nociception GO:0019233 sensory perception of pain The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. 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. GOC:curators 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. biological_process GO:0019234 sensory perception of fast pain 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. PMID:38704307 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. biological_process GO:0019235 sensory perception of slow pain 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. PMID:38704307 http://www.people.vcu.edu/~mikuleck/ssspain/ Any biological process, occurring at the level of a multicellular organism, pertinent to its function. https://github.com/geneontology/go-ontology/issues/27189 jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 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. multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb 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). biological_process GO:0033555 multicellular organismal response to stress 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). GOC:mah 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. biological_process GO:0042391 regulation of membrane potential 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. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 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. unconditional response biological_process GO:0046958 nonassociative learning 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. ISBN:0582227089 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. Wikipedia:Sensitization biological_process GO:0046960 sensitization 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. ISBN:0582227089 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. GO:0048267 physiological response to pain biological_process GO:0048265 response to pain 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. GOC:jid PMID:10203867 PMID:12723742 PMID:12843304 Wikipedia:Pain 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. behavioural response to pain biological_process GO:0048266 behavioral response to pain 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. GOC:jid An organ system process carried out by any of the organs or tissues of the neurological system. https://github.com/geneontology/go-ontology/issues/13824 neurological system process neurophysiological process biological_process pan-neural process GO:0050877 nervous system process An organ system process carried out by any of the organs or tissues of the neurological system. GOC:ai GOC:mtg_cardio 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. Wikipedia:Cognition biological_process GO:0050890 cognition cognitive process 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. ISBN:0721619908 Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect. biological_process GO:0050893 sensory processing Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect. GOC:dph ISBN:0721662544 Any process in which an emotional response is associated with a particular sensory stimulation. biological_process GO:0050894 determination of affect Any process in which an emotional response is associated with a particular sensory stimulation. GOC:ai GOC:dph ISBN:0721662544 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. Wikipedia:Transduction_(physiology) sensory detection of stimulus sensory perception, sensory transduction of stimulus sensory perception, stimulus detection sensory transduction biological_process GO:0050906 detection of stimulus involved in sensory perception The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. GOC:ai GOC:dos GOC:dph The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of chemical stimulus sensory detection of chemical stimulus during sensory perception sensory perception, sensory detection of chemical stimulus sensory perception, sensory transduction of chemical stimulus sensory transduction of chemical stimulus sensory transduction of chemical stimulus during sensory perception biological_process GO:0050907 detection of chemical stimulus involved in sensory perception The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of temperature stimulus sensory detection of temperature stimulus during sensory perception sensory detection of thermal stimulus during sensory perception sensory perception, sensory detection of temperature stimulus sensory perception, sensory detection of thermal stimulus sensory perception, sensory transduction of temperature stimulus sensory perception, sensory transduction of thermal stimulus sensory transduction of temperature stimulus sensory transduction of temperature stimulus during sensory perception sensory transduction of thermal stimulus during sensory perception sensory detection of heat stimulus during sensory perception sensory perception, sensory detection of heat stimulus sensory perception, sensory transduction of heat stimulus sensory transduction of heat stimulus