Bairong Shen Danting Li Hui Zong Jiao Wang Ke Zhang Min Jiang Ting Bao Tong Tang Xingyun Liu Yin Yang A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise. EXMO Exercise Medicine Ontology https://creativecommons.org/licenses/by/4.0/ Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example 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 example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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. 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> no DEFINITION definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note editor_note editor note editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor 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 alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source 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 URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand 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 An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. PERSON:Alan Ruttenberg first order logic expression OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has 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 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 An association that specifies one of three data types for a particular variable, String, Code or Number. A23 Conceptual Entity Has_PCDC_Data_Type Has_PCDC_Data_Type Has_PCDC_Data_Type An association that shows which PCDC AML Authorized Values are possible for a specific Variable. A26 Conceptual Entity Has_PCDC_AML_Authorized_Value Has_PCDC_AML_Authorized_Value Has_PCDC_AML_Authorized_Value An association connecting a CTDC Property concept to its dedicated value concept(s). A27 Conceptual Entity Has_CTDC_Value Has_CTDC_Value Has_CTDC_Value An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept. A29 Conceptual Entity Has_PCDC_EWS_Authorized_Value Has_PCDC_EWS_Authorized_Value Has_PCDC_EWS_Authorized_Value An association that connects a concept representing a GDC property to its dedicated value concept(s). A31 Conceptual Entity Has_GDC_Value Has_GDC_Value Has_GDC_Value An association that that connects a concept representing a GDC value to any associated GDC property concept(s). A32 Conceptual Entity Is_Value_For_GDC_Property Is_Value_For_GDC_Property Is_Value_For_GDC_Property An association that shows which Authorized Values are possible for a specific PCDC GCT Variable. A34 Conceptual Entity Has_PCDC_GCT_Authorized_Value Has_PCDC_GCT_Authorized_Value Has_PCDC_GCT_Authorized_Value An association that shows which PCDC ALL Authorized Values are possible for a specific Variable. A36 Conceptual Entity Has_PCDC_ALL_Authorized_Value Has_PCDC_ALL_Authorized_Value Has_PCDC_ALL_Authorized_Value An association that shows which Authorized Values are possible for a specific SeroNet Variable. A37 Conceptual Entity Has_SeroNet_Authorized_Value Has_SeroNet_Authorized_Value Has_SeroNet_Authorized_Value An association that shows which Authorized Values are possible for a specific PCDC OS Variable. A38 Conceptual Entity Has_PCDC_OS_Authorized_Value Has_PCDC_OS_Authorized_Value Has_PCDC_OS_Authorized_Value An association that shows which Authorized Values are possible for a specific PCDC HL Variable. A39 Conceptual Entity Has_PCDC_HL_Authorized_Value Has_PCDC_HL_Authorized_Value Has_PCDC_HL_Authorized_Value An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable. A40 Conceptual Entity Has_DIPG_DMG_Authorized_Value Has_DIPG_DMG_Authorized_Value Has_DIPG_DMG_Authorized_Value An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute. A42 Conceptual Entity Has_OORO_PC_Value Has_OORO_PC_Value Has_OORO_PC_Value true A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. NHC0 Conceptual Entity code code code A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. P106 Conceptual Entity Semantic Type Semantic_Type In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic_Type A property representing an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name A property representing the word or phrase that NCI uses by preference to refer to the concept. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name A property used to store the name of parent concepts present at the time a concept was retired. P200 Conceptual Entity OLD PARENT OLD_PARENT OLD_PARENT OLD_PARENT A property used to store the name of children concepts present at the time a concept was retired. P201 Conceptual Entity OLD CHILD OLD_CHILD OLD_CHILD OLD_CHILD Used to store the name of the concept's kind at the time a concept was retired. P203 Conceptual Entity OLD KIND OLD_KIND OLD_KIND OLD_KIND A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS). P208 Conceptual Entity NCI Metathesaurus CUI NCI_META_CUI NCI_META_CUI NCI_META_CUI A property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used. P310 Conceptual Entity Concept Status Concept_Status Concept_Status Concept_Status A property used to flag terms that are part of an FDA data standard manual, including Route of Administration, Dosage Form, Package Type and Potency. P317 Conceptual Entity FDA Table FDA_Table FDA_Table FDA_Table A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source A property representing the English language definition of a concept from a source other than NCI. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION true A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name Legacy Concept Name A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms. P375 Conceptual Entity Maps_To Maps_To Maps_To A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote An alternative term used by the IEDB. IEDB alternative term Oliver He Sam Smith US Standard Occupational Classification (SOC) ID https://www.bls.gov/oes/current/oes_stru.htm https://www.bls.gov/soc/ US SOC ID '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 A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term Oliver He term mapping to NCIT ID An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] ambiguous for taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon defined by inverse An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. annotation property cardinality A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. dispositional interpretation 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) has no connections with inherited annotation property Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) curator guidance link brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in always present in taxon This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. temporal logical macro assertion on a class measurement property has unit has start time value has end time value Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. start, days post fertilization Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. end, days post fertilization Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. start, years post birth Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 end, years post birth Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. start, months post birth Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 end, months post birth Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. month of gestation A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process has developmental stage marker Count of number of days intervening between the start of the stage and the time of coitum. For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) start, days post coitum Count of number of days intervening between the end of the stage and the time of coitum. end, days post coitum start, weeks post birth end, weeks post birth If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p is asymmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p is symmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process is relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y is indirect form of logical macro assertion on an axiom If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. is relational form of a class A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" is approximately equivalent to 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is indistinguishable from evidential logical macro assertion on an axiom A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom has evidence A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom contradicted by evidence In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. nominally disjoint with Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" 2018-03-13T23:59:29Z is directional form of 2018-03-14T00:03:16Z is positive form of 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for An administrative note of use for a curator but of no use for a user. no organizational term IAO:0000232 editor_notes curator note A source from where the formal description was derived. This can be in the form of a link to a relevant webpage, the IRI of a term in an existing ontology, a reference to specific literature, etc. yes metadata complete - requires restrictions and relationships IAO:0000119 definition source description source An assertion of whether or not the term/class description is an adaptation of the description in the description source. Requested inclusion of this property into RO. Check details here again after inclusion. metadata complete - requires restrictions and relationships SCDO description adapted from source Description inherent in name (not provided by source) Only label adapted organizational term property has curation status An indication of whether a term/class already exists in other ontologies. Only used for term (descriptions) that were not taken directly from an existing ontology. SCDO (Jade Hotchkiss) existence in other ontologies Used to record the identifier that had been used previously but is no longer in use. SCDO (Jade Hotchkiss) previous identifier An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. uberon external_definition external_definition 2020-09-22T11:05:29Z valid_for_go_annotation_extension 2020-09-22T11:05:18Z valid_for_go_gp2term 2020-09-22T11:04:12Z valid_for_go_ontology 2020-09-22T11:05:45Z valid_for_gocam Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 human_stages_ontology end_ypb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. end, years post birth human_stages_ontology has_unit true Used to associate a measurement property (e.g. days post fertilization) with a unit (e.g. days) has unit Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. human_stages_ontology start_ypb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. start, years post birth eco subset An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group or a curator.) The SCDO uses this especially to apply to term descriptions. no ready for release dc:creator Creator relation is referenced by relation subset_property creation date ID of merged class. has_alternative_id 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 A database cross-reference. An annotation which directs one to information contained within a database. A property representing a reference to an identical or very similar object in another database. Reference database or publication source. Conceptual Entity xRef metadata complete - requires restrictions and relationships SBO:0000554 DbXref Xref database cross-reference database_cross_reference db xref hasDbXref database cross reference database_cross_reference has database cross reference xRef A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle. An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. Exact synonym. Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 no pending vetting by the SCDO developers FULL_SYN Synonym with Source Data has exact synonym has exact synonym hasExactSynonym 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 has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has_obo_format_version Name space of the ontology. disease_ontology has_obo_namespace 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. Has related synonym. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 An identifier for an individual entity. An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. id An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. In subset. Concept_In_Subset in subset in_subset shorthand Comment. comment comment is defined by is defined by This is an experimental annotation label A human readable name for this class. A human-readable name for the class/term. yes A human-readable name for the subject. label label rdfs:label equivalent property A skos concept mapping used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably. has exact match A preferred label. yes pending vetting by the SCDO developers skos:prefLabel alternate name library_of_congress_subject_headings Library of Congress Subject Headings http://purl.org/dc/terms/LCSH https://viaf.org/viaf/174475040 library_of_congress_classification Library of Congress Classification viaf_id VIAF ID medical_dictionary_for_regulatory_activities_id Medical Dictionary for Regulatory Activities ID derived_from derived from snomed_ct_identifier SNOMED CT Identifier is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 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 Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 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 occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in https://wiki.geneontology.org/Occurs_in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process is about 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 A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic https://github.com/oborel/obo-relations/pull/284 A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is allergic trigger for A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is autoimmune trigger for penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has allergic trigger A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has autoimmune trigger located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of surface of 2D boundary of May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 aligned with my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary A relation that holds between two neurons that are electrically coupled via gap junctions. electrically_synapsed_to The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). tracheates innervated_by has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y cell expresses x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). regulates in other organism regulates in another organism A relationship that holds between a process that regulates a transport process and the entity transported by that process. regulates transport of A part of relation that applies only between occurrents. occurrent part of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. 2017-07-19T17:30:36Z has ligand Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. 2017-07-20T17:11:08Z transports A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. 2017-07-20T17:19:37Z occurs across 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. 2017-12-07T12:58:06Z in register with A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time. David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of RO:0002087 immediately_preceded_by David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland starts before ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during https://wiki.geneontology.org/Happens_during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Ib_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Is_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type II bouton. BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_II_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type II bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_II_bouton Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Ib_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in has neurotransmitter releases neurotransmitter Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Is_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in A relation between a motor neuron and a muscle that it synapses to via a type III bouton. BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_III_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type III bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_III_bouton Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) dendrite synapsed in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has synaptic terminal in x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) has fasciculating neuron projection Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) innervates X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) continuous with FMA:85972 x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom proper overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) partially overlaps d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. ancestral_stucture_of evolutionarily_descended_from derived by descent from inverse of derived by descent from has derived by descendant two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' VBO calls this homologous_to shares ancestor with serially homologous to lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) attached to part of true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure supplies Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). has phenotype inverse of has phenotype phenotype of x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y This is the transitive form of the develops from relation develops from inverse of develops from develops into definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. gene product of every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y has gene product 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process expressed in Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. FBbt has developmental precursor TODO - add child relations from DOS directly develops from A parasite that kills or sterilizes its host parasitoid of inverse of parasitoid of has parasitoid inverse of directly develops from developmental precursor of directly develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. has prototype 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 For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". 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 capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by surrounds Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. 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 inverse of starts with Chris Mungall Allen starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y develops from part of x develops_in y if x is located in y whilst x is developing EHDAA2 Jonathan Bard, EHDAA2 develops in A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of inverse of ends with ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y ends with process that occurs in has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. 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 A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. hemiparasite of X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. has component participant A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. ExO:0000001 has exposure receptor A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 has exposure stressor A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 has exposure route A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 has exposure transport path Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. over-expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. under-expressed in Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance has active pharmaceutical ingredient has active ingredient inverse of has active ingredient active ingredient in In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. connecting branch of inverse of connecting branch of has connecting branch Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] developmentally induced by Inverse of developmentally induced by developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) has chemical role A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage replaces developmentally replaces Inverse of developmentally preceded by developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue part of developmental precursor of x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. ubiquitously expressed in y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses inverse of ubiquiotously expressed in ubiquitously expresses p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. http://www.geneontology.org/GO.doc.development.shtml results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) GOC:mtg_berkeley_2013 results in formation of anatomical entity an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. GOC:mtg_berkeley_2013 results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. GOC:mtg_berkeley_2013 results in maturation of foramen ovale closure SubClassOf results in disappearance of foramen ovale May be merged into parent relation results in disappearance of every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) May be merged into parent relation results in developmental regression of Inverse of 'is substance that treats' is treated by substance Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. 