during sensory perception biological_process GO:0050961 detection of temperature stimulus involved in sensory perception The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal. perception of pain, detection of temperature stimulus perception of pain, sensory detection of temperature stimulus perception of pain, sensory transduction of temperature stimulus sensory detection of temperature stimulus during perception of pain sensory detection of thermal stimulus during sensory perception of pain sensory perception of pain, sensory detection of thermal stimulus sensory perception of pain, sensory transduction of thermal stimulus sensory transduction of temperature stimulus during perception of pain sensory transduction of thermal stimulus during sensory perception of pain biological_process thermal nociception GO:0050965 detection of temperature stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal. GOC:ai GOC:dos thermal nociception GOC:pr The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal. perception of pain, detection of mechanical stimulus perception of pain, sensory detection of mechanical stimulus perception of pain, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of pain sensory transduction of mechanical stimulus during perception of pain biological_process mechanical nociception GO:0050966 detection of mechanical stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos mechanical nociception GOC:pr 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. https://github.com/geneontology/go-ontology/issues/31306 perception of pain, detection of electrical stimulus perception of pain, sensory detection of electrical stimulus perception of pain, sensory transduction of electrical stimulus biological_process detection of electrical stimulus during sensory perception of pain sensory detection of electrical stimulus during perception of pain sensory transduction of electrical stimulus during perception of pain GO:0050967 This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model. obsolete detection of electrical stimulus involved in sensory perception of pain true 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. GOC:ai GOC:dos GOC:dph GOC:tb detection of electrical stimulus during sensory perception of pain GOC:dph GOC:tb The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. perception of pain, detection of chemical stimulus perception of pain, sensory detection of chemical stimulus perception of pain, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of pain sensory transduction of chemical stimulus during perception of pain biological_process chemical nociception GO:0050968 detection of chemical stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. GOC:ai chemical nociception GOC:pr The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of mechanical stimulus sensory detection of mechanical stimulus during sensory perception sensory perception, sensory detection of mechanical stimulus sensory perception, sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus during sensory perception biological_process GO:0050974 detection of mechanical stimulus involved in sensory perception The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events by which a mechanical stimulus is received and converted into a molecular signal. biological_process GO:0050982 detection of mechanical stimulus The series of events by which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. stimulus detection biological_process perception of stimulus stimulus sensing GO:0051606 detection of stimulus The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. GOC:add GOC:ai GOC:dph GOC:mah OBSOLETE. The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. https://github.com/geneontology/go-ontology/issues/31330 dph 2019-09-13T13:48:47Z biological_process GO:0062149 This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model. obsolete detection of stimulus involved in sensory perception of pain true OBSOLETE. The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. PMID:19837031 Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates 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. https://github.com/geneontology/go-ontology/issues/30599 regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality 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. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATO:0000132 PATO:0001565 distribution quality pattern PATO:0000060 spatial pattern A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. quality PATO:0000389 acute A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. dictionary:reference A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. focal localised quality PATO:0000627 localized A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. WordNet:WordNet A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. quality PATO:0001020 damage A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. quality PATO:0001167 damaged A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. WordNet:WordNet A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up. PATO:0001513 diffuse scattered quality PATO:0001566 distributed A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up. WordNet:WordNet A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations. multi-focal quality PATO:0001791 multi-localised A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations. PATOC:GVG A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. quality PATO:0001863 chronic A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. PATOC:cjm 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process Extremely acute and aggressive onset of a pathological process. 2012-09-15T02:57:46Z per-acute quality PATO:0002387 peracute Extremely acute and aggressive onset of a pathological process. PATOC:PNS A quality of duration having progressive course of indefinite duration with active, acute-like elements. 2012-12-17T10:59:58Z quality PATO:0002414 chronic-active A quality of duration having progressive course of indefinite duration with active, acute-like elements. PATOC:MPATH 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. 2019-07-18T18:49:08Z quality PATO:0010005 spatial distribution of a process 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. https://orcid.org/0000-0002-7073-9172 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FAO:0000001 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure UBERON:0000061 anatomical structure anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 FBbt:00007001 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) anatomical unit body organ element UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. Wikipedia:Organ_(anatomy) Wikipedia Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element http://orcid.org/0000-0002-6601-2165 A multicellular structure that is a part of an organ. AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. http://orcid.org/0000-0002-6601-2165 cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision skeletal system part UBERON:0000075 subdivision of skeletal system Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 SCTID:21082005 TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 Wikipedia:Mouth XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg regio oralis adult mouth cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg https://cdn.humanatlas.io/digital-objects/ref-organ/mouth-female/v1.0/assets/3d-vh-f-mouth.glb https://cdn.humanatlas.io/digital-objects/ref-organ/mouth-male/v1.0/assets/3d-vh-m-mouth.glb 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). Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) http://bgee.unil.ch/ in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA FBbt:00003126 regio oralis BTO:0004698 FMA:49184 FMA:TA cavital oralis Wikipedia:Mouth cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus http://orcid.org/0000-0002-6601-2165 vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 UBERON:0000465 material anatomical entity material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007016 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. AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 Wikipedia:Body_part XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region body part body region cardinal body part UBERON:0000475 organism subdivision Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS http://orcid.org/0000-0001-9114-8737 FBbt:00007009 UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 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. AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue UBERON:0000479 tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 FBbt:00007003 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 SCTID:302550007 UMLS:C0027530 Wikipedia:Neck galen:Neck collum neck (volume) UBERON:0000974 neck https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. http://orcid.org/0000-0002-6601-2165 ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum Wikipedia:Neck neck (volume) FMA:7155 The portion of the hindlimb that contains both the stylopod and zeugopod. 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] 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 BTO:0000721 CALOHA:TS-2206 EFO:0001411 EHDAA2:0000972 EHDAA:5151 EHDAA:6176 EHDAA:8289 EMAPA:17489 GAID:49 MA:0000047 MESH:D035002 VHOG:0000345 Wikipedia:Leg#Limb tetrapod leg lower extremity UBERON:0000978 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 leg The portion of the hindlimb that contains both the stylopod and zeugopod. Wikipedia:Leg#Limb 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] 2012-09-17 VHOG:0000345 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ 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 3 lower extremity MESH:A01.378.610 Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 RETIRED_EHDAA2:0003182 SCTID:302536002 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 Wikipedia:Joint XAO:0000171 ZFA:0001596 galen:Joint articular joint joints UBERON:0000982 skeletal joint Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 UBERON:0001062 anatomical entity anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 FBbt:10000000 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:D001415 NCIT:C13062 SCTID:123961009 UMLS:C0004600 Wikipedia:Dorsum_(anatomy) galen:Back back back of body proper dorsal part of organism UBERON:0001137 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 Wikipedia:Dorsum_(anatomy) UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 FMA:24218 SCTID:123852005 XAO:0000040 head subdivision head region region of head UBERON:0001444 subdivision of head A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 SCTID:302549007 UMLS:C0015450 Wikipedia:Face galen:Face facia/facies visage UBERON:0001456 face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg 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). http://orcid.org/0000-0002-6601-2165 Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 http://api.hymao.org/api/ref/67791 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies Wikipedia:Face visage BTO:0003369 The part of the forelimb extending from the shoulder to the autopod[cjm]. 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] BTO:0001435 CALOHA:TS-2204 EFO:0001410 EHDAA2:0000140 EHDAA:4164 EHDAA:6210 EHDAA:8275 EMAPA:17413 GAID:52 MA:0000033 MESH:D001132 VHOG:0000339 Wikipedia:Arm brachium upper extremity UBERON:0001460 arm http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg The part of the forelimb extending from the shoulder to the autopod[cjm]. Wikipedia:Arm 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] 2012-09-17 VHOG:0000339 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ brachium Wikipedia:Arm upper extremity MESH:A01.378.800 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]. cubital Naming conventions for pod terms under discussion within phenoscape group CALOHA:TS-2222 EFO:0003069 EHDAA2:0000429 EHDAA:4166 EHDAA:6212 EMAPA:17414 FMA:24901 GAID:54 MA:0000036 MESH:D004550 SCTID:76248009 VHOG:0000340 Wikipedia:Elbow galen:Elbow cubital region elbow limb segment elbow region articulatio cubiti UBERON:0001461 elbow https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG 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]. Wikipedia:Elbow articulatio cubiti Wikipedia:Elbow A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. BTO:0003595 CALOHA:TS-2220 EHDAA2:0000895 EHDAA:5159 EHDAA:6184 EMAPA:17493 FMA:24974 GAID:48 MA:0000046 MESH:D007717 SCTID:361291001 VHOG:0000347 galen:Knee knee region UBERON:0001465 knee http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. https://orcid.org/0000-0002-6601-2165 A digit that is part of a pes (foot). UBERON:0000027 AAO:0000888 BTO:0002348 EMAPA:32649 FMA:25046 GAID:44 MA:0000048 NCIT:C33788 SCTID:116667001 UMLS:C0040357 Wikipedia:Toe XAO:0003035 galen:Toe digit of foot digit of terminal segment of lower limb digiti pedis digitus pedis foot digit hind digit hind_digit hindlimb digit pedal digit (phalangeal portion) plus soft tissue pes digit toe digiti pedis digitipedis UBERON:0001466 pedal digit http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg A digit that is part of a pes (foot). https://orcid.org/0000-0002-6601-2165 UMLS:C0040357 ncithesaurus:Toe digit of terminal segment of lower limb OBOL:automatic digiti pedis FMA:70664 FMA:TA foot digit MA:0000048 hind digit XAO:0003035 hind_digit AAO:0000888 pedal digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 toe FMA:25046 digiti pedis Wikipedia:Toe digitipedis BTO:0002348 A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] 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 CALOHA:TS-2229 EFO:0003068 EHDAA2:0001834 EHDAA:4180 EHDAA:6228 EMAPA:17421 FMA:25202 GAID:60 MA:0000038 MESH:D012782 NCIT:C25203 SCTID:361103004 UMLS:C0037004 VHOG:0000342 Wikipedia:Shoulder galen:Shoulder shoulder region articulatio humeri UBERON:0001467 shoulder http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). http://orcid.org/0000-0002-6601-2165 (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] 2012-09-17 VHOG:0000342 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332 http://bgee.unil.ch/ 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 FMA UMLS:C0037004 ncithesaurus:Shoulder articulatio humeri Wikipedia:Shoulder Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 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] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 SCTID:90780006 TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 Wikipedia:Bone XAO:0000169 ZFA:0001514 galen:Bone bone organ bone bones UBERON:0001474 bone element Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 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] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO 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] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) http://bgee.unil.ch/ UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton. mandibular 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 'mandible' also refers to either the upper OR lower part of the beak in birds lower jaw lower jaw bone BTO:0001748 CALOHA:TS-2225 EFO:0001965 EHDAA2:0001059 EHDAA:8007 EMAPA:18290 FMA:52748 GAID:68 MA:0001487 MESH:D008334 NCIT:C12290 SCTID:181812008 UMLS:C0024687 Wikipedia:Human_mandible galen:Mandible inferior maxillary bone mammaliam mandible mandibulla lower mandibula mandibula mandibular series UBERON:0001684 mandible http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton. Wikipedia:Human_mandible Wikipedia:Mandible 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 ZFA lower jaw lower jaw bone UMLS:C0024687 ncithesaurus:Mandible lower mandibula Wikipedia:Mandible mandibula BTO:0001748 Wikipedia:Human_mandible mandibular series ZFA:0001273 Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 SCTID:113234001 TAO:0005153 Wikipedia:Synovial_joint ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. FMA:7501 Wikipedia:Synovial_joint Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 Distal portion of the hind limb, including tarsal region, metatarsal region and digits. pedal BTO:0000476 CALOHA:TS-0377 EFO:0003065 EHDAA2:0000546 EMAPA:17459 FMA:9664 GAID:40 MA:0000044 MESH:D005528 NCIT:C32622 SCTID:302545001 UMLS:C0016504 VHOG:0000350 Wikipedia:Pes_(anatomy) galen:Foot foot hindlimb autopod hindlimb autopodium hindlimb distal free limb segment pes terminal segment of free lower limb hind foot hind paw hind-paw hindfeet hindfoot hindfoot of quadruped hindpaw hind limb autopodium UBERON:0002387 pes http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg Distal portion of the hind limb, including tarsal region, metatarsal region and digits. Wikipedia:Foot Wikipedia:Pes_(anatomy) UMLS:C0016504 ncithesaurus:Foot foot MA:0000044 hindlimb autopod OBOL:automatic hindlimb autopodium OBOL:automatic hindlimb distal free limb segment OBOL:automatic pes https://orcid.org/0000-0002-6601-2165 hind paw EMAPA:17428 OBOL:automatic hind-paw EMAPA:17428 hindfeet hindpaw MA:0000044 hind limb autopodium VHOG:0000350 A digit that is part of a manus (hand). One of the fingers of the manus.[AAO] UBERON:0000028 AAO:0000857 BTO:0004669 EHDAA2:0000404 EMAPA:32642 FMA:9666 GAID:57 MA:0000041 MESH:D005385 NCIT:C32608 NLXANAT:20090602 SCTID:283992002 UMLS:C0016129 Wikipedia:Finger XAO:0003036 galen:Finger digit of hand digit of manus digitus manus finger fore digit forelimb digit hand digit manual digit (phalangeal portion) plus soft tissue UBERON:0002389 manual digit A digit that is part of a manus (hand). http://orcid.org/0000-0002-6601-2165 One of the fingers of the manus.[AAO] 2012-06-20 AAO:0000857 AAO AAO:LAP UMLS:C0016129 ncithesaurus:Finger digit of hand FMA:9666 finger FMA:9666 fore digit AAO:0000857 XAO:0003036 hand digit MA:0000041 manual digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods. Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO] Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO] relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO] relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO] 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] maxillary upper jaw bone AAO:0000285 CALOHA:TS-2217 EHDAA2:0001068 EHDAA:8043 EMAPA:17639 FMA:9711 GAID:220 MA:0001491 MESH:D008437 NCIT:C26470 SCTID:181813003 TAO:0000270 UMLS:C0024947 VHOG:0001021 VSAO:0000207 Wikipedia:Maxilla ZFA:0000270 galen:Maxilla maxillae maxillary bone UBERON:0002397 Fusion of maxilla + premaxilla maxilla http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods. Wikipedia:Maxilla http://palaeos.com/vertebrates/glossary/glossaryM.html Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO] 2012-08-14 TAO:0000270 TAO TAO:GA_TG Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO] 2012-06-20 AAO:0000285 AAO AAO:LAP relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO] 2012-08-14 TAO:0000270 TAO relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO] 2012-08-14 TAO:0000270 TAO 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] 2012-09-06 TAO:0000270 TAO Curator UMLS:C0024947 ncithesaurus:Maxilla maxillae maxillary bone Wikipedia:Maxilla Distal segment of the fore limb, including carpal region, metacarpal region and digits. manual AAO:0010803 BTO:0004668 CALOHA:TS-2213 EHDAA2:0000728 EMAPA:17428 FMA:9712 GAID:56 MA:0000037 MESH:D006225 NCIT:C32712 NLXANAT:20090603 SCTID:302539009 UMLS:C0018563 VHOG:0000344 Wikipedia:Manus_(anatomy) galen:Hand forelimb autopod forelimb autopodium hand hand region terminal segment of free upper limb fore foot fore paw fore-paw forefeet forefoot forefoot of quadruped forepaw UBERON:0002398 manus http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg Distal segment of the fore limb, including carpal region, metacarpal region and digits. Wikipedia:Hand Wikipedia:Manus_(anatomy) UMLS:C0018563 ncithesaurus:Hand forelimb autopod OBOL:automatic forelimb autopodium OBOL:automatic hand MA:0000037 hand region EHDAA2:0000728 fore foot fore paw EMAPA:17428 OBOL:automatic fore-paw EMAPA:17428 forefeet forefoot forepaw MA:0000037 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. Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton. autopod BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 NCIT:C77660 SCTID:95936004 UMLS:C0687080 autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb autopodial element distal segment of limb manus/pes paw paw/hand/foot/hoof pod UBERON:0002470 autopod region 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. https://github.com/obophenotype/uberon/issues/303 https://orcid.org/0000-0002-6601-2165 autopod MA:0002714 UMLS:C0687080 ncithesaurus:Paw autopodial limb segment MA:th distal free limb segment FMA:83015 distal segment of free limb FMA:83015 distal segment of limb EMAPA:32722 Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] EMAPA:36615 TAO:0001644 Wikipedia:Intramembranous_ossification ZFA:0001635 intramembranous bones membrane bone UBERON:0002514 intramembranous bone 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]. GO:0001957 Wikipedia:Intramembranous_ossification https://github.com/obophenotype/uberon/issues/267 Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] 2012-08-14 TAO:0001644 TAO TAO:wd [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] 2012-09-06 TAO:0001644 TAO Curator intramembranous bones ZFA:0001635 membrane bone AEO:0000085 A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA:241863 MA:0002889 NCIT:C38630 UMLS:C1268195 free limb segment segment of limb subdivision of limb extremity part limb region region of limb UBERON:0002529 limb segment 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. https://orcid.org/0000-0002-6601-2165 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 FMA UMLS:C1268195 ncithesaurus:Extremity_Part free limb segment FMA:241863 A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] digital AAO:0011126 EFO:0000881 EMAPA:32725 FMA:85518 MA:0000690 MAT:0000285 MIAA:0000285 NCIT:C40186 SCTID:361367007 UMLS:C0582802 VHOG:0000944 Wikipedia:Digit_(anatomy) XAO:0003032 galen:Digit acropodial unit digit (phalangeal portion) plus soft tissue limb digit UBERON:0002544 digit 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). http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/420 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] 2012-09-17 VHOG:0000944 VHOG DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008) http://bgee.unil.ch/ FMA:85518 GAT UMLS:C0582802 ncithesaurus:Digit digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 limb digit MA:0000690 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 SCTID:110530005 UMLS:C0037303 Wikipedia:Skull WikipediaCategory:Skull galen:Skull cranial skeleton skeletal system of head UBERON:0003129 skull Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. PMID:11523816 Wikipedia:Skull http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376 in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 SCTID:118646007 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone http://orcid.org/0000-0002-6601-2165 A bone that is part of a facial skeleton [Automatically generated definition]. EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 MESH:D005147 NCIT:C63706 SCTID:181799005 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic MESH:D005147 UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A synovial joint of the jaw that connects the mandible to the temporal bone. BTO:0003674 EMAPA:19196 FMA:54832 GAID:272 MA:0002899 MESH:D013704 NCIT:C32888 SCTID:181814009 UMLS:C0039493 Wikipedia:Temporomandibular_joint TMJ temperomandibular joint articulatio temporomandibularis dentary-squamosal joint squamosal-dentary joint tempero-mandibular joint temporalmandibular joint temporomandibular temporomandibular articulation temporomandibular joint UBERON:0003700 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]. temporomandibular joint http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray309.png A synovial joint of the jaw that connects the mandible to the temporal bone. Wikipedia:Temporomandibular_joint UMLS:C0039493 ncithesaurus:Jaw_Joint TMJ BTO:0003674 Wikipedia:Temporomandibular_joint temperomandibular joint HP:0010754 articulatio temporomandibularis Wikipedia:Temporomandibular_joint dentary-squamosal joint http://palaeos.com/vertebrates/glossary/glossaryT.html squamosal-dentary joint http://palaeos.com/vertebrates/glossary/glossaryT.html tempero-mandibular joint Wikipedia:Temporomandibular_joint temporalmandibular joint Wikipedia:Temporomandibular_joint temporomandibular Wikipedia:Temporomandibular_joint temporomandibular articulation Wikipedia:Temporomandibular_joint temporomandibular joint Wikipedia:Temporomandibular_joint Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 SCTID:91728009 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. https://orcid.org/0000-0002-6601-2165 ectodermal deriviative FBbt:00025990 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]. 