2017-06-05T17:35:04Z has exposure stimulus evolutionary variant of Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. regulates localization of transports or maintains localization of 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. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity GOC:mtg_berkeley_2013 results in acquisition of features of A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. adapted for confers advantage in A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] colocalizes with ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to https://wiki.geneontology.org/Contributes_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 This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables 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. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in https://wiki.geneontology.org/Involved_in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of (process to entity) regulates levels of inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by A relationship that holds via some process of localization Do not use this relation directly. It is a grouping relation. related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. has target end location Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. imports Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l results in transport along Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. results in transport across 'pollen tube growth' results_in growth_of some 'pollen tube' results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) results in transport to from or in Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. exports an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. results in commitment to p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. results in determination of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input input of inverse of has output output of formed as result of A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. results in structural organization of The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. results in specification of p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. results in developmental induction of http://neurolex.org/wiki/Property:DendriteLocation has dendrite location a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a attached to (anatomical structure to anatomical structure) attached to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) has muscle origin m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) has muscle insertion false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. derived from ancestral fusion of A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) tributary of http://en.wikipedia.org/wiki/Tributary Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x branch of distributary channel of http://en.wikipedia.org/wiki/Distributary This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes distributary of x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. anastomoses with anabranch of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y branching part of FMA:85994 In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. main stem of x proper_distributary_of y iff x distributary_of y and x does not flow back into y proper distributary of x proper_tributary_of y iff x tributary_of y and x does not originate from y proper tributary of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to 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 immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. directly provides input for directly provides input for (process to process) provides input for https://wiki.geneontology.org/Provides_input_for transitive form of directly_provides_input_for This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) transitively provides input for p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within false This is an exploratory relation differs in https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions differs in attribute of differs in attribute inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) genetically interacts with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. interacts with on organism level biotically interacts with http://eol.org/schema/terms/interactsWith An interaction relationship in which the partners are related via a feeding relationship. trophically interacts with A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members is subject of predation interaction with preys upon preys on http://eol.org/schema/terms/preysUpon http://www.inaturalist.org/observations/2942824 A biotic interaction in which the two organisms live together in more or less intimate association. http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism symbiotically interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 commensually interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 mutualistically interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by interacts with via parasite-host interaction Pediculus humanus capitis parasite of human A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of parasite of http://eol.org/schema/terms/parasitizes Inverse of parasite of has parasite parasitised by directly parasitized by parasitized by http://eol.org/schema/terms/hasParasite Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. semibiotically interacts with participates in a abiotic-biotic interaction with Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints transmitted by A relation that holds between a disease or an organism and a phenotype has symptom The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y has host http://eol.org/schema/terms/hasHost Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. is subject of pollination interaction with pollinates http://eol.org/schema/terms/pollinates has polinator is target of pollination interaction with pollinated by http://eol.org/schema/terms/hasPollinator Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from inverse of preys on has predator is target of predation interaction with preyed upon by http://eol.org/schema/terms/HasPredator http://polytraits.lifewatchgreece.eu/terms/PRED Anopheles is a vector for Plasmodium a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for has vector Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is symbiosis is commensalism is mutualism is parasitism A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with eats Inverse of eats eaten by is target of eating interaction with is eaten by A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. is evidence for 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. composed primarily of ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. child nucleus of A child nucleus relationship in which the cells are part of a hermaphroditic organism child nucleus of in hermaphrodite A child nucleus relationship in which the cells are part of a male organism child nucleus of in male p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later ubiquitinates is kinase activity is ubiquitination See notes for inverse relation receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. sends output to Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). existence starts during x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). existence starts with x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t immediate transformation of x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. towards 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c has intermediate product has intermediate The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future determined by (system to material entity) determined by inverse of determined by determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. determined by part of true x is transcribed from y if and only if x is synthesized from template y http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from inverse of transcribed from http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of inverse of ribosomal translation of http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to A relation that holds between two entities that have the property of being sequences or having sequences. http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. sequentially related to Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 has start sequence inverse of has start sequence starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 is start sequence of Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 has end sequence inverse of has end sequence ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 is end sequence of x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering is sequentially aligned with The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y bounds sequence of inverse of bounds sequence of is bound by sequence of x has subsequence y iff all of the sequence parts of y are sequence parts of x contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 has subsequence inverse of has subsequence contained by is subsequence of x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. overlaps sequence of x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. disconnected from does not overlap sequence of inverse of downstream of sequence of is upstream of sequence of x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. is downstream of sequence of A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y is immediately downstream of sequence of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of is immediately upstream of sequence of Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. results in ending of x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of epiparasite of hyperparasite of inverse of hyperparasite of has epiparasite has hyperparasite hyperparasitoidized by hyperparasitized by http://en.wikipedia.org/wiki/Allelopathy allelopath of http://eol.org/schema/terms/allelopathyYes x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y Inverse of has pathogen pathogen of A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen inverse of is evidence for x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. has evidence causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c results in movement of The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Vasundra Touré causally influences (entity-centric) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Wikipedia:Antagonist_(muscle) has muscle antagonist inverse of branching part of has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity luminal space of A relation that holds between an attribute or a qualifier and another attribute. This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. has modifier participates in a biotic-biotic interaction with inverse of has skeleton skeleton of p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). existence starts at end of gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of results in synthesis of results in assembly of p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. results in catabolism of results in disassembly of results in remodeling of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). existence ends at start of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating pazopanib -> pathological angiogenesis Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. treats The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. capable of inhibiting or preventing pathological process treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship benzene -> cancer [CHEBI] Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. causes disease capable of upregulating or causing pathological process c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. treats is substance that treats c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI is marker for Inverse of 'causal agent in process' process has causal agent A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. In the Gene Ontology association model, this corresponds to the With/From field is evidence with support from Inverse of is-model-of has model Do not use this relation directly. It is a grouping relation. related via evidence or inference to visits https://github.com/oborel/obo-relations/issues/74 visited by visits flowers of has flowers visited by lays eggs in has eggs laid in by https://github.com/jhpoelen/eol-globi-data/issues/143 kills is killed by p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host ectoparasite of inverse of ectoparasite of has ectoparasite A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system lives inside of endoparasite of has endoparasite A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite mesoparasite of inverse of mesoparasite of has mesoparasite A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. intercellular endoparasite of inverse of intercellular endoparasite of has intercellular endoparasite A sub-relation of endoparasite-of in which the parasite inhabits host cells. intracellular endoparasite of inverse of intracellular endoparasite of has intracellular endoparasite Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. co-roosts with An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. reservoir host of An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. inverse of reservoir host of has reservoir host a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. produced by Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. represses expression of Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. increases expression of A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. is used to study The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. has role in modeling The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. causes condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. contributes to expressivity of condition contributes to severity of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. contributes to penetrance of condition contributes to frequency of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. is preventative for condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. ameliorates condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. correlated with condition A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. exacerbates condition A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. condition ameliorated by A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. condition exacerbated by Do not use this relation directly. It is intended as a grouping for a more specific relations 2017-11-05T02:38:20Z condition has genetic basis in 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in 2017-11-05T02:45:54Z has material basis in germline mutation in 2017-11-05T02:46:07Z has material basis in somatic mutation in 2017-11-05T02:46:26Z has major susceptibility factor 2017-11-05T02:46:57Z has partial material basis in germline mutation in p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. 2018-12-13T11:26:17Z has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. 2018-12-13T11:26:32Z has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. 2018-12-13T11:26:56Z has primary input p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 Do not use this relation directly. It is intended as a grouping for a more specific relations 2017-11-05T02:53:08Z is genetic basis for condition Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:55:51Z is causal gain of function germline mutation of in Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:56:06Z is causal loss of function germline mutation of in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:56:40Z is causal germline mutation in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. 2017-11-05T02:57:07Z is causal somatic mutation in Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. 2017-11-05T02:57:43Z is causal susceptibility factor for Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to 2017-11-05T03:20:01Z realizable has basis in 2017-11-05T03:20:29Z is basis for realizable 2017-11-05T03:26:47Z disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) 2017-11-05T03:29:32Z disease has basis in dysfunction of A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) 2017-11-05T03:37:52Z disease has basis in disruption of A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. 2017-11-05T03:46:07Z disease has basis in feature Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. 2017-11-05T03:50:54Z causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) 2017-11-05T03:51:09Z disease causes disruption of disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z disease causes dysfunction of A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. 2017-11-05T04:06:02Z disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity 2017-12-26T19:37:31Z disease has inflammation site A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. 2017-12-26T19:45:49Z realized in response to stimulus A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. 2017-12-26T19:50:53Z disease has feature A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z disease arises from alteration in structure Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. has driver A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. has disease driver An interaction relationship wherein a plant or algae is living on the outside surface of another plant. https://en.wikipedia.org/wiki/Epiphyte epiphyte of inverse of epiphyte of has epiphyte A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material https://en.wikipedia.org/wiki/Kleptoparasitism kleptoparasite of inverse of kleptoparasite of kleptoparasitized by An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. lays eggs on inverse of lays eggs on has eggs laid on by Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. 2023-01-18T14:28:21Z A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. has roost muffin 'has substance added' some 'baking soda' "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. has substance added 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. has substance removed sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. immersed in sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. has consumer bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. has primary substance added A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. 2023-05-23T15:24:15Z assay measures characteristic Inverse of 'assay measures characteristic' 2023-05-23T15:29:50Z characteristic measured by assay A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. [072-ISO] g-depends on generically depends on Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] is carrier of The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. regulates quantity of The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. indirectly regulates activity of The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. decreases by repression quantity of The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. increases by expression quantity of The entity A has an activity that directly positively regulates the quantity of B. directly positively regulates quantity of The entity A has an activity that directly negatively regulates the quantity of B. directly negatively regulates quantity of The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. indirectly activates indirectly positively regulates activity of AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. destabilizes quantity of AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. stabilizes quantity of The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. indirectly inhibits indirectly negatively regulates activity of The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. directly regulates quantity of The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. indirectly regulates quantity of The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. indirectly negatively regulates quantity of The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. indirectly positively regulates quantity of a relation between a process and a continuant, in which the process is regulated by the small molecule continuant 2020-04-22T20:27:26Z has small molecule regulator a relation between a process and a continuant, in which the process is activated by the small molecule continuant 2020-04-22T20:28:37Z has small molecule activator a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant 2020-04-22T20:28:54Z has small molecule inhibitor p acts on population of c iff c' is a collection, has members of type c, and p has participant c 2020-06-08T17:21:33Z acts on population of a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process 2020-06-24T13:15:17Z is small molecule regulator of a relation between a continuant and a process, in which the continuant is a small molecule that activates the process 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process 2020-06-24T13:15:35Z is small molecule inhibitor of https://wiki.geneontology.org/Is_small_molecule_inhibitor_of The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. 2020-08-27T08:13:59Z results in adhesion of 2021-02-26T07:28:29Z results in fusion of p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. 2022-09-26T06:01:01Z constitutively upstream of https://wiki.geneontology.org/Constitutively_upstream_of p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. 2022-09-26T06:06:20Z removes input for https://wiki.geneontology.org/Removes_input_for p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z indirectly regulates x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). 2023-10-12T10:02:28Z positively regulates in other organism positively regulates in another organism x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). 2023-10-12T10:02:42Z negatively regulates in other organism negatively regulates in another organism A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. 2020-07-17T09:42:23Z receives synaptic input in region A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. 2020-07-17T09:45:06Z sends synaptic output to region A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:52:19Z has synaptic IO throughout A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:55:36Z receives synaptic input throughout A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:57:27Z sends synaptic output throughout Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in has sensory terminal location has sensory dendrite in A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. 2021-05-26T08:40:18Z receives synaptic input from neuron A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. disease has infectious agent transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. This relation is not meant to capture the relation between occurrents and data. has exemplar data exemplar data of A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. subcluster of 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. has marker gene combination has marker signature set has characterizing marker set q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. different in magnitude relative to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. similar in magnitude relative to q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 has relative magnitude s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. https://orcid.org/0000-0002-6601-2165 q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. https://orcid.org/0000-0002-6601-2165 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. has high plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. PMID:19243617 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. has low plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. PMID:19243617 Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 2021-12-14T20:41:45Z has exposure medium A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relation between entities in which one increases or decreases as the other does the same. directly correlated with positively correlated with A relation between entities in which one increases as the other decreases. inversely correlated with negatively correlated with anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. A relation between a container and measurement datum that specifies the actual amount of material in the container. contains measured amount anticoagulant-containing test tube has maximum capacity 10 ml. A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. has maximum capacity biobank organization owns a specimen hospital owns a laboratory facility A primitive relation that holds between entities x and y in which y is at x's full disposal. This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. 2023-03-29T16:57:03Z owns freezer is owned by a biobank organization Inverse of the owns relation. 2023-03-29T17:06:06Z is owned by Helper relation for OWL definition of RO:0018002 myristoylates is myristoyltransferase activity A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input myristoylates inverse of myristoylates myristoylated by mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor is agonist of pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level is inverse agonist of tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level is antagonist of Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. chemical relationship pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. is direct conjugate base of neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. is direct conjugate acid of (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. obo:chebi#is_conjugate_base_of is deprotonated form of (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. obo:chebi#is_conjugate_acid_of is protonated form of phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. 2023-02-28T18:53:32Z is MMP with is matched molecular pair with is matched small molecular pair with A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. 2023-03-18T23:49:31Z obo:chebi#is_tautomer_of is desmotrope of is tautomer of 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. 2023-03-18T23:49:31Z obo:chebi#is_substituent_group_from is substitutent group from carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. 2023-03-18T23:49:31Z obo:chebi#has_functional_parent has functional parent hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). 2023-03-18T23:49:31Z obo:chebi#is_enantiomer_of is optical isomer of is enantiomer of dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. 2023-03-18T23:49:31Z obo:chebi#has_parent_hydride has parent hydride pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. confers susceptibility to condition brachial artery vessel supplies blood to brachialis muscle x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. 2024-02-01T10:09:22Z vessel supplies blood to cystic vein vessel drains blood from gallbladder x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. 2024-02-01T10:09:41Z vessel drains blood from alveolar capillary directly supplies and drains some alveolus x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. 2024-02-01T10:09:59Z directly supplies and drains A relationship between a ratio or proportion and its dividend. has dividend has numerator A relationship between a ratio or proportion and its divisor. has divisor has denominator This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. 2018-09-26T00:00:32Z disease relationship p has anatomical participant c iff p has participant c, and c is an anatomical entity 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom ECO:0000041 SO:similar_to sameness similar to correspondence resemblance in similarity relationship with Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. BGEE:curator correspondence Similarity that results from common evolutionary origin. homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with Similarity that results from common evolutionary origin. Similarity that results from independent evolution. homoplasous to analogy in homoplasy relationship with Similarity that results from independent evolution. Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. in homocracy relationship with Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. Homoplasy that involves different underlying mechanisms or structures. analogy Convergence usually implies a notion of adaptation. in convergence relationship with Homoplasy that involves different underlying mechanisms or structures. Homoplasy that involves homologous underlying mechanisms or structures. parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with Homoplasy that involves homologous underlying mechanisms or structures. Homology that is defined by similarity with regard to selected structural parameters. ECO:0000071 MI:2163 structural homologous to idealistic homology in structural homology relationship with Homology that is defined by similarity with regard to selected structural parameters. ISBN:0123195837 Homology that is defined by common descent. homology ECO:0000080 RO_proposed_relation:homologous_to SO:0000330 SO:0000853 SO:0000857 SO:homologous_to TAO:homologous_to cladistic homology historical homologous to phylogenetic homology taxic homology true homology in historical homology relationship with Homology that is defined by common descent. ISBN:0123195837 Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. ECO:0000067 biological homologous to transformational homology Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. in biological homology relationship with Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. atavism rudiment reversion in reversal relationship with Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. Structural homology that is detected by similarity in content and organization between chromosomes. MeSH:Synteny SO:0000860 SO:0005858 syntenic homologous to synteny in syntenic homology relationship with Structural homology that is detected by similarity in content and organization between chromosomes. MeSH:Synteny Historical homology that involves genes that diverged after a duplication event. SO:0000854 SO:0000859 SO:paralogous_to paralogous to in paralogy relationship with Historical homology that involves genes that diverged after a duplication event. Paralogy that involves sets of syntenic blocks. syntenic paralogous to duplicon paralogon in syntenic paralogy relationship with Paralogy that involves sets of syntenic blocks. DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y Syntenic homology that involves chromosomes of different species. syntenic orthologous to in syntenic orthology relationship with Syntenic homology that involves chromosomes of different species. Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. fractional homology partial homologous to segmental homology mixed homology modular homology partial correspondence percent homology in partial homology relationship with Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. ISBN:0123195837 ISBN:978-0471984931 Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. Structural homology that involves a pseudogenic feature and its functional ancestor. pseudogene SO:non_functional_homolog_of non functional homologous to in non functional homology relationship with Structural homology that involves a pseudogenic feature and its functional ancestor. SO:non_functional_homolog_of Historical homology that involves genes that diverged after a speciation event. ECO:00000060 SO:0000855 SO:0000858 SO:orthologous_to orthologous to The term is sometimes also used for anatomical structures. in orthology relationship with Historical homology that involves genes that diverged after a speciation event. Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. Historical homology that involves two members sharing no other homologs in the lineages considered. 1 to 1 homologous to 1:1 homology one-to-one homology in 1 to 1 homology relationship with Historical homology that involves two members sharing no other homologs in the lineages considered. BGEE:curator Orthology that involves two genes that did not experience any duplication after the speciation event that created them. 1 to 1 orthologous to 1:1 orthology one-to-one orthology in 1 to 1 orthology relationship with Orthology that involves two genes that did not experience any duplication after the speciation event that created them. Paralogy that results from a whole genome duplication event. ohnologous to homoeology in ohnology relationship with Paralogy that results from a whole genome duplication event. Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. in-paralogous to inparalogy symparalogy in in-paralogy relationship with Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. Paralogy that results from a duplication preceding a given speciation event. alloparalogy out-paralogous to outparalogy in out-paralogy relationship with Paralogy that results from a duplication preceding a given speciation event. 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. pro-orthologous to in pro-orthology relationship with 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. Iterative homology that involves structures arranged along the main body axis. serial homologous to homonomy in serial homology relationship with Iterative homology that involves structures arranged along the main body axis. Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. heterochronous homologous to heterochrony in heterochronous homology relationship with Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. ISBN:978-0674639416 Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. juvenification pedomorphosis in paedomorphorsis relationship with Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. ISBN:978-0674639416 Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. in peramorphosis relationship with Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. in progenesis relationship with Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. ISBN:978-0674639416 Paedomorphosis that is produced by a retardation of somatic development. juvenilization neotenous to in neoteny relationship with Paedomorphosis that is produced by a retardation of somatic development. ISBN:978-0674639416 Convergence that results from co-evolution usually involving an evolutionary arms race. mimicrous to in mimicry relationship with Convergence that results from co-evolution usually involving an evolutionary arms race. Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. 1 to many orthologous to 1:many orthology one-to-many orthology co-orthology many to 1 orthology in 1 to many orthology relationship with Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. Historical homology that involves two members of a larger set of homologs. many to many homologous to many-to-many homology many:many homology in many to many homology relationship with Historical homology that involves two members of a larger set of homologs. Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. 1 to many homologous to one-to-many homology 1:many homology in 1 to many homology relationship with Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. BGEE:curator Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. apomorphous to synapomorphy in apomorphy relationship with Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. ISBN:978-0252068140 Historical homology that is based on distant shared ancestry. plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. in plesiomorphy relationship with Historical homology that is based on distant shared ancestry. ISBN:978-0252068140 Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. deep genetic homology deep homologous to generative homology homoiology Used for structures in distantly related taxa. in deep homology relationship with Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. hemiplasous to in hemiplasy relationship with Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. Historical homology that involves not recombining and subsequently differentiated sex chromosomes. gametologous to in gametology relationship with Historical homology that involves not recombining and subsequently differentiated sex chromosomes. Historical homology that involves the chromosomes able to pair (synapse) during meiosis. MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with Historical homology that involves the chromosomes able to pair (synapse) during meiosis. ISBN:0195307615 Orthology that involves two genes that experienced duplications more recent than the species split that created them. many to many orthologous to many-to-many orthology many:many orthology trans-orthology co-orthology trans-homology in many to many orthology relationship with Orthology that involves two genes that experienced duplications more recent than the species split that created them. Paralogy that involves genes from the same species. within-species paralogous to in within-species paralogy relationship with Paralogy that involves genes from the same species. Paralogy that involves genes from different species. between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with Paralogy that involves genes from different species. Paedomorphosis that is produced by delayed growth of immature structures into the adult form. post-displacement in postdisplacement relationship with Paedomorphosis that is produced by delayed growth of immature structures into the adult form. Peramorphosis that is produced by a delay in the offset of development. in hypermorphosis relationship with Peramorphosis that is produced by a delay in the offset of development. ISBN:978-0674639416 Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. synologous to in synology relationship with Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. Orthology that involves functional equivalent genes with retention of the ancestral function. ECO:0000080 isoorthologous to in isoorthology relationship with Orthology that involves functional equivalent genes with retention of the ancestral function. Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. tandem paralogous to iterative paralogy serial paralogy in tandem paralogy relationship with Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. ISBN:978-0878932665 Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). apomorphic tendency cryptic homology latent homologous to underlying synapomorphy homoiology homoplastic tendency re-awakening Used for structures in closely related taxa. in latent homology relationship with Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). ISBN:0199141118 Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. in syngeny relationship with Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. 1:1 paralogy apparent 1:1 orthology apparent orthologous to pseudoorthology The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. in apparent orthology relationship with Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. Historical homology that involves functional equivalent genes with retention of the ancestral function. equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with Historical homology that involves functional equivalent genes with retention of the ancestral function. Historical homology that involves orthologous pairs of interacting molecules in different organisms. interologous to in interology relationship with Historical homology that involves orthologous pairs of interacting molecules in different organisms. Similarity that is characterized by interchangeability in function. functional similarity in functional equivalence relationship with Similarity that is characterized by interchangeability in function. Biological homology that involves parts of the same organism. iterative homologous to in iterative homology relationship with Biological homology that involves parts of the same organism. Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. duplicate xenology multiple xenology paraxenologous to in paraxenology relationship with Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. Structural homology that involves structures with the same or similar relative positions. homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with Structural homology that involves structures with the same or similar relative positions. ISBN:0123195837 Biological homology that involves an ectopic structure and the normally positioned structure. heterotopy in homeosis relationship with Biological homology that involves an ectopic structure and the normally positioned structure. Synology that results from allopolyploidy. homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with Synology that results from allopolyploidy. Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. axis paramorphism in paramorphism relationship with Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. regulogous to in regulogy relationship with Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. contains 0 100 Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. PMID:24138933 Wikipedia:Infant_mortality BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 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]) An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) A polypeptide consisting of 31 amino acid residues in the sequence Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-Leu-Phe-Lys-Asn-Ala-Ile-Ile-Lys-Asn-Ala-Tyr-Lys-Lys-Gly-Glu. It is an endogenous opioid peptide neurotransmitter found in the neurons of both the central and peripheral nervous system and results from processing of the precursor protein proopiomelanocortin (POMC). 