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] 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] 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] relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] 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] 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. AAO:0000124 EFO:0003508 TAO:0000191 VHOG:0001022 ZFA:0000191 http://palaeos.com/vertebrates/bones/dermal/images/Dentary1.gif dentaries dentary bone dentale os dentale sur-angulaire UBERON:0004742 dentary 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]. VHOG:0001022 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] 2012-08-14 TAO:0000191 TAO TAO:GA_TG 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] 2012-06-20 AAO:0000124 AAO AAO:LAP 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] 2012-09-17 VHOG:0001022 VHOG http://bgee.unil.ch/ relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] 2012-08-14 TAO:0000191 TAO 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] 2012-09-17 VHOG:0001022 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248 http://bgee.unil.ch/ dentaries TAO:0000191 dentary bone ZFA:0000191 dentale AAO:0000124 os dentale AAO:0000124 sur-angulaire AAO:0000124 Dermis-derived entity that is made of skeletal tissue. dermal element UBERON:0004756 dermal skeletal element Dermis-derived entity that is made of skeletal tissue. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/206 dermal element VSAO:curator Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure UBERON:0004765 skeletal element Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. lower jaw bone UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. https://orcid.org/0000-0002-6601-2165 Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint UBERON:0004905 articulation Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 FBbt:00005811 A proximal-distal subdivision of the digestive tract. FBbt:00100315 FMA:71131 alimentary system subdivision gut section intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 FBbt:00100315 alimentary system subdivision FMA:71131 gut section FBbt:00100315 subdivision of alimentary system FMA:71131 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]. lumbar lumbar region BTO:0001505 EMAPA:36623 FMA:61681 MA:0000027 NCIT:C34004 SCTID:182343007 UMLS:C0024090 abdominal back back of abdomen dorsum of abdomen lower back lumbar part of back lumbar region of back posterior part of abdomen regio lumbalis loin lombus lumbos UBERON:0005462 overlaps with region sometimes called 'loin' lower back 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]. FMA:61681 lumbar region FMA:61681 UMLS:C0024090 ncithesaurus:Lumbar_Region abdominal back FMA:61681 back of abdomen FMA:61681 dorsum of abdomen FMA:61681 lower back MA:0000027 lumbar part of back FMA:61681 lumbar region of back https://orcid.org/0000-0002-6601-2165 posterior part of abdomen FMA:61681 regio lumbalis FMA:61681 FMA:TA loin BTO:0001505 Wikipedia:Loin A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. digit or predigit limb outgrowth UBERON:0005881 encompasses digits and prepollex. requires review autopodial extension A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. http://orcid.org/0000-0002-6601-2165 A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). UBERON:0006058 multi-limb segment region https://github.com/obophenotype/uberon/issues/514 A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). https://orcid.org/0000-0002-6601-2165 That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] BTO:0004150 EHDAA:5063 EMAPA:17396 FMA:9140 MA:0003155 NCIT:C69315 SCTID:243931006 UMLS:C0581269 axial skeleton thoracic region columna vertebralis thoracicus thoracic spine thoracic vertebrae series thoracic vertebral column UBERON:0006073 thoracic region of vertebral column That part of the spine comprising the thoracic vertebrae. http://medical-dictionary.thefreedictionary.com/ Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0581269 ncithesaurus:Thoracic_Spine axial skeleton thoracic region MA:0003155 columna vertebralis thoracicus FMA:9140 thoracic spine FMA:9140 thoracic vertebral column FMA:9140 A collection of all skeletal elements in some subdivision of the vertebral column. FMA:16201 subdivision of vertebral skeleton vertebrae series vertebral column subdivision vertebral series vertebral region vertebral subdivision UBERON:0006077 subdivision of vertebral column A collection of all skeletal elements in some subdivision of the vertebral column. https://orcid.org/0000-0002-6601-2165 subdivision of vertebral skeleton https://orcid.org/0000-0002-6601-2165 vertebral column subdivision FMA:16201 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 membrane bones UBERON:0007842 membrane bone Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone cranial bone UBERON:0007914 bone of craniocervical region A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. 