0 C158H253N41O44S InChI=1S/C158H253N41O44S/c1-17-84(9)126(153(237)184-102(44-29-34-65-163)137(221)188-112(74-120(168)210)142(226)173-86(11)131(215)185-110(73-94-48-52-96(206)53-49-94)146(230)179-99(41-26-31-62-160)135(219)177-98(40-25-30-61-159)134(218)172-78-124(214)175-106(158(242)243)56-59-119(167)209)195-154(238)127(85(10)18-2)194-132(216)87(12)174-143(227)113(75-121(169)211)187-136(220)100(42-27-32-63-161)180-147(231)111(72-92-38-23-20-24-39-92)186-144(228)107(68-81(3)4)190-155(239)129(89(14)203)197-152(236)125(83(7)8)193-148(232)108(69-82(5)6)189-151(235)116-45-35-66-199(116)157(241)130(90(15)204)198-140(224)104(55-58-118(166)208)182-149(233)114(79-200)191-138(222)101(43-28-33-64-162)178-139(223)103(54-57-117(165)207)181-150(234)115(80-201)192-156(240)128(88(13)202)196-141(225)105(60-67-244-16)183-145(229)109(71-91-36-21-19-22-37-91)176-123(213)77-170-122(212)76-171-133(217)97(164)70-93-46-50-95(205)51-47-93/h19-24,36-39,46-53,81-90,97-116,125-130,200-206H,17-18,25-35,40-45,54-80,159-164H2,1-16H3,(H2,165,207)(H2,166,208)(H2,167,209)(H2,168,210)(H2,169,211)(H,170,212)(H,171,217)(H,172,218)(H,173,226)(H,174,227)(H,175,214)(H,176,213)(H,177,219)(H,178,223)(H,179,230)(H,180,231)(H,181,234)(H,182,233)(H,183,229)(H,184,237)(H,185,215)(H,186,228)(H,187,220)(H,188,221)(H,189,235)(H,190,239)(H,191,222)(H,192,240)(H,193,232)(H,194,216)(H,195,238)(H,196,225)(H,197,236)(H,198,224)(H,242,243)/t84-,85-,86-,87-,88+,89+,90+,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,107-,108-,109-,110-,111-,112-,113-,114-,115-,116-,125-,126-,127-,128-,129-,130-/m0/s1 WOPZMFQRCBYPJU-NTXHZHDSSA-N 3463.01300 3460.85408 CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCCCN)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](CCSC)NC(=O)[C@H](Cc1ccccc1)NC(=O)CNC(=O)CNC(=O)[C@@H](N)Cc1ccc(O)cc1)[C@@H](C)O)[C@@H](C)O)C(C)C)[C@@H](C)O)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)N[C@@H](CCC(N)=O)C(O)=O CAS:60617-12-1 KEGG:C02210 PMID:21044625 PMID:21187108 PMID:21775068 PMID:22014186 PMID:22080997 PMID:22101356 PMID:22574561 PMID:22578170 PMID:22626645 Wikipedia:Beta-endorphin L-tyrosylglycylglycyl-L-phenylalanyl-L-methionyl-L-threonyl-L-seryl-L-glutaminyl-L-lysyl-L-seryl-L-glutaminyl-L-threonyl-L-prolyl-L-leucyl-L-valyl-L-threonyl-L-leucyl-L-phenylalanyl-L-lysyl-L-asparaginyl-L-alanyl-L-isoleucyl-L-isoleucyl-L-lysyl-L-asparaginyl-L-alanyl-L-tyrosyl-L-lysyl-L-lysylglycyl-L-glutamine beta-Endorphin chebi_ontology Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-Leu-Phe-Lys-Asn-Ala-Ile-Ile-Lys-Asn-Ala-Tyr-Lys-Lys-Gly-Glu CHEBI:10415 beta-endorphin CHEBI:10415 An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) CHEBI:14321 An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. 0 C10H16N5O13P3 InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 ZKHQWZAMYRWXGA-KQYNXXCUSA-N 507.18100 506.99575 Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O CHEBI:10789 CHEBI:10841 CHEBI:13236 CHEBI:22249 CHEBI:2359 CHEBI:40938 CAS:56-65-5 DrugBank:DB00171 Drug_Central:91 Gmelin:34857 HMDB:HMDB0000538 KEGG:C00002 KEGG:D08646 KNApSAcK:C00001491 PDBeChem:ATP Patent:US3079379 Reaxys:73010 Wikipedia:Adenosine_triphosphate ATP adenosine 5'-(tetrahydrogen triphosphate) chebi_ontology ADENOSINE-5'-TRIPHOSPHATE Adenosine 5'-triphosphate Adenosine triphosphate H4atp CHEBI:15422 ATP CHEBI:15422 Catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group. 0 C8H11NO2 InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2 VYFYYTLLBUKUHU-UHFFFAOYSA-N 153.17840 153.07898 NCCc1ccc(O)c(O)c1 CHEBI:11695 CHEBI:11930 CHEBI:14203 CHEBI:1764 CHEBI:23886 CHEBI:43686 CAS:51-61-6 DrugBank:DB00988 Drug_Central:947 HMDB:HMDB0000073 KEGG:C03758 KEGG:D07870 KNApSAcK:C00001408 LINCS:LSM-4630 MetaCyc:DOPAMINE PMID:10629745 PMID:11149432 PMID:9422813 Reaxys:1072822 Wikipedia:Dopamine 4-(2-aminoethyl)benzene-1,2-diol Dopamine chebi_ontology 2-(3,4-Dihydroxyphenyl)ethylamine 2-(3,4-dihydroxyphenyl)ethylamine 3,4-Dihydroxyphenethylamine 3-Hydroxytyramine 4-(2-Aminoethyl)-1,2-benzenediol 4-(2-Aminoethyl)benzene-1,2-diol 4-(2-aminoethyl)-1,2-benzenediol 4-(2-aminoethyl)catechol 4-(2-aminoethyl)pyrocatechol Deoxyepinephrine Hydroxytyramin dopamina dopamine dopaminum CHEBI:18243 dopamine CHEBI:18243 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity CHEBI:23367 A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role CHEBI:24432 An endogenous compound that is used to transmit information across the synapse between a neuron and another cell. Wikipedia:Neurotransmitter chebi_ontology neurotransmitters CHEBI:25512 neurotransmitter CHEBI:25512 A primary amino compound that is the 5-hydroxy derivative of tryptamine. 0 C10H12N2O InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2 QZAYGJVTTNCVMB-UHFFFAOYSA-N 176.215 176.09496 C1=CC(=CC=2C(=CNC12)CCN)O CHEBI:1420 CHEBI:26652 CHEBI:49894 CAS:50-67-9 Gmelin:1861995 HMDB:HMDB0000259 KEGG:C00780 KNApSAcK:C00001429 LINCS:LSM-6589 MetaCyc:SEROTONIN PDBeChem:SRO PMID:18593914 PMID:22770225 PMID:24136337 Reaxys:143524 Wikipedia:Serotonin 3-(2-aminoethyl)-1H-indol-5-ol SEROTONIN Serotonin chebi_ontology 3-(2-Aminoethyl)-1H-indol-5-ol 5-HT 5-Hydroxytryptamine Enteramine serotonine thrombocytin thrombotonin CHEBI:28790 serotonin CHEBI:28790 A catecholamine in which C-1 of the aminoethyl side-chain is hydroxy-substituted. 0 C8H11NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2 SFLSHLFXELFNJZ-UHFFFAOYSA-N 169.17788 169.07389 NCC(O)c1ccc(O)c(O)c1 Beilstein:2210994 CAS:138-65-8 Gmelin:863925 LINCS:LSM-5181 4-(2-amino-1-hydroxyethyl)benzene-1,2-diol chebi_ontology noradrenalina norepinephrine CHEBI:33569 noradrenaline CHEBI:33569 A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. clinical_measurement_ontology CMO:0000000 clinical measurement CMO:0000000 The number of contractions of the cardiac ventricles per unit of time. EFO:0004326 EFO:0004351 resting heart rate clinical_measurement_ontology CMO:0000002 heart rate CMO:0000002 Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. EFO:0004325 blood pressure clinical_measurement_ontology Not4Curation CMO:0000003 blood pressure measurement CMO:0000003 The maximum arterial pressure within the cardiac cycle, i.e. at the point at which the heart is in its maximal state of contraction. This is the time when the blood is forced from the ventricles of the heart into the pulmonary artery and the aorta. EFO:0006335 clinical_measurement_ontology CMO:0000004 systolic blood pressure CMO:0000004 The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood. EFO:0006336 clinical_measurement_ontology CMO:0000005 diastolic blood pressure CMO:0000005 The level of heat in an organism. clinical_measurement_ontology CMO:0000015 body temperature CMO:0000015 The circumference of the body at the level of the navel divided by the circumference at the widest point around the buttocks, often used to assess distribution of sub-cutaneous and intra-abdominal adipose tissue. mshimoyama 2010-06-18T10:40:52Z EFO:0004343 waist-hip ratio clinical_measurement_ontology waist/hip ratio CMO:0000020 waist to hip ratio (WHR) CMO:0000020 Measurement of the amount of glucose, the monosaccharide sugar, C6H12O6, occurring widely in plant and animal tissues which is one of the three dietary monosaccharides that are absorbed directly into the bloodstream during digestion, is the end product of carbohydrate metabolism, and is the chief source of energy for living organisms, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. mshimoyama 2009-12-17T10:41:54Z glucose measurement EFO:0004468 VT:0000188 fasting blood glucose measurement clinical_measurement_ontology CMO:0000046 blood glucose level CMO:0000046 Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure. lipid or lipoprotein measurement EFO:0004529 EFO:0005105 EFO:0006811 EFO:0008350 lipid measurement alpha-linoleic acid measurement linolenic acid measurement clinical_measurement_ontology CMO:0000050 blood lipid measurement CMO:0000050 Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. EFO:0004574 EFO:0007806 total cholesterol measurement total cholesterol change measurement clinical_measurement_ontology blood TC level CMO:0000051 blood total cholesterol level CMO:0000051 Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml. EFO:0004612 EFO:0007805 EFO:0022157 blood HDL-C high density lipoprotein cholesterol measurement HDL cholesterol change measurement free cholesterol in large HDL measurement clinical_measurement_ontology blood HDL level CMO:0000052 Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided. blood high density lipoprotein cholesterol level CMO:0000052 Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1. EFO:0004611 EFO:0007804 low density lipoprotein cholesterol measurement LDL cholesterol change measurement clinical_measurement_ontology blood LDL level blood LDL-C level CMO:0000053 Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided. blood low density lipoprotein cholesterol level CMO:0000053 Measurement of adipose tissue in entire body or region of body of an organism. mshimoyama 2010-06-23T04:14:20Z EFO:0004341 EFO:0004764 adipose tissue measurement body fat distribution clinical_measurement_ontology CMO:0000089 body fat morphological measurement CMO:0000089 The vertical measurement of a body. EFO:0004339 EFO:0005201 EFO:0006784 EFO:0006785 body height at birth infant body height clinical_measurement_ontology height growth measurement CMO:0000106 body height CMO:0000106 The amount of triglycerides in a specific volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Triglycerides are any of a group of lipids that are esters formed from one molecule of glycerol and three molecules of one or more fatty acids, are widespread in adipose tissue, and commonly circulate in the blood in the form of lipoproteins. mshimoyama 2009-12-17T10:19:44Z triglyceride measurement EFO:0004530 EFO:0007681 triglyceride change measurement clinical_measurement_ontology CMO:0000118 blood triglyceride level CMO:0000118 Total volume of gas inhaled and exhaled from the lungs per one minute. mshimoyama 2009-12-17T11:12:05Z MV Q Ve clinical_measurement_ontology CMO:0000132 minute ventilation CMO:0000132 VO2 max (maximal oxygen consumption), refers to the maximum amount of oxygen that an individual can utilize during intense or maximal exercise. The more oxygen a person can use during high level exercise, the more energy a person can produce. This test is the gold standard for determining cardiorespiratory fitness because the muscles need oxygen for prolonged aerobic exercise, and the heart must pump adequate amounts of blood through the circulation to meet the demands of aerobic exercise. mshimoyama 2009-12-17T11:14:04Z EFO:0004887 maximal oxygen uptake measurement maximum oxygen consumption clinical_measurement_ontology VO2 max maximal aerobic capacity maximal oxygen uptake peak oxygen uptake CMO:0000135 maximal oxygen consumption CMO:0000135 Percentage of blood pumped out of the left ventricle with each heart beat. mshimoyama 2010-06-10T09:06:25Z EF EFO:0005527 EFO:0008373 PMID:32207065 LVEF ejection fraction measurement heart left ventricle ejection fraction left ventricle ejection fraction left ventricular ejection fraction left ventricular ejection fraction measurement clinical_measurement_ontology CMO:0000180 ejection fraction CMO:0000180 The volume of blood pumped from the right or left ventricle per minute, also used to calculate - stroke volume X heart rate. mshimoyama 2010-06-10T09:51:29Z clinical_measurement_ontology CMO:0000197 cardiac output CMO:0000197 Volume of gas inhaled and exhaled during one respiratory cycle. mshimoyama 2010-06-10T03:57:56Z clinical_measurement_ontology CMO:0000222 tidal volume CMO:0000222 Volume of blood pumped from one ventricle of the heart with each beat, calculated by subtracting the volume of blood in the ventricle at the end of a beat (end-systolic volume) from the volume of blood just prior to the beat (end-diastolic volume). mshimoyama 2010-06-11T01:32:10Z SV clinical_measurement_ontology CMO:0000223 stroke volume CMO:0000223 Distance completely around the body in the area between the thorax and hips. In humans, this is commonly at the umbilicus. mshimoyama 2010-06-17T11:28:45Z EFO:0004342 clinical_measurement_ontology waist girth CMO:0000242 waist circumference CMO:0000242 The volume of air that can be forcibly expelled from a maximally inflated lung. mshimoyama 2010-06-17T12:18:18Z clinical_measurement_ontology forced expired vital capacity CMO:0000251 forced vital capacity (FVC) CMO:0000251 Maximal rate of air flow through the pulmonary tree during forced expiration. mshimoyama 2010-06-17T12:19:05Z EFO:0004313 EFO:0009718 maximal midexpiratory flow rate clinical_measurement_ontology PEF peak expiratory flow CMO:0000253 maximum mid-expiratory flow (MMEF) CMO:0000253 Fraction of forced vital capacity that is exhaled in a specific number of seconds. mshimoyama 2010-06-17T12:19:28Z EFO:0004314 clinical_measurement_ontology CMO:0000254 forced expiratory volume CMO:0000254 Maximum volume of air that an organism can breathe in and out during a specified period of time, often 1 minute. mshimoyama 2010-12-17T09:50:05Z MVV clinical_measurement_ontology maximum breathing capacity CMO:0000255 maximal volume ventilation CMO:0000255 The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart. mshimoyama 2010-08-04T10:37:40Z clinical_measurement_ontology CMO:0000294 pulse CMO:0000294 mshimoyama 2010-08-05T08:53:40Z EFO:0007800 clinical_measurement_ontology CMO:0000302 body fat percentage CMO:0000302 mshimoyama 2010-08-05T09:19:24Z EFO:0005409 fat body mass clinical_measurement_ontology total body fat weight CMO:0000305 total body fat mass CMO:0000305 The amount of gas remaining in the lung at the end of a maximal exhalation. mshimoyama 2010-08-05T09:28:36Z clinical_measurement_ontology CMO:0000307 residual lung volume CMO:0000307 Total volume to which lungs can be expanded with greatest inspiratory effort. mshimoyama 2010-12-16T01:24:14Z EFO:0600046 lung volume clinical_measurement_ontology CMO:0000380 total lung capacity CMO:0000380 Temperature measured at the surface of or within the head of an experimental subject. Because the temperature of the head/brain can influence neurological measurements, head temperature is or can be considered to be distinct from core body temperature. jsmith 2012-08-23T03:27:50Z clinical_measurement_ontology cranial temperature CMO:0001035 head temperature CMO:0001035 The temperature of the internal tissues and organs of the body. jsmith 2012-08-23T04:06:16Z clinical_measurement_ontology core temperature CMO:0001036 core body temperature CMO:0001036 Measurement of the mineral mass per unit area of bone, the hard, rigid form of connective tissue constituting most of the skeleton of vertebrates and composed chiefly of calcium salts. JSmith 2012-12-18T17:04:40Z EFO:0003923 EFO:0007701 EFO:0007702 EFO:0007785 EFO:0007933 EFO:0009270 BMD areal BMD areal bone mineral density bone density femoral neck bone mineral density heel bone mineral density hip bone mineral density radius bone mineral density spine bone mineral density clinical_measurement_ontology CMO:0001226 bone mineral density CMO:0001226 The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity. JSmith 2013-01-09T16:37:31Z oxygen saturation measurement EFO:0005682 percent oxygen saturation clinical_measurement_ontology CMO:0001324 oxygen saturation CMO:0001324 A calculated measurement in which the mass of mineral in any or all of the bones of the body is divided by the total weight of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the size of the organism. JSmith 2013-05-07T17:43:08Z clinical_measurement_ontology BMC/BW CMO:0001556 bone mineral content to body weight ratio CMO:0001556 A calculated measurement of the force necessary to fracture a bone under specified conditions and thus a measure of the biomechanical strength of that bone. Bone is the hard, rigid form of connective tissue constituting most of the skeleton of vertebrates and composed chiefly of calcium salts. JSmith 2013-05-07T18:45:42Z force at failure of bone ultimate load of bone clinical_measurement_ontology CMO:0001561 bone ultimate force CMO:0001561 Measurement of the capacity of an individual's body to transport and utilize oxygen, measured as volume of oxygen per unit of time. JSmith 2014-02-04T12:19:38Z clinical_measurement_ontology VO2 oxygen uptake CMO:0002169 oxygen consumption CMO:0002169 A calculated measurement in which the cardiac output is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage. sjwang 2018-11-27T15:09:41Z clinical_measurement_ontology CMO:0002881 cardiac index CMO:0002881 This is a calculated value which is a measure of the rate of energy expenditure per unit time by endothermic animals at rest. It represents the minimum amount of energy required to sustain life while at complete rest, including the body being in a post-absorptive state (ie the digestive system is inactive. slaulede 2023-09-29T10:44:25Z BMR base metabolic rate base metabolic rate measurement clinical_measurement_ontology CMO:0003955 basal metabolic rate CMO:0003955 A specific developmental disorder that involves significant limitations both in mental functioning and in adaptive behavior such as communicating, taking care of him or herself, and social skills. NCI:C84392 SNOMEDCT_US_2023_03_01:1855002 UMLS_CUI:C0025362 disease_ontology mental retardation DOID:1059 OMIM mapping submitted by NeuroDevNet. [LS]. intellectual disability DOID:1059 A nerve compression syndrome characterized by pressure on the median nerve at the wrist resulting in numbness, tingling, pain, and muscle weakness in the hand and forearm. ICD10CM:G56.0 ICD9CM:354.0 MESH:D002349 MIM:PS115430 NCI:C34450 SNOMEDCT_US_2023_03_01:193126005 UMLS_CUI:C0007286 CTS - Carpal tunnel syndrome Median nerve entrapment carpal tunnel median neuropathy disease_ontology DOID:12169 carpal tunnel syndrome DOID:12169 A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. DOID:73 ICD9CM:429.2 MESH:D002318 NCI:C2931 SNOMEDCT_US_2023_03_01:266275004 UMLS_CUI:C0007222 disease of subdivision of hemolymphoid system disease_ontology DOID:1287 cardiovascular system disease DOID:1287 A central nervous system disease that results in the progressive deterioration of function or structure of neurons. DOID:4874 ICD10CM:G31.9 MESH:D019636 NCI:C27090 SNOMEDCT_US_2023_03_01:362975008 UMLS_CUI:C0524851 UMLS_CUI:C1285162 degenerative disease disease_ontology DOID:1289 neurodegenerative disease DOID:1289 A bone inflammation disease that results_in inflammation located_in epicondyle. DOID:14162 ICD10CM:M77.1 ICD9CM:726.32 MESH:D013716 NCI:C34589 NCI:C35067 SNOMEDCT_US_2023_03_01:156659008 SNOMEDCT_US_2023_03_01:268088003 UMLS_CUI:C0014488 UMLS_CUI:C0039516 Lateral epicondylitis andrel epicondylitis archer's elbow golfer's elbow hockey elbow medial epicondylitis disease_ontology shooter's elbow tennis elbow DOID:14087 epicondylitis DOID:14087 ICD10CM:M65.4 ICD9CM:727.04 MESH:D053684 SNOMEDCT_US_2023_03_01:202905002 UMLS_CUI:C0149870 Radial styloid tenosynovitis Tenosynovitis, de Quervain's disease_ontology DOID:14107 De Quervain disease DOID:14107 A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80.1 ICD9CM:199 ICDO:8000/3 MESH:D009369 NCI:C9305 SNOMEDCT_US_2023_03_01:269513004 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer DOID:162 A disease of anatomical entity that occurs in the muscular and/or skeletal system. MESH:D009140 NCI:C107377 SNOMEDCT_US_2023_03_01:268047003 UMLS_CUI:C0026857 disease_ontology DOID:17 musculoskeletal system disease DOID:17 A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2023_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease DOID:4 A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both. DOID:0081062 ICD10CM:E08-E13 ICD9CM:250 MESH:D003920 NCI:C2985 SNOMEDCT_US_2023_03_01:267467004 UMLS_CUI:C0011849 diabetes disease_ontology DOID:9351 diabetes mellitus DOID:9351 ENVO:01000614 A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other. bike cycle bicycle EXMO:0000008 The relative amounts of various components in the body, such as percentage of body fat. mesh:D001823 snomedct:68592003 umls:C0005885 body composition The relative amounts of various components in the body, such as percentage of body fat. mesh:D001823 EXMO:0000010 The amount of an individual's total body mass that is protein, expressed as a percent. percentage of body protein body protein percentage EXMO:0000012 The amount of an individual's total body mass that is water, expressed as a percent. percentage of body water body water percentage EXMO:0000013 equipment used in exercise snomedct:708542002 umls:C0497977 exercise device exercise equipment exercise device snomedct:708542002 EXMO:0000015 Exercise prescription commonly refers to the specific plan of fitness-related activities that are designed for a specified purpose, which is often developed by a fitness or rehabilitation specialist for the client or patient. exercise prescription Exercise prescription commonly refers to the specific plan of fitness-related activities that are designed for a specified purpose, which is often developed by a fitness or rehabilitation specialist for the client or patient. https://emedicine.medscape.com/article/88648-overview EXMO:0000016 Concept used to describe exercise characteristic of exercise EXMO:0000017 what is the mode of exercise type of exercise what is the mode of exercise https://www.ssisa-academy.com/blog/fittvp-principle-for-resistance-training EXMO:0000018 Exercise frequency refers to the number of physical activity sessions performed within a specific time period, typically measured per week. exercise frequence Exercise frequency refers to the number of physical activity sessions performed within a specific time period, typically measured per week. https://www.weightcrafters.com/training-concepts/frequency EXMO:0000020 how long is the exercise duration exercise time how long is the exercise duration https://www.ssisa-academy.com/blog/fittvp-principle-for-resistance-training EXMO:0000046 Right ventricular ejection fraction (RVEF), is a measure of the efficiency of pumping into the pulmonary circulation. snomedct:250939002 umls:C0428781 right ventricular ejection fraction Right ventricular ejection fraction (RVEF), is a measure of the efficiency of pumping into the pulmonary circulation. https://en.wikipedia.org/wiki/Ejection_fraction right ventricular ejection fraction RVEF EXMO:0000048 Functions of pumping the blood in adequate or required amounts and pressure throughout the body. snomedct:106053004 umls:C0232164 heart function cardiac function Functions of pumping the blood in adequate or required amounts and pressure throughout the body. https://icd.who.int/browse/2024-01/icf/en#222589883 heart function umls:C0232164 EXMO:0000049 Pulmonary function refers to the physiological processes and capabilities of the lungs and respiratory system that enable effective gas exchange. snomedct:106053004 umls:C0231921 lung function pulmonary function EXMO:0000053 Peak filling rate (PFR) defined as the maximum dV/dt divided by LV end-diastolic volume was obtained as the index of LV diastolic function. pubmed:30650017 peak filling rate Peak filling rate (PFR) defined as the maximum dV/dt divided by LV end-diastolic volume was obtained as the index of LV diastolic function. pubmed:30650017 peak filling rate PFR EXMO:0000054 The interval, in milliseconds, between the point of minimal ventricular volume and the point at which the peak filling rate occurs is labeled as the time to peak filling rate. umls:C4284945 time to peak filling rate The interval, in milliseconds, between the point of minimal ventricular volume and the point at which the peak filling rate occurs is labeled as the time to peak filling rate. pubmed:2198392 time to peak filling rate TPFR EXMO:0000064 Alveolar ventilation is the exchange of gas between the alveoli and the external environment. It is the process by which oxygen is brought into the lungs from the atmosphere and by which the carbon dioxide carried into the lungs in the mixed venous blood is expelled from the body. umls:C4068542 alveolar ventilation Alveolar ventilation is the exchange of gas between the alveoli and the external environment. It is the process by which oxygen is brought into the lungs from the atmosphere and by which the carbon dioxide carried into the lungs in the mixed venous blood is expelled from the body. https://accessmedicine.mhmedical.com/content.aspx?bookid=2288&sectionid=178856748 alveolar ventilation VA EXMO:0000065 The lung volume at which the dependent lung zones cease to ventilate presumably as a result of airway closure. mesh:D003011 snomedct:251905008 umls:C0009050 closing volume The lung volume at which the dependent lung zones cease to ventilate presumably as a result of airway closure. mesh:D003011 closing volume CV EXMO:0000068 The flow (or speed) of air coming out of the lung during the middle portion of a forced expiration. umls:C3804964 forced expiratory flow The flow (or speed) of air coming out of the lung during the middle portion of a forced expiration. https://en.wikipedia.org/wiki/Spirometry#Forced_expiratory_flow_(FEF) forced expiratory flow FEF EXMO:0000080 The number of times heart beats per minute when a person is at rest – such as relaxed, sitting or lying down. umls:C1821417 resting heart rate The number of times heart beats per minute when a person is at rest – such as relaxed, sitting or lying down. https://www.healthdirect.gov.au/resting-heart-rate EXMO:0000081 The maxium number of times heart beats per minute during exercise test. pubmed:20146781 pubmed:23877260 peak heart rate during exercise testing EXMO:0000088 The amount of force generated by MUSCLE CONTRACTION. Muscle strength can be measured during isometric, isotonic, or isokinetic contraction, either manually or using a device such as a MUSCLE STRENGTH DYNAMOMETER. mesh:D053580 umls:C0517349 muscle strength EXMO:0000090 video games that are also a form of exercise exer-gaming exergame fitness game gamercising exergaming video games that are also a form of exercise https://en.wikipedia.org/wiki/Exergaming exer-gaming https://en.wikipedia.org/wiki/Exergaming exergame https://en.wikipedia.org/wiki/Exergaming fitness game https://en.wikipedia.org/wiki/Exergaming gamercising https://en.wikipedia.org/wiki/Exergaming EXMO:0000091 Home exercise refers to physical activity performed within one’s residence or personal space, designed to improve fitness, strength, flexibility, or overall health without requiring specialized gym equipment or facilities. home exercise EXMO:0000094 what is the total amount of exercise exercise volume what is the total amount of exercise https://www.ssisa-academy.com/blog/fittvp-principle-for-resistance-training EXMO:0000095 how is the program advanced exercise progression how is the program advanced https://www.ssisa-academy.com/blog/fittvp-principle-for-resistance-training EXMO:0000099 a technique for systematically categorizing patients based on their health status and other factors risk stratification a technique for systematically categorizing patients based on their health status and other factors pubmed:31083868 EXMO:0000101 General Health Evaluation refers to a comprehensive assessment of an individual's overall physical, mental, and functional well-being. general health evaluation EXMO:0000102 Body composition assessment quantifies the fat, water, protein, and bone content of the body. body composition assessment body composition testing Body composition assessment quantifies the fat, water, protein, and bone content of the body. https://www.sciencedirect.com/topics/medicine-and-dentistry/body-composition-assessment EXMO:0000103 Cardiovascular endurance testing is a systematic evaluation of the body's ability to perform continuous, rhythmic exercise over time, reflecting the integrated efficiency of the heart, blood vessels, and lungs in supporting sustained physical effort. cardiovascular endurance testing EXMO:0000104 Strength and endurance testing refers to the systematic evaluation of an individual's physical capacity to exert force (strength) and sustain prolonged physical or mental effort (endurance). strength and endurance testing EXMO:0000105 Flexibility Testing refers to the assessment of an individual's ability to move a joint or series of joints through their full, pain-free range of motion (ROM). flexibility testing EXMO:0000106 The Cooper test, a 12-minute run fitness test, was developed by Kenneth Cooper, MD, in 1968. The test is an easy way to measure aerobic fitness and provide an estimate of VO2 max for military personnel, and it's still used today as a field test for determining aerobic fitness. 12-minute run fitness test Cooper test 12-minute run test EXMO:0000108 measure maximum rate of oxygen consumption during an activity VO2 max testing measure maximum rate of oxygen consumption during an activity https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000109 measures the length of time a muscle group can contract and release before it fatigues muscle endurance testing measures the length of time a muscle group can contract and release before it fatigues https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000110 zipper test evaluate the flexibility and mobility of shoulder joint shoulder flexibility testing zipper test https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 evaluate the flexibility and mobility of shoulder joint https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000111 measure tightness in lower back and hamstring muscles sit-and-reach testing measure tightness in lower back and hamstring muscles https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000112 measure tightness in lower back trunk lift testing measure tightness in lower back https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000114 Skinfold measurement is an anthropometric method used to estimate body fat percentage by measuring the thickness of subcutaneous adipose tissue (fat beneath the skin) at specific anatomical sites on the body. umls:C1963769 skinfold measurement EXMO:0000115 measure the maximal amount of force a muscle group can exert at one time strength testing measure the maximal amount of force a muscle group can exert at one time https://www.verywellfit.com/what-a-fitness-test-can-tell-you-about-your-health-3120283 EXMO:0000116 The push-up test is a widely used physical fitness assessment that measures upper body muscular endurance and strength, primarily targeting the chest, shoulders, triceps, and core stabilizing muscles. It evaluates an individual’s ability to perform repetitive push-ups with proper form over a set duration or until failure, providing insight into overall upper-body conditioning and endurance capacity. push-up test EXMO:0000117 Core strength and stability testing refers to the systematic evaluation of an individual's ability to generate force through the muscles of the torso (core strength) and maintain control of spinal and pelvic positioning during static or dynamic movements (core stability). core strength and stability test EXMO:0000119 Use of active or passive body movement to maintain or restore joint flexibility snomedct:386294003 umls:C0419122 joint mobility exercise Use of active or passive body movement to maintain or restore joint flexibility umls:C0419122 EXMO:0000120 Ankle mobility exercise refers to targeted physical movements or routines designed to enhance the range of motion, flexibility, and strength of the ankle joint. ankle mobility exercise EXMO:0000121 Hip joint exercise refers to physical movements or routines designed to improve the mobility, strength, flexibility, and stability of the hip joint and its surrounding musculature. umls:C0846692 hip joint exercise EXMO:0000123 Lower limb strength training refers to a structured exercise regimen designed to enhance the muscular strength, power, endurance, and functional capacity of the lower body. lower limb strength training EXMO:0000124 Core training refers to exercises that target the muscles of the lumbo-pelvic-hip complex, including the abdominal muscles (rectus abdominis, transverse abdominis, internal and external obliques), back extensors (erector spinae), hip musculature (gluteals, iliopsoas), and deeper stabilizing muscles like the multifidus and diaphragm. core training Core training refers to exercises that target the muscles of the lumbo-pelvic-hip complex, including the abdominal muscles (rectus abdominis, transverse abdominis, internal and external obliques), back extensors (erector spinae), hip musculature (gluteals, iliopsoas), and deeper stabilizing muscles like the multifidus and diaphragm. https://www.statecollegestrength.com/blog/core-training-explained EXMO:0000125 Jumping exercise refers to physical activities that involve repeated or explosive propelling of the body off the ground using the lower limbs, often to improve power, strength, cardiovascular fitness, or neuromuscular coordination. umls:C5387952 jumping exercise EXMO:0000126 running exerciseA form of aerobic or anaerobic physical activity involving rhythmic, repetitive movement of the legs at a pace faster than walking. running exercise EXMO:0000128 Cardiopulmonary exercise refers to physical activity that engages and challenges both the cardiovascular system (heart and blood vessels) and the respiratory system (lungs and airways) to meet the increased metabolic demands of working muscles. cardiopulmonary exercise EXMO:0000130 Agility exercise refers to a type of physical training designed to improve an individual's ability to rapidly and efficiently change direction, speed, or body position while maintaining control and balance. agility exercise EXMO:0000131 Flexibility Exercise refers to physical activities aimed at enhancing the ability of muscles and connective tissues to elongate, thereby increasing the range of motion (ROM) around joints and improving overall flexibility. flexibility exercise EXMO:0000132 The FMS was developed in the late 1990s by Gray Cook, a physical therapist and strength coach, and Dr. Lee Burton, an athletic trainer. The goal was to create a practical and standardised system for evaluating movement patterns that are foundational to athletic activities. pubmed:28360142 functional movement screen The FMS was developed in the late 1990s by Gray Cook, a physical therapist and strength coach, and Dr. Lee Burton, an athletic trainer. The goal was to create a practical and standardised system for evaluating movement patterns that are foundational to athletic activities. https://coachathletics.com.au/coaching-education/the-functional-movement-screen functional movement screen FMS EXMO:0000134 The SFMA is a clinical model used to assist diagnosis and treatment of musculoskeletal disorders by identifying dysfunctions in movement patterns. selective functional movement assessment The SFMA is a clinical model used to assist diagnosis and treatment of musculoskeletal disorders by identifying dysfunctions in movement patterns. https://www.physio-pedia.com/Selective_Functional_Movement_Assessment_(SFMA) selective functional movement assessment SFMA EXMO:0000135 a simple, yet reliable, test used to measure dynamic balance umls:C5389416 Y-balance test a simple, yet reliable, test used to measure dynamic balance pubmed:25761134 EXMO:0000136 Hop test refers to a functional performance assessment used in sports medicine, physical therapy, and rehabilitation to evaluate lower limb strength, balance, and neuromuscular control. It involves a series of unilateral (single-leg) hopping tasks, such as the single-leg hop, triple hop, crossover hop, or timed hop, where an individual jumps forward or laterally as far or as quickly as possible on one leg. hopping hop test EXMO:0000137 Drop jump landing refers to the biomechanical phase immediately following a drop jump, where an individual descends from a predetermined height (e.g., a platform or box) and contacts the ground, transitioning force through the lower extremities. drop jump landing EXMO:0000139 The ability to carry out daily tasks and perform physical activities in a highly functional state, often as a result of physical conditioning. mesh:D010809 umls:C0031812 physical fitness The ability to carry out daily tasks and perform physical activities in a highly functional state, often as a result of physical conditioning. mesh:D010809 EXMO:0000143 Tummy time is a colloquialism for placing infant children in the prone position while awake and supervised, to encourage development of the neck and trunk muscles and prevent skull deformations. tummy time Tummy time is a colloquialism for placing infant children in the prone position while awake and supervised, to encourage development of the neck and trunk muscles and prevent skull deformations. https://en.wikipedia.org/wiki/Tummy_time EXMO:0000144 the maximum rate at which oxygen can be used during a specified period, usually during intense exercise maximal aerobic power the maximum rate at which oxygen can be used during a specified period, usually during intense exercise https://journals.lww.com/acsm-healthfitness/Fulltext/2011/11000/Maximal_Aerobic_Power__An_Important_Clinical_and.12.aspx Maximal aerobic power describes the functional capacity of the cardiorespiratory system. EXMO:0000145 submaximal endurance capacity. increased by endurance training. average absolute power output a person can maintain during a fixed period of time on cycle ergometer, OR average speed a person can maintain during a fixed period of time. submaximal endurance capacity submaximal endurance submaximal endurance capacity. increased by endurance training. average absolute power output a person can maintain during a fixed period of time on cycle ergometer, OR average speed a person can maintain during a fixed period of time. https://askingthelot.com/what-is-a-submaximal-exercise/#what_is_submaximal_endurance_capacity submaximal endurance capacity https://askingthelot.com/what-is-a-submaximal-exercise/#what_is_submaximal_endurance_capacity EXMO:0000146 A non-performance component of physical fitness related to body composition factors such as body circumferences, body fat content and regional body fat distribution. morphplogical fitness A non-performance component of physical fitness related to body composition factors such as body circumferences, body fat content and regional body fat distribution. www.health-galaxy.com/components-of-physical-fitness.html EXMO:0000150 Muscular fitness is a general term that describes the general health, strength, and endurance of one's muscles. muscular fitness Muscular fitness is a general term that describes the general health, strength, and endurance of one's muscles. https://www.thehealthboard.com/what-is-muscular-strength.htm EXMO:0000151 Muscular power is mainly determined by muscular strength, maximum movement velocity, and neuromuscular activation. muscular power Muscular power is mainly determined by muscular strength, maximum movement velocity, and neuromuscular activation. pubmed:19675484 EXMO:0000153 Isometric strength is defined as the capacity to produce force or torque with a voluntary isometric (muscle[s] maintain[s] a constant length) contraction. isometric strength Isometric strength is defined as the capacity to produce force or torque with a voluntary isometric (muscle[s] maintain[s] a constant length) contraction. https://stacks.cdc.gov/view/cdc/9182 EXMO:0000154 The concept of metabolic fitness is a broader term that encompasses the overall efficacy of the metabolic processes in the body. It includes the conversion of food into energy, the utilization of nutrients, and the elimination of waste products. metabolic fitness The concept of metabolic fitness is a broader term that encompasses the overall efficacy of the metabolic processes in the body. It includes the conversion of food into energy, the utilization of nutrients, and the elimination of waste products. https://vanahealth.com/metabolic-fitness EXMO:0000155 physiological ability of the body to properly metabolize glucose. umls:C0178665 glucose tolerance EXMO:0000157 Motor fitness is a term that describes an athlete’s ability to perform effectively during sports or other physical activity. motor fitness Motor fitness is a term that describes an athlete’s ability to perform effectively during sports or other physical activity. https://www.thehealthboard.com/what-is-motor-fitness.htm EXMO:0000158 umls:C0237464 Agility is an ability to change the body's position efficiently and requires the integration of isolated movement skills using a combination of balance, coordination, speed, reflexes, strength and endurance. nimbleness physical agility agility Agility is an ability to change the body's position efficiently and requires the integration of isolated movement skills using a combination of balance, coordination, speed, reflexes, strength and endurance. https://en.wikipedia.org/wiki/Agility EXMO:0000161 The rate at which an object covers distance over time, measured as a scalar quantity representing the magnitude of velocity (without direction). umls:C0517932 speed of movement EXMO:0000166 Aerobics is a form of physical exercise that combines rhythmic aerobic exercise with stretching and strength training routines with the goal of improving all elements of fitness (flexibility, muscular strength, and cardio-vascular fitness). umls:C3842693 aerobic dance aerobic dancing aerobics Aerobics is a form of physical exercise that combines rhythmic aerobic exercise with stretching and strength training routines with the goal of improving all