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] FMA:7478 SCTID:333008005 Wikipedia:Skeletal_pneumaticity galen:PneumaticBone os pneumaticum pneumatic bone hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. http://www.medilexicon.com/medicaldictionary.php?t=11303 os pneumaticum FMA:7478 pneumatic bone FMA:7478 A limb segment that is part of a hindlimb. FMA:24877 free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb UBERON:0008784 lower limb segment A limb segment that is part of a hindlimb. OBOL:automatic free lower limb segment FMA:24877 free lower limb subdivision FMA:24877 segment of free lower limb FMA:24877 subdivision of free lower limb FMA:24877 A limb segment that is part of a forelimb. FMA:24876 free upper limb segment free upper limb subdivision segment of free upper limb subdivision of free upper limb UBERON:0008785 upper limb segment A limb segment that is part of a forelimb. OBOL:automatic free upper limb segment FMA:24876 free upper limb subdivision FMA:24876 segment of free upper limb FMA:24876 subdivision of free upper limb FMA:24876 Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 Wikipedia:Dermal_bone XAO:0004015 ZFA:0001590 dermal bones UBERON:0008907 dermal bone Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 FMA:25054 SCTID:22943007 region of trunk trunk subdivision UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure UBERON:0010000 multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure FBbt:00100313 An anatomical structure that develops from the neural crest. UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 An anatomical structure that has some part that develops from the neural crest. UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 An appendage segment that is part of a limb/fin. limb/fin segment UBERON:0010538 paired limb/fin segment An appendage segment that is part of a limb/fin. OBOL:automatic 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. FBbt:00007018 appendage segment appendicular segment UBERON:0010758 subdivision of organism along appendicular axis A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. https://orcid.org/0000-0002-6601-2165 FBbt:00007018 appendage segment FBbt:00007018 Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 Wikipedia:Facial_skeleton facial skeleton facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg Subdivision of skull that consists of the facial bones. MP:0005274 Wikipedia:Facial_skeleton http://www.bartleby.com/107/37.html https://orcid.org/0000-0002-6601-2165 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia Wikipedia:Facial_skeleton ossa faciei Wikipedia:Facial_skeleton viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton. FMA:54964 skull subdivision subdivision of skull UBERON:0011158 primary subdivision of skull The skull can be divided into two: the neurocranium and the facial skeleton. http://orcid.org/0000-0002-6601-2165 skull subdivision FMA:54964 subdivision of skull FMA:54964 Synovial joint that articulates bones of upper and lower jaw. Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long jaw joint craniomandibular joint UBERON:0011171 joint connecting upper and lower jaws Synovial joint that articulates bones of upper and lower jaw. http://evolution.berkeley.edu/evolibrary/article/evograms_05 https://orcid.org/0000-0002-6601-2165 Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long http://evolution.berkeley.edu A subdivision of an anatomical system. FBbt:00007330 FMA:67509 SCTID:91690000 UBERON:0011216 organ system subdivision A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 FBbt:00007330 Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). upper jaw bone UBERON:0011597 bone of upper jaw Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). https://orcid.org/0000-0002-6601-2165 A bone element that is part of a jaw region. EMAPA:35453 MA:0003130 SCTID:369003004 jaw bone UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic UBERON:0013522 subdivision of tube A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. https://orcid.org/0000-0002-6601-2165 Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 SCTID:272627002 digestive organ digestive system organ UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. http://orcid.org/0000-0002-6601-2165 EMAPA:37843 MA:th Any structure that is placed on one side of the left-right axis of a bilaterian. UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://orcid.org/0000-0002-6601-2165 An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster UBERON:0034921 multi organ part structure An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 obsolete class Mattew Diller Bill Duncan Alexander D. Diehl Daniel W. McNeil John Beverley Finn Wilson Ava E. Cunningham Gopikrishnan M Chandrasekharan Jisoo Seo