elements of fitness (flexibility, muscular strength, and cardio-vascular fitness). https://en.wikipedia.org/wiki/Aerobics aerobic dancing umls:C3842693 EXMO:0000167 Badminton is a racquet sport played using racquets to hit a shuttlecock across a net. umls:C0004678 badminton Badminton is a racquet sport played using racquets to hit a shuttlecock across a net. https://en.wikipedia.org/wiki/Badminton EXMO:0000168 A competitive team sport played on a rectangular court having a raised basket at each end. mesh:D001490 snomedct:25731005 umls:C0004818 Basketball basketball game A competitive team sport played on a rectangular court having a raised basket at each end. mesh:D001490 Basketball snomedct:25731005 mesh:D001490 EXMO:0000169 A two-person sport in which the fists are skillfully used to attack and defend. mesh:D001914 umls:C0006080 boxing A two-person sport in which the fists are skillfully used to attack and defend. mesh:D001914 EXMO:0000175 Long-distance running is a form of continuous running over distances of at least 3 km (1.9 mi). endurance running long-distance running Long-distance running is a form of continuous running over distances of at least 3 km (1.9 mi). https://en.wikipedia.org/wiki/Long-distance_running endurance running https://en.wikipedia.org/wiki/Long-distance_running EXMO:0000176 Gateball is a mallet team sport inspired by croquet. gate ball Gateball is a mallet team sport inspired by croquet. https://en.wikipedia.org/wiki/Gateball EXMO:0000178 Hiking in mountains refers to the recreational outdoor activity of walking or trekking on trails or off-path routes in mountainous terrain, typically for enjoyment, exercise, or exploration. umls:C2030962 hiking uphill uphill hiking hiking in mountains EXMO:0000179 Hiking on flat ground refers to the recreational activity of walking on trails, paths, or open terrain with minimal elevation changes. hiking on flat ground EXMO:0000183 Moderate walking refers to brisk walking at a pace that increases heart rate and breathing noticeably but still allows for comfortable conversation. moderate walk moderate-intensity walking moderate walking EXMO:0000184 Brisk walking is a type of exercise where a person walks quickly in order to increase the heart rate and get in shape. brisk walk speed walking brisk walking Brisk walking is a type of exercise where a person walks quickly in order to increase the heart rate and get in shape. https://www.thehealthboard.com/what-is-brisk-walking.htm EXMO:0000186 Fencing is a group of three related combat sports. The three disciplines in modern fencing are the foil, the épée, and the sabre (also saber); winning points are made through the weapon's contact with an opponent. fencing Fencing is a group of three related combat sports. The three disciplines in modern fencing are the foil, the épée, and the sabre (also saber); winning points are made through the weapon's contact with an opponent. https://en.wikipedia.org/wiki/Fencing EXMO:0000187 A game whose object is to sink a ball into each of 9 or 18 successive holes on a golf course using as few strokes as possible. mesh:D006055 golfing golf A game whose object is to sink a ball into each of 9 or 18 successive holes on a golf course using as few strokes as possible. mesh:D006055 golfing snomedct:15530008 EXMO:0000188 Netball is a ball sport played by two teams of seven players. netball umls:C0840974 netball game Netball is a ball sport played by two teams of seven players. https://en.wikipedia.org/wiki/Netball EXMO:0000189 Table tennis, also known as ping-pong and whiff-whaff, is a sport in which two or four players hit a lightweight ball, also known as the ping-pong ball, back and forth across a table using small rackets. ping-pong whiff-whaff table tennis Table tennis, also known as ping-pong and whiff-whaff, is a sport in which two or four players hit a lightweight ball, also known as the ping-pong ball, back and forth across a table using small rackets. https://en.wikipedia.org/wiki/Table_tennis ping-pong https://en.wikipedia.org/wiki/Table_tennis whiff-whaff https://en.wikipedia.org/wiki/Table_tennis EXMO:0000190 A snow sport which uses skis to glide over the snow. mesh:D012865 snomedct:45033006 umls:C0037264 snow skiing skiing A snow sport which uses skis to glide over the snow. mesh:D012865 It does not include water-skiing. snow skiing mesh:D012865 EXMO:0000191 Alpine skiing, or downhill skiing, is the pastime of sliding down snow-covered slopes on skis with fixed-heel bindings, unlike other types of skiing (cross-country, Telemark, or ski jumping), which use skis with free-heel bindings. alpine ski downhill skiing ski slope alpine skiing Alpine skiing, or downhill skiing, is the pastime of sliding down snow-covered slopes on skis with fixed-heel bindings, unlike other types of skiing (cross-country, Telemark, or ski jumping), which use skis with free-heel bindings. https://en.wikipedia.org/wiki/Alpine_skiing alpine ski https://en.wikipedia.org/wiki/Alpine_skiing downhill skiing https://en.wikipedia.org/wiki/Alpine_skiing ski slope https://en.wikipedia.org/wiki/Alpine_skiing EXMO:0000192 Cross-country skiing is a form of skiing where skiers rely on their own locomotion to move across snow-covered terrain, rather than using ski lifts or other forms of assistance. umls:C2712399 cross country skiing cross-country skiing Cross-country skiing is a form of skiing where skiers rely on their own locomotion to move across snow-covered terrain, rather than using ski lifts or other forms of assistance. https://en.wikipedia.org/wiki/Cross-country_skiing EXMO:0000193 Taekwondo is a Korean form of martial arts, characterized by punching and kicking techniques, with emphasis on head-height kicks, jumping spinning kicks, and fast kicking techniques. umls:C0080204 tae kwon tae kwon do taekwon-do taekwondo Taekwondo is a Korean form of martial arts, characterized by punching and kicking techniques, with emphasis on head-height kicks, jumping spinning kicks, and fast kicking techniques. https://en.wikipedia.org/wiki/Taekwondo EXMO:0000194 A game played by two or four players with rackets and an elastic ball on a level court divided by a low net. umls:C0039515 tennis EXMO:0000195 Softball is a game similar to baseball played with a larger ball (11 to 16 inches or 28 to 40 cm circumference) on a field that has base lengths of 60 feet, a pitcher's mound that ranges from 35 to 43 (professional is 43) feet away from home plate, and a home run fence that is 220–300 feet away from home plate, depending on the type of softball being played. softball soft-ball softball game Softball is a game similar to baseball played with a larger ball (11 to 16 inches or 28 to 40 cm circumference) on a field that has base lengths of 60 feet, a pitcher's mound that ranges from 35 to 43 (professional is 43) feet away from home plate, and a home run fence that is 220–300 feet away from home plate, depending on the type of softball being played. https://en.wikipedia.org/wiki/Softball EXMO:0000196 A game in which a round inflated ball is advanced by kicking or propelling with any part of the body except the hands or arms. The object of the game is to place the ball in opposite goals. association football football mesh:D012916 snomedct:88289009 soccer umls:C0037393 association football game A game in which a round inflated ball is advanced by kicking or propelling with any part of the body except the hands or arms. The object of the game is to place the ball in opposite goals. mesh:D012916 football snomedct:88289009 soccer snomedct:88289009 EXMO:0000197 Squash is a racket and ball sport played by two players in a four-walled court with a small, hollow rubber ball. mesh:D015865 snomedct:415578009 umls:C0038076 squash Squash is a racket and ball sport played by two players in a four-walled court with a small, hollow rubber ball. https://en.wikipedia.org/wiki/Squash_(sport) EXMO:0000198 A form of physical training performed using a large, inflatable ball (commonly known as a Swiss ball, exercise ball, stability ball, or physio ball), designed to improve strength, balance, flexibility, and core stability. umls:C2147987 swiss ball exercise EXMO:0000199 umls:C2712409 a sport involving rhythmic jumping over a rope swung underfoot and overhead jump rope a sport involving rhythmic jumping over a rope swung underfoot and overhead https://en.wikipedia.org/wiki/Skipping_rope EXMO:0000200 Cultivation of PLANTS; (FRUIT; VEGETABLES; MEDICINAL HERBS) on small plots of ground or in containers. mesh:D051639 umls:C0868963 gardening Cultivation of PLANTS; (FRUIT; VEGETABLES; MEDICINAL HERBS) on small plots of ground or in containers. mesh:D051639 EXMO:0000202 Stair climbing is the climbing of a flight of stairs. stair climbing Stair climbing is the climbing of a flight of stairs. https://en.wikipedia.org/wiki/Stair_climbing EXMO:0000203 A team sport in which two teams hit an inflated ball back and forth over a high net using their hands. mesh:D054798 umls:C1956059 volleyball game A team sport in which two teams hit an inflated ball back and forth over a high net using their hands. mesh:D054798 EXMO:0000204 Sprinting is running over a short distance at the top-most speed of the body in a limited period of time. umls:C2319308 sprinting Sprinting is running over a short distance at the top-most speed of the body in a limited period of time. https://en.wikipedia.org/wiki/Sprint_(running) EXMO:0000205 Bodybuilding is the use of progressive resistance exercise to control and develop one's muscles (muscle building) by muscle hypertrophy for aesthetic purposes. bodybuilding Bodybuilding is the use of progressive resistance exercise to control and develop one's muscles (muscle building) by muscle hypertrophy for aesthetic purposes. https://en.wikipedia.org/wiki/Bodybuilding EXMO:0000207 Bodyweight exercises (also called bodyweight workouts) are strength-training exercises that use an individual's own weight to provide resistance against gravity. bodyweight workout bodyweight exercise Bodyweight exercises (also called bodyweight workouts) are strength-training exercises that use an individual's own weight to provide resistance against gravity. https://en.wikipedia.org/wiki/Bodyweight_exercise EXMO:0000208 The term suspension training refers to an approach to strength training that uses a system of ropes and webbing called a "suspension trainer" to allow users to work against their own body weight. suspension training The term suspension training refers to an approach to strength training that uses a system of ropes and webbing called a "suspension trainer" to allow users to work against their own body weight. https://en.wikipedia.org/wiki/Suspension_training EXMO:0000211 Circuit training is a form of body conditioning that involves endurance training, resistance training, high-intensity aerobics, and exercises performed in a circuit, similar to high-intensity interval training. umls:C2712423 circuit training Circuit training is a form of body conditioning that involves endurance training, resistance training, high-intensity aerobics, and exercises performed in a circuit, similar to high-intensity interval training. https://en.wikipedia.org/wiki/Circuit_training EXMO:0000212 Cross-training is athletic training in sports other than the athlete's usual sport. The goal is improving overall performance. It takes advantage of the particular effectiveness of one training method to negate the shortcomings of another. cross-training Cross-training is athletic training in sports other than the athlete's usual sport. The goal is improving overall performance. It takes advantage of the particular effectiveness of one training method to negate the shortcomings of another. https://en.wikipedia.org/wiki/Cross-training EXMO:0000215 Interval training is a type of training exercise that involves a series of high-intensity workouts interspersed with rest or relief periods. interval training Interval training is a type of training exercise that involves a series of high-intensity workouts interspersed with rest or relief periods. https://en.wikipedia.org/wiki/Interval_training EXMO:0000218 Outdoor fitness consists of exercise undertaken outside a building for the purpose of improving physical fitness. outdoor fitness Outdoor fitness consists of exercise undertaken outside a building for the purpose of improving physical fitness. https://en.wikipedia.org/wiki/Outdoor_fitness EXMO:0000220 Virtual reality exercise refers to physical activity performed within a digitally simulated environment, using VR (virtual reality) headsets, motion-tracking sensors, and interactive software. pubmed:34663191 VR exercise exercise with VR exercising with virtual reality virtual reality exercise EXMO:0000221 A barbell is a piece of exercise equipment used in weight training, bodybuilding, weightlifting and powerlifting, consisting of a long bar, usually with weights attached at each end. barbell A barbell is a piece of exercise equipment used in weight training, bodybuilding, weightlifting and powerlifting, consisting of a long bar, usually with weights attached at each end. https://en.wikipedia.org/wiki/Barbell EXMO:0000222 Weight training benches may be of various designs: fixed horizontal, fixed inclined, fixed in a folded position, with one adjustable portion, with two or more adjustable portions, with racks to hold bars, etc. In the limit, the definition of a bench blurs into that of combinations that mix a bench and associated equipment. Benches are manufactured by many different vendors, in an array of qualities, features, and prices. bench Weight training benches may be of various designs: fixed horizontal, fixed inclined, fixed in a folded position, with one adjustable portion, with two or more adjustable portions, with racks to hold bars, etc. In the limit, the definition of a bench blurs into that of combinations that mix a bench and associated equipment. Benches are manufactured by many different vendors, in an array of qualities, features, and prices. https://en.wikipedia.org/wiki/Bench_(weight_training) EXMO:0000223 A BOSU Balance Trainer (or BOSU ball) is a fitness training device, invented in 1999 by David Weck.[1] It consists of an inflated rubber hemisphere attached to a rigid platform. The device is often used for balance training. BOSU Balance Trainer BOSU Trainer BOSU ball BOSU A BOSU Balance Trainer (or BOSU ball) is a fitness training device, invented in 1999 by David Weck.[1] It consists of an inflated rubber hemisphere attached to a rigid platform. The device is often used for balance training. https://en.wikipedia.org/wiki/BOSU EXMO:0000224 A lightweight, brightly colored (typically orange, yellow, or fluorescent) marker made of flexible plastic, rubber, or foam, shaped like a cone. It is used in sports, training, and fitness activities to designate boundaries, create obstacle courses, mark distances, or outline drills. Cones are portable, stackable, and designed for quick setup and repositioning during exercises. cone EXMO:0000225 The dumbbell, a type of free weight, is a piece of equipment used in weight training. It can be used individually or in pairs, with one in each hand. dumbbell The dumbbell, a type of free weight, is a piece of equipment used in weight training. It can be used individually or in pairs, with one in each hand. https://en.wikipedia.org/wiki/Dumbbell EXMO:0000226 Battling ropes are used for fitness training to increase full body strength and conditioning. battle ropes battling ropes heavy ropes Battling ropes are used for fitness training to increase full body strength and conditioning. https://en.wikipedia.org/wiki/Battling_ropes EXMO:0000227 A hurdle is a moveable section of light fence. hurdle A hurdle is a moveable section of light fence. https://en.wikipedia.org/wiki/Hurdle EXMO:0000228 The kettlebell is a cast iron or cast steel ball with a handle attached to the top (resembling a cannonball with a handle). It is used to perform many types of exercises, including ballistic exercises that combine cardiovascular, strength and flexibility training. They are also the primary equipment used in the weight lifting sport of kettlebell lifting. umls:C2721233 kettlebell The kettlebell is a cast iron or cast steel ball with a handle attached to the top (resembling a cannonball with a handle). It is used to perform many types of exercises, including ballistic exercises that combine cardiovascular, strength and flexibility training. They are also the primary equipment used in the weight lifting sport of kettlebell lifting. https://en.wikipedia.org/wiki/Kettlebell EXMO:0000229 Portable structures typically consisting of two pairs of legs and a series of evenly spaced perpendicular rungs or steps used for climbing. Ladders are typically around 6-10 feet tall, although some shorter ladders (often called stepladders) are approximately 3-4 feet tall and some (called telescoping or extension ladders) may reach up to 20 feet in length. Ladders are typically made of fiberglass, aluminum, or wood. umls:C0336762 ladder Portable structures typically consisting of two pairs of legs and a series of evenly spaced perpendicular rungs or steps used for climbing. Ladders are typically around 6-10 feet tall, although some shorter ladders (often called stepladders) are approximately 3-4 feet tall and some (called telescoping or extension ladders) may reach up to 20 feet in length. Ladders are typically made of fiberglass, aluminum, or wood. umls:C0336762 EXMO:0000230 A medicine ball (also known as an exercise ball, a med ball, or a fitness ball) is a weighted ball whose diameter is about a shoulder-width, (approx. 13.7 inches (350 mm)), often used for rehabilitation and strength training. exercise ball fitness ball med ball medicine ball A medicine ball (also known as an exercise ball, a med ball, or a fitness ball) is a weighted ball whose diameter is about a shoulder-width, (approx. 13.7 inches (350 mm)), often used for rehabilitation and strength training. https://en.wikipedia.org/wiki/Medicine_ball EXMO:0000231 A pull-up bar is a horizontal bar, typically made of metal or durable material, fixed securely between two supports (e.g., on a wall, doorframe, or freestanding structure). It is designed for performing upper-body exercises such as pull-ups, chin-ups, hanging leg raises, and other strength-training movements that involve gripping the bar and lifting or suspending one's body weight. pull-up bar EXMO:0000232 A resistance band is an elastic band used for strength training. They are also commonly used in physical therapy, specifically by convalescents of muscular injuries, including cardiac rehab patients to allow slow rebuilding of strength. resistance cable resistance band A resistance band is an elastic band used for strength training. They are also commonly used in physical therapy, specifically by convalescents of muscular injuries, including cardiac rehab patients to allow slow rebuilding of strength. https://en.wikipedia.org/wiki/Resistance_band EXMO:0000233 An exercise ball is a ball constructed of soft elastic, typically in 5 diameters of 10 cm increments, from 35 to 95 cm (14 to 37 in), and filled with air. The air pressure is changed by removing a valve stem and either filling with air or letting the ball deflate. It is most often used in physical therapy, athletic training and exercise. It can also be used for weight training. balance ball exercise ball fitness ball swiss ball swiss exercise ball stability ball An exercise ball is a ball constructed of soft elastic, typically in 5 diameters of 10 cm increments, from 35 to 95 cm (14 to 37 in), and filled with air. The air pressure is changed by removing a valve stem and either filling with air or letting the ball deflate. It is most often used in physical therapy, athletic training and exercise. It can also be used for weight training. https://en.wikipedia.org/wiki/Exercise_ball EXMO:0000234 a performance training tool that leverages gravity and the user’s body weight to complete the exercises TRX TRX suspension trainer a performance training tool that leverages gravity and the user’s body weight to complete the exercises https://en.wikipedia.org/wiki/TRX_System EXMO:0000235 A weight machine is an exercise machine used for weight training that uses gravity as the primary source of resistance and a combination of simple machines to convey that resistance to the person using the machine. Each of the simple machines (pulley, lever, wheel, incline) changes the mechanical advantage of the overall machine relative to the weight. weight machine A weight machine is an exercise machine used for weight training that uses gravity as the primary source of resistance and a combination of simple machines to convey that resistance to the person using the machine. Each of the simple machines (pulley, lever, wheel, incline) changes the mechanical advantage of the overall machine relative to the weight. https://en.wikipedia.org/wiki/Weight_machine EXMO:0000236 A racket or racquet is a sports implement consisting of a handled frame with an open hoop across which a network of strings or catgut is stretched tightly. racquet racket A racket or racquet is a sports implement consisting of a handled frame with an open hoop across which a network of strings or catgut is stretched tightly. https://en.wikipedia.org/wiki/Racket_(sports_equipment) EXMO:0000237 Badminton rackets are light, with top quality rackets weighing between about 70 and 95 grams. Modern rackets are composed of carbon fiber composite (graphite reinforced plastic), which may be augmented by a variety of materials. badminton racket Badminton rackets are light, with top quality rackets weighing between about 70 and 95 grams. Modern rackets are composed of carbon fiber composite (graphite reinforced plastic), which may be augmented by a variety of materials. https://en.wikipedia.org/wiki/Racket_(sports_equipment)#Badminton EXMO:0000240 A shuttlecock (also called a birdie or shuttle) is a high-drag projectile used in the sport of badminton. It has an open conical shape formed by feathers or plastic (or a synthetic alternative) embedded into a rounded cork (or rubber) base. The shuttlecock's shape makes it extremely aerodynamically stable. Regardless of initial orientation, it will turn to fly cork first, and remain in the cork-first orientation. birdie shuttle shuttlecock A shuttlecock (also called a birdie or shuttle) is a high-drag projectile used in the sport of badminton. It has an open conical shape formed by feathers or plastic (or a synthetic alternative) embedded into a rounded cork (or rubber) base. The shuttlecock's shape makes it extremely aerodynamically stable. Regardless of initial orientation, it will turn to fly cork first, and remain in the cork-first orientation. https://en.wikipedia.org/wiki/Shuttlecock EXMO:0000241 A basketball is a spherical ball used in basketball games. basketball A basketball is a spherical ball used in basketball games. https://en.wikipedia.org/wiki/Basketball_(ball) EXMO:0000243 A golf ball is a ball designed to be used in golf. Under the rules of golf, a golf ball has a mass no more than 1.620 oz (45.93 g), has a diameter not less than 1.680 inches (42.67 mm), and performs within specified velocity, distance, and symmetry limits. golf ball A golf ball is a ball designed to be used in golf. Under the rules of golf, a golf ball has a mass no more than 1.620 oz (45.93 g), has a diameter not less than 1.680 inches (42.67 mm), and performs within specified velocity, distance, and symmetry limits. https://en.wikipedia.org/wiki/Golf_ball EXMO:0000244 A golf club is a club used to hit a golf ball in a game of golf. golf club A golf club is a club used to hit a golf ball in a game of golf. https://en.wikipedia.org/wiki/Golf_club EXMO:0000245 A rope is a group of yarns, plies, fibers or strands that are twisted or braided together into a larger and stronger form. rope A rope is a group of yarns, plies, fibers or strands that are twisted or braided together into a larger and stronger form. https://en.wikipedia.org/wiki/Rope EXMO:0000246 Ball games (or ballgames), also ball sports, are any form of game or sport which feature a ball as part of play. ball sport ball game Ball games (or ballgames), also ball sports, are any form of game or sport which feature a ball as part of play. https://en.wikipedia.org/wiki/Ball_game EXMO:0000247 Netball is a ball used in netball game. It is around 70 cm in circumference and weighs 400 to 450 grams. It is typically constructed from leather, rubber, or similar material. netball Netball is a ball used in netball game. It is around 70 cm in circumference and weighs 400 to 450 grams. It is typically constructed from leather, rubber, or similar material. https://en.wikipedia.org/wiki/Netball EXMO:0000248 A ski is a narrow strip of semi-rigid material worn underfoot to glide over snow. ski A ski is a narrow strip of semi-rigid material worn underfoot to glide over snow. https://en.wikipedia.org/wiki/Ski EXMO:0000249 Ski poles, also referred to as poles (in North America), sticks (UK), or stocks (Australia),[1][2] are used by skiers for balance and propulsion. pole stick stock ski pole EXMO:0000250 The Baduanjin qigong is one of the most common forms of Chinese qigong used as exercise. baduanjin The Baduanjin qigong is one of the most common forms of Chinese qigong used as exercise. https://en.wikipedia.org/wiki/Baduanjin_qigong EXMO:0000251 football EXMO:0000252 Football is a family of team sports that involve, to varying degrees, kicking a ball to score a goal. football football game Football is a family of team sports that involve, to varying degrees, kicking a ball to score a goal. https://en.wikipedia.org/wiki/Football EXMO:0000253 A football, soccer ball, football ball, or association football ball is the ball used in the sport of association football. football association football ball soccer ball association football A football, soccer ball, football ball, or association football ball is the ball used in the sport of association football. https://en.wikipedia.org/wiki/Ball_(association_football) EXMO:0000254 Rugby football is a collective name for the family of team sports of rugby union and rugby league, as well as the earlier forms of football from which both games, as well as Australian rules football and gridiron football, evolved. rugby football Rugby football is a collective name for the family of team sports of rugby union and rugby league, as well as the earlier forms of football from which both games, as well as Australian rules football and gridiron football, evolved. https://en.wikipedia.org/wiki/Rugby_football EXMO:0000255 A rugby ball is an elongated ellipsoidal ball used in both codes of rugby football. rugby ball A rugby ball is an elongated ellipsoidal ball used in both codes of rugby football. https://en.wikipedia.org/wiki/Rugby_ball EXMO:0000256 Gridiron football, also known as North American football or, in North America, simply football, is a family of football team sports primarily played in the United States and Canada. gridiron football game Gridiron football, also known as North American football or, in North America, simply football, is a family of football team sports primarily played in the United States and Canada. https://en.wikipedia.org/wiki/Gridiron_football EXMO:0000257 In Canada and the United States, a football (also called a pigskin) is a ball, roughly in the form of a prolate spheroid, used in the context of playing gridiron football. gridiron football In Canada and the United States, a football (also called a pigskin) is a ball, roughly in the form of a prolate spheroid, used in the context of playing gridiron football. https://en.wikipedia.org/wiki/Ball_(gridiron_football) EXMO:0000258 American football, referred to simply as football in the United States and also known as gridiron, is a team sport played by two teams of eleven players on a rectangular field with goalposts at each end. football American football American football, referred to simply as football in the United States and also known as gridiron, is a team sport played by two teams of eleven players on a rectangular field with goalposts at each end. https://en.wikipedia.org/wiki/American_football EXMO:0000259 Canadian football is a sport played in Canada in which two teams of 12 players each compete for territorial control of a field of play 110 yards (101 m) long and 65 yards (59 m) wide attempting to advance a pointed oval-shaped ball into the opposing team's scoring area (end zone). Canadian football Canadian football is a sport played in Canada in which two teams of 12 players each compete for territorial control of a field of play 110 yards (101 m) long and 65 yards (59 m) wide attempting to advance a pointed oval-shaped ball into the opposing team's scoring area (end zone). https://en.wikipedia.org/wiki/Canadian_football EXMO:0000260 Softball is a variation of baseball, the difference being that it is played with a larger ball, on a smaller field, and with only underhand pitches (where the ball is released while the hand is primarily below the ball) permitted. softball Softball is a variation of baseball, the difference being that it is played with a larger ball, on a smaller field, and with only underhand pitches (where the ball is released while the hand is primarily below the ball) permitted. https://en.wikipedia.org/wiki/Softball EXMO:0000261 Baseball is a bat-and-ball game played between two opposing teams, typically of nine players each, that take turns batting and fielding. baseball game Baseball is a bat-and-ball game played between two opposing teams, typically of nine players each, that take turns batting and fielding. https://en.wikipedia.org/wiki/Baseball EXMO:0000262 A baseball is the ball used in the sport of baseball. It consists of a rubber or cork center wrapped in yarn and covered with white natural horsehide or cowhide, or a synthetic composite leather. baseball A baseball is the ball used in the sport of baseball. It consists of a rubber or cork center wrapped in yarn and covered with white natural horsehide or cowhide, or a synthetic composite leather. https://en.wikipedia.org/wiki/Baseball_(ball) EXMO:0000263 The stick-like implement used to hit the ball in bat-and-ball sports. bat EXMO:0000264 The bat used by the batter can be made of wood, aluminum, or composite materials such as carbon fiber. Sizes may vary but they may be no more than 34 inches (86 cm) long, 2.4 inches (6 cm) in diameter, or 38 ounces (1.1 kg) in mass. softball bat The bat used by the batter can be made of wood, aluminum, or composite materials such as carbon fiber. Sizes may vary but they may be no more than 34 inches (86 cm) long, 2.4 inches (6 cm) in diameter, or 38 ounces (1.1 kg) in mass. https://en.wikipedia.org/wiki/Softball#Bat EXMO:0000265 A baseball bat is a smooth wooden or metal club used in the sport of baseball to hit the ball after it is thrown by the pitcher. baseball bat A baseball bat is a smooth wooden or metal club used in the sport of baseball to hit the ball after it is thrown by the pitcher. https://en.wikipedia.org/wiki/Baseball_bat EXMO:0000267 A baseball glove or mitt is a large glove (traditionally made of leather, today other options do exist) worn by baseball players of the defending team, which assists players in catching and fielding balls hit by a batter or thrown by a teammate. mitt baseball glove A baseball glove or mitt is a large glove (traditionally made of leather, today other options do exist) worn by baseball players of the defending team, which assists players in catching and fielding balls hit by a batter or thrown by a teammate. https://en.wikipedia.org/wiki/Baseball_glove EXMO:0000268 Batting gloves are a component in bat-and-ball games sportswear. Typically consisting of a leather palm and back made of nylon or another synthetic fabric, the glove covers one or both hands of a batter, providing comfort, prevention of blisters, warmth, improved grip, and shock absorption when hitting the ball. Batting gloves are considered an essential part of cricket equipment, though they are not mandatory at any level of the game. batting glove Batting gloves are a component in bat-and-ball games sportswear. Typically consisting of a leather palm and back made of nylon or another synthetic fabric, the glove covers one or both hands of a batter, providing comfort, prevention of blisters, warmth, improved grip, and shock absorption when hitting the ball. Batting gloves are considered an essential part of cricket equipment, though they are not mandatory at any level of the game. https://en.wikipedia.org/wiki/Batting_glove EXMO:0000269 Bat-and-ball games (or safe haven games) are field games played by two opposing teams, in which the action starts when the defending team throws a ball at a dedicated player of the attacking team, who tries to hit it with a bat and run between various safe areas in the field to score runs (points), while the defending team can use the ball in various ways against the attacking team's players to force them off the field when they are not in safe zones, and thus prevent them from further scoring. safe haven game bat-and-ball game Bat-and-ball games (or safe haven games) are field games played by two opposing teams, in which the action starts when the defending team throws a ball at a dedicated player of the attacking team, who tries to hit it with a bat and run between various safe areas in the field to score runs (points), while the defending team can use the ball in various ways against the attacking team's players to force them off the field when they are not in safe zones, and thus prevent them from further scoring. https://en.wikipedia.org/wiki/Bat-and-ball_games EXMO:0000270 All defensive players wear fielding gloves, made of leather or similar material. softball glove All defensive players wear fielding gloves, made of leather or similar material. https://en.wikipedia.org/wiki/Softball#Gloves EXMO:0000271 Squash rackets have maximum dimensions of 686 mm (27.0 in) long and 215 mm (8.5 in) wide, with a maximum strung area of 500 square centimeters (77.5 sq in). The permitted maximum weight is 255 grams (9.0 oz), but most have a weight between 90 and 150 grams (3–5.3 oz.). The strings of the racket usually have a tension of 25-30. squash racket Squash rackets have maximum dimensions of 686 mm (27.0 in) long and 215 mm (8.5 in) wide, with a maximum strung area of 500 square centimeters (77.5 sq in). The permitted maximum weight is 255 grams (9.0 oz), but most have a weight between 90 and 150 grams (3–5.3 oz.). The strings of the racket usually have a tension of 25-30. https://en.wikipedia.org/wiki/Squash_(sport)#Racket EXMO:0000272 Squash balls are between 39.5 and 40.5 mm in diameter, and weigh 23 to 25 grams. They are made with two pieces of rubber compound, glued together to form a hollow sphere and buffed to a matte finish. squash ball Squash balls are between 39.5 and 40.5 mm in diameter, and weigh 23 to 25 grams. They are made with two pieces of rubber compound, glued together to form a hollow sphere and buffed to a matte finish. https://en.wikipedia.org/wiki/Squash_(sport)#Ball EXMO:0000274 A table tennis racket is used by table tennis players. It is usually made from laminated wood covered with rubber on one or two sides depending on the player's grip. paddle table tennis bat table tennis racket A table tennis racket is used by table tennis players. It is usually made from laminated wood covered with rubber on one or two sides depending on the player's grip. https://en.wikipedia.org/wiki/Table_tennis_racket EXMO:0000275 The international rules specify that the game is played with a sphere having a mass of 2.7 grams (0.095 oz) and a diameter of 40 millimetres (1.57 in). table tennis ball The international rules specify that the game is played with a sphere having a mass of 2.7 grams (0.095 oz) and a diameter of 40 millimetres (1.57 in). https://en.wikipedia.org/wiki/Table_tennis#Ball EXMO:0000276 A tennis ball is a ball designed for the sport of tennis. Tennis balls are fluorescent yellow in organised competitions, but in recreational play can be virtually any color. Tennis balls are covered in a fibrous felt which modifies their aerodynamic properties, and each has a white curvilinear oval covering it. tennis ball A tennis ball is a ball designed for the sport of tennis. Tennis balls are fluorescent yellow in organised competitions, but in recreational play can be virtually any color. Tennis balls are covered in a fibrous felt which modifies their aerodynamic properties, and each has a white curvilinear oval covering it. https://en.wikipedia.org/wiki/Tennis_ball EXMO:0000277 A tennis racket is a specialized sports equipment used to hit a tennis ball during a match or practice. It consists of a frame with an open hoop, tightly strung with strings (traditionally made of natural gut, now often synthetic materials like nylon or polyester), and a handle (grip) for holding and swinging. Modern rackets are typically constructed from lightweight, durable materials such as graphite, carbon fiber, or aluminum. tennis racket EXMO:0000278 A volleyball is a ball used to play indoor volleyball, beach volleyball, or other less common variations of the sport. Volleyballs are round and traditionally consist of eighteen nearly rectangular panels of synthetic or genuine leather, arranged in six identical sections of three panels each, wrapped around a bladder. A valve permits the internal air pressure to be adjusted. volleyball A volleyball is a ball used to play indoor volleyball, beach volleyball, or other less common variations of the sport. Volleyballs are round and traditionally consist of eighteen nearly rectangular panels of synthetic or genuine leather, arranged in six identical sections of three panels each, wrapped around a bladder. A valve permits the internal air pressure to be adjusted. https://en.wikipedia.org/wiki/Volleyball_(ball) EXMO:0000285 A chronic condition is a long-lasting health issue that persists over an extended period (typically three months or more), progresses gradually, and often cannot be cured completely. umls:C5545294 chronic condition EXMO:0000287 An electrocardiogram sensor is a medical or wearable device that detects, measures, and records the electrical activity of the heart over time. electrocardiogram sensor electrocardiogram sensor ECG sensor EXMO:0000288 An air flow sensor is a device that measures the rate of air flow through a system, including combustion engines, HVAC (Heating, Ventilation, and Air Conditioning), and industrial processes. airflow sensor An air flow sensor is a device that measures the rate of air flow through a system, including combustion engines, HVAC (Heating, Ventilation, and Air Conditioning), and industrial processes. https://www.azosensors.com/article.aspx?ArticleID=2840 EXMO:0000290 An electromyography (EMG) sensor is a device that detects and measures electrical activity produced by skeletal muscles during contraction and relaxation. electromyography sensor electromyography sensor EMG sensor EXMO:0000291 A body temperature sensor is a device designed to measure the temperature of a human body. These sensors find application in wearable fitness trackers and medical thermometers. body temperature sensor A body temperature sensor is a device designed to measure the temperature of a human body. These sensors find application in wearable fitness trackers and medical thermometers. https://www.rfwireless-world.com/terminology/measurements/body-temperature-sensor-basics EXMO:0000292 A patient position sensor is a medical device component or system designed to detect, monitor, and/or record the physical orientation, posture, or movement of a patient during medical procedures, imaging, or therapeutic interventions. patient position sensor EXMO:0000294 A pulse oximeter is a non-invasive device used to measure oxygen saturation in the blood. This article will cover pulse oximetry, including its limitations and clinical application. pulse oximeter A pulse oximeter is a non-invasive device used to measure oxygen saturation in the blood. This article will cover pulse oximetry, including its limitations and clinical application. https://geekymedics.com/pulse-oximetry EXMO:0000295 Galvanic skin response (GSR) sensors read the change in electrical conductance between two regions of the skin to measure skin conductance activity. galvanic skin response sensor Galvanic skin response (GSR) sensors read the change in electrical conductance between two regions of the skin to measure skin conductance activity. doi:10.1016/j.snb.2018.06.125 galvanic skin response sensor GSR sensor EXMO:0000296 Electronic implements worn on the body as an implant or as an accessory. mesh:D000076251 umls:C4505348 wearable device wearable electronic device Electronic implements worn on the body as an implant or as an accessory. mesh:D000076251 wearable device mesh:D000076251 EXMO:0000297 Computerized eyewear with multiple technological applications for advanced computing and interoperability. Smart glasses are optimized to facilitate information and data access, capture, display, transfer, and manipulation. mesh:D000080310 umls:C5197727 smart glasses Computerized eyewear with multiple technological applications for advanced computing and interoperability. Smart glasses are optimized to facilitate information and data access, capture, display, transfer, and manipulation. mesh:D000080310 EXMO:0000298 A smartwatch is a wearable computer in the form of a watch; modern smartwatches provide a local touchscreen interface for daily use, while an associated smartphone app provides for management and telemetry. smart watch A smartwatch is a wearable computer in the form of a watch; modern smartwatches provide a local touchscreen interface for daily use, while an associated smartphone app provides for management and telemetry. https://en.wikipedia.org/wiki/Smartwatch EXMO:0000301 A stationary bicycle is a device used as exercise equipment for indoor cycling. umls:C2712863 exercise bicycle exercise bike exercycle spinning bike stationary bike A stationary bicycle is a device used as exercise equipment for indoor cycling. https://en.wikipedia.org/wiki/Stationary_bicycle EXMO:0000303 Fasting plasma glucose (FPG) levels are determined by taking a blood sample from participants who have fasted for at least 8 hours. It can be measured in mmol/L or in mg/dL. For comparability, these values are converted in mmol/L. Other related biomarkers, such as haemoglobin A1c (HbA1c), can be used to help calculate national estimates. fasting plasma glucose Fasting plasma glucose (FPG) levels are determined by taking a blood sample from participants who have fasted for at least 8 hours. It can be measured in mmol/L or in mg/dL. For comparability, these values are converted in mmol/L. Other related biomarkers, such as haemoglobin A1c (HbA1c), can be used to help calculate national estimates. https://www.who.int/data/gho/indicator-metadata-registry/imr-details/2380 fasting plasma glucose FPG EXMO:0000305 Exercise addiction is a state characterized by a compulsive engagement in any form of physical exercise, despite negative consequences. umls:C0860095 exercise addiction Exercise addiction is a state characterized by a compulsive engagement in any form of physical exercise, despite negative consequences. https://en.wikipedia.org/wiki/Exercise_addiction EXMO:0000310 Any waking behaviour characterized by an energy expenditure of 1.5 METS or lower while sitting, reclining, or lying. Most desk-based office work, driving a car, and watching television are examples of sedentary behaviours; these can also apply to those unable to stand, such as wheelchair users. sedentary behavior Any waking behaviour characterized by an energy expenditure of 1.5 METS or lower while sitting, reclining, or lying. Most desk-based office work, driving a car, and watching television are examples of sedentary behaviours; these can also apply to those unable to stand, such as wheelchair users. https://www.who.int/publications/i/item/9789240015128 EXMO:0000311 exercise performed in water umls:C2147841 aquatic exercise EXMO:0000318 The sit-up is an abdominal endurance training exercise to strengthen, tighten and tone the abdominal muscles. umls:C0454359 sit-up strength exercise sit up exercise The sit-up is an abdominal endurance training exercise to strengthen, tighten and tone the abdominal muscles. https://en.wikipedia.org/wiki/Sit-up EXMO:0000326 umls:C0429629 total energy expenditure EXMO:0000327 the Basal Metabolic Rate (BMR) + the Thermic Effect of Activity (TEA) + the Thermic Effect of Food (TEF) total daily energy expenditure the Basal Metabolic Rate (BMR) + the Thermic Effect of Activity (TEA) + the Thermic Effect of Food (TEF) https://healthyweightlossperweek.org/knowledge-base/total-daily-energy-expenditure-tdee-formula-and-examples/ total daily energy expenditure TDEE EXMO:0000328 The thermic effect of physical activity (TEPA) is the amount of energy burned during all physical activity. thermic effect of activity thermic effect of exercise thermic effect of physical activity The thermic effect of physical activity (TEPA) is the amount of energy burned during all physical activity. https://wikipedikia.org/what-is-the-thermic-effect-of-exercise/ TEPA can range anywhere from 15 to 30% of TDEE. thermic effect of activity TEA thermic effect of physical activity TEPA EXMO:0000329 Specific dynamic action (SDA), also known as thermic effect of food (TEF) or dietary induced thermogenesis (DIT), is the amount of energy expenditure above the basal metabolic rate due to the cost of processing food for use and storage. dietary induced thermogenesis specific dynamic action thermic effect of food Specific dynamic action (SDA), also known as thermic effect of food (TEF) or dietary induced thermogenesis (DIT), is the amount of energy expenditure above the basal metabolic rate due to the cost of processing food for use and storage. https://en.wikipedia.org/wiki/Specific_dynamic_action dietary induced thermogenesis DIT specific dynamic action SDA thermic effect of food TEF EXMO:0000330 Physical activity performed by an individual that is not required as an essential activity of daily living and is performed at the discretion of the individual. Such activities include sports participation, exercise conditioning or training, and recreational activities such as going for a walk, dancing, and gardening. umls:C0336910 leisure- domain physical activity leisure physical activity Physical activity performed by an individual that is not required as an essential activity of daily living and is performed at the discretion of the individual. Such activities include sports participation, exercise conditioning or training, and recreational activities such as going for a walk, dancing, and gardening. https://www.who.int/publications/i/item/9789240015128 EXMO:0000331 On an absolute scale, moderate-intensity refers to the physical activity that is performed between 3 and less than 6 times the intensity of rest. On a scale relative to an individual’s personal capacity, moderate-intensity physical activity is usually a 5 or 6 on a scale of 0–10. umls:C4482418 moderate-intensity physical activity moderate physical activity On an absolute scale, moderate-intensity refers to the physical activity that is performed between 3 and less than 6 times the intensity of rest. On a scale relative to an individual’s personal capacity, moderate-intensity physical activity is usually a 5 or 6 on a scale of 0–10. https://www.who.int/publications/i/item/9789240015128 EXMO:0000332 On an absolute scale, vigorous-intensity refers to physical activity that is performed at 6.0 or more METS. On a scale relative to an individual’s personal capacity, vigorous-intensity physical activity is usually a 7 or 8 on a scale of 0–10. umls:C4267713 vigorous-intensity physical activity vigorous physical activity On an absolute scale, vigorous-intensity refers to physical activity that is performed at 6.0 or more METS. On a scale relative to an individual’s personal capacity, vigorous-intensity physical activity is usually a 7 or 8 on a scale of 0–10. https://www.who.int/publications/i/item/9789240015128 EXMO:0000333 Moderate-to-vigorous physical activity (MVPA) refers to physical activities that require sustained, rhythmic movement and elevate heart rate and breathing to a level where exertion is perceived as moderate or intense. moderate-to-vigorous physical activity moderate-to-vigorous physical activity MVPA EXMO:0000335 Tapering-off physical activity from vigorous to light, to gradually return the body to pre-exercise condition and metabolic state. mesh:D064590 umls:C3658227 cool down exercise cooldown exercise cooling down exercise cooling-down exercise warm-down exercise warming-down exercise cool-down exercise Tapering-off physical activity from vigorous to light, to gradually return the body to pre-exercise condition and metabolic state. mesh:D064590 cool down exercise mesh:D064590 cooldown exercise mesh:D064590 cooling down exercise mesh:D064590 cooling-down exercise mesh:D064590 warm-down exercise mesh:D064590 warming-down exercise mesh:D064590 EXMO:0000341 Muscle tone is traditionally defined as ‘the tension in the relaxed muscle’ or ‘the resistance, felt by the examiner during passive stretching of a joint when the muscles are at rest’. muscle tone Muscle tone is traditionally defined as ‘the tension in the relaxed muscle’ or ‘the resistance, felt by the examiner during passive stretching of a joint when the muscles are at rest’. doi:10.3390/toxins13040282 EXMO:0000345 Physical activity performed primarily for enjoyment, relaxation, or social interaction rather than for competitive, occupational, or structured fitness goals. recreational exercise EXMO:0000346 High-intensity functional training (HIFT) is an exercise modality that emphasizes functional, multi-joint movements that can be modified to any fitness level and elicit greater muscle recruitment than more traditional exercise. high-intensity functional training High-intensity functional training (HIFT) is an exercise modality that emphasizes functional, multi-joint movements that can be modified to any fitness level and elicit greater muscle recruitment than more traditional exercise. pubmed:30087252 high-intensity functional training HIFT EXMO:0000347 Cardiopulmonary endurance is the ability of body to perform aerobic exercise or activity for long periods of time without tiring. cardiopulmonary endurance Cardiopulmonary endurance is the ability of body to perform aerobic exercise or activity for long periods of time without tiring. pubmed:32132378 EXMO:0000349 The Six Healing Sounds or Liu Zi Jue is one of the common forms of Chinese qigong, and involves the coordination of movement and breathing patterns with specific sounds. Liu Zi Jue Liuzijue Qigong Six Healing Sounds liuzijue The Six Healing Sounds or Liu Zi Jue is one of the common forms of Chinese qigong, and involves the coordination of movement and breathing patterns with specific sounds. https://en.wikipedia.org/wiki/Liu_Zi_Jue Liuzijue Qigong pubmed:35242094 LQG EXMO:0000350 Anaerobic exercise is a type of exercise that breaks down glucose in the body without using oxygen; anaerobic means "without oxygen". This type of exercise leads to a buildup of lactic acid. In practical terms, this means that anaerobic exercise is more intense, but shorter in duration than aerobic exercise. umls:C3841233 anaerobic exercise Anaerobic exercise is a type of exercise that breaks down glucose in the body without using oxygen; anaerobic means "without oxygen". This type of exercise leads to a buildup of lactic acid. In practical terms, this means that anaerobic exercise is more intense, but shorter in duration than aerobic exercise. https://en.wikipedia.org/wiki/Anaerobic_exercise EXMO:0000352 Actions performed to provide the active or passive exercises to maintain joint function umls:C0150220 range of motion exercise EXMO:0000353 A clinical or rehabilitative assessment that measures the maximum movement potential of a joint or body part in specific directions (e.g., flexion, extension, rotation). snomedct:69212005 umls:C0204061 range of motion testing EXMO:0000356 An ability to perform all the mental processes of cognition, including the ability to learn and judge, use language, and remember. brain health An ability to perform all the mental processes of cognition, including the ability to learn and judge, use language, and remember. pubmed:33037002 EXMO:0000361 Injuries to the ROTATOR CUFF of the shoulder joint. mesh:D000070636 snomedct:718539004 rotator cuff injury Injuries to the ROTATOR CUFF of the shoulder joint. mesh:D000070636 EXMO:0000363 umls:C2732289 injury of cruciate ligament of knee EXMO:0000364 Acute ankle sprains are commonly seen in both primary care and sports medicine practices as well as emergency departments and can result in significant short-term morbidity, recurrent injuries, and functional instability. acute ankle sprain acute sprain of ankle joint Acute ankle sprains are commonly seen in both primary care and sports medicine practices as well as emergency departments and can result in significant short-term morbidity, recurrent injuries, and functional instability. https://www.ncbi.nlm.nih.gov/books/NBK459212/ EXMO:0000365 acute lumbar muscle sprain EXMO:0000366 musculi piriformis syndrome EXMO:0000379 A structured and personalized schedule outlining specific physical activities, routines, and goals designed to improve or maintain an individual's physical fitness, health, or athletic performance. exercise plan EXMO:0000382 A systematic process of identifying, assessing, and minimizing risks associated with physical activity to prevent injuries, accidents, or harm to participants, staff, and facilities. It involves implementing protocols, policies, and practices to ensure a safe environment for training, competition, and recreational exercise. safety and risk management EXMO:0000383 Static and dynamic exercises that are designed to improve an individual’s ability to withstand challenges from postural sway or destabilizing stimuli caused by self-motion, the environment, or other objects. balance training Static and dynamic exercises that are designed to improve an individual’s ability to withstand challenges from postural sway or destabilizing stimuli caused by self-motion, the environment, or other objects. https://www.who.int/publications/i/item/9789240015128 EXMO:0000384 Physical activity primarily designed to increase the strength of specific sites in bones that make up the skeletal system. Bone-strengthening activities produce an impact or tension force on the bones that promotes bone growth and strength. bone-strengthening activity Physical activity primarily designed to increase the strength of specific sites in bones that make up the skeletal system. Bone-strengthening activities produce an impact or tension force on the bones that promotes bone growth and strength. https://www.who.int/publications/i/item/9789240015128 EXMO:0000385 A measure of the body's ability to function efficiently and effectively in work and leisure activities, and includes, for example, physical fitness and cardiorespiratory fitness. fitness A measure of the body's ability to function efficiently and effectively in work and leisure activities, and includes, for example, physical fitness and cardiorespiratory fitness. https://www.who.int/publications/i/item/9789240015128 EXMO:0000386 Exercises that can be embedded into everyday tasks to improve lower-body strength, balance, and motor performance. functional exercise Exercises that can be embedded into everyday tasks to improve lower-body strength, balance, and motor performance. https://www.who.int/publications/i/item/9789240015128 EXMO:0000387 Tandem stance (TS) is a recognised clinical measure of standing balance and it has been shown that the performance deteriorates with age. tandem stance tandem stand Tandem stance (TS) is a recognised clinical measure of standing balance and it has been shown that the performance deteriorates with age. doi:10.1016/j.clinbiomech.2004.09.008 EXMO:0000388 The one-leg stand is a physical test or exercise in which an individual is required to stand upright on one leg while maintaining balance, often with the other leg lifted off the ground (e.g., bent at the knee or extended forward/backward). one-leg stand EXMO:0000389 A functional assessment exercise used to evaluate lower body strength, endurance, and mobility, particularly in older adults or individuals undergoing rehabilitation. chair stand EXMO:0000390 Toe Raise refers to a strength and mobility exercise that involves lifting the toes and forefoot upward while keeping the heel planted on the ground. toe raise EXMO:0000391 Stepping over obstacles is a functional exercise that involves lifting one or both legs to clear physical barriers, mimicking real-life movements to enhance strength, balance, coordination, and adaptability. stepping over obstacles EXMO:0000392 Physical activity undertaken in the home for domestic duties (such as cleaning, caring for children, gardening etc.). household domain physical activity Physical activity undertaken in the home for domestic duties (such as cleaning, caring for children, gardening etc.). https://www.who.int/publications/i/item/9789240015128 EXMO:0000393 The action of removing dirt, filth, or unwanted substances from. ncit:C65076 umls:C1947930 cleaning The action of removing dirt, filth, or unwanted substances from. ncit:C65076 EXMO:0000395 Light-intensity physical activity is between 1.5 and 3 METs, i.e. activities with energy cost less than 3 times the energy expenditure at rest for that person. light-intensity physical activity Light-intensity physical activity is between 1.5 and 3 METs, i.e. activities with energy cost less than 3 times the energy expenditure at rest for that person. https://www.who.int/publications/i/item/9789240015128 EXMO:0000396 Physical activity and exercise that increase skeletal muscle strength, power, endurance, and mass (e.g. strength training, resistance training, or muscular strength and endurance exercises). muscle-strengthening activity Physical activity and exercise that increase skeletal muscle strength, power, endurance, and mass (e.g. strength training, resistance training, or muscular strength and endurance exercises). https://www.who.int/publications/i/item/9789240015128 EXMO:0000397 Multicomponent physical activity refers to exercise programs or routines that combine multiple types of physical activities to target different aspects of physical fitness and health. multicomponent physical activity EXMO:0000398 An insufficient physical activity level to meet present physical activity recommendations. physical inactivity An insufficient physical activity level to meet present physical activity recommendations. https://www.who.int/publications/i/item/9789240015128 EXMO:0000399 Screen time is the amount of time spent using an electronic device with a display screen such as a smartphone, computer, television, video game console, or tablet. screen time Screen time is the amount of time spent using an electronic device with a display screen such as a smartphone, computer, television, video game console, or tablet. https://en.wikipedia.org/wiki/Screen_time EXMO:0000400 Time spent watching screens (television (TV), computer, mobile devices) for purposes other than those related to education/study or work. recreational screen time Time spent watching screens (television (TV), computer, mobile devices) for purposes other than those related to education/study or work. https://www.who.int/publications/i/item/9789240015128 EXMO:0000401 Time spent watching screen-based entertainment (TV, computer, mobile devices). Does not include active screen-based games where physical activity or movement is required. sedentary screen time Time spent watching screen-based entertainment (TV, computer, mobile devices). Does not include active screen-based games where physical activity or movement is required. https://www.who.int/publications/i/item/9789240015128 EXMO:0000402 Physical activity performed for the purpose of getting to and from places, and refers to walking, cycling and wheeling (the use of non-motorized means of locomotion with wheels, such as scooters, rollerblades, manual wheelchair etc.). transport domain physical activity Physical activity performed for the purpose of getting to and from places, and refers to walking, cycling and wheeling (the use of non-motorized means of locomotion with wheels, such as scooters, rollerblades, manual wheelchair etc.). https://www.who.int/publications/i/item/9789240015128 EXMO:0000403 Physical activity undertaken during paid or voluntary work. occupation domain physical activity work domain physical activity Physical activity undertaken during paid or voluntary work. https://www.who.int/publications/i/item/9789240015128 occupation domain physical activity https://www.who.int/publications/i/item/9789240015128 EXMO:0000404 Conditioning refers to the systematic process of improving physical fitness, endurance, strength, speed, flexibility, and overall athletic performance through targeted training programs. conditioning The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy. Wikipedia:Muscle_hypertrophy biological_process GO:0014896 muscle hypertrophy GO:0014896 GSSO:000924 Intellectual processes which allow for knowledge acquisition. cognitive function cognitive functions GSSO:001811 A limitation on a person's physical functioning, mobility, dexterity or stamina. https://en.wikipedia.org/wiki/Physical_disability https://www.wikidata.org/wiki/Q1179623 physical handicap physical disability http://purl.bioontology.org/ontology/MEDDRA/10048624 physical GSSO:005059 A garment covering the whole hand. Gloves usually have separate sheaths or openings for each finger and the thumb. https://en.wikipedia.org/wiki/Category:Gloves https://en.wikipedia.org/wiki/Glove https://www.wikidata.org/wiki/Q169031 glove gloves http://id.loc.gov/authorities/subjects/sh85055348 GT2170 TS2160 TT666 glóf http://purl.bioontology.org/ontology/SNOMEDCT/52291003 GSSO:005898 A person who actively participates in physical sports, especially with great skill; a sportsperson. athlete athletes http://id.loc.gov/authorities/subjects/sh85009135 GV697 GSSO:008521 A person who has a form of physical disability. person with a physical disability people with physical disabilities persons with physical disabilities GSSO:010636 A woman who is pregnant. https://www.wikidata.org/wiki/Q104720811 pregnant woman pregnant women http://id.loc.gov/authorities/subjects/sh85106300 http://purl.bioontology.org/ontology/SNOMEDCT/255409004 Medical history of maternal diseases, exposures, or other relevant findings during the pregnancy of which the index person was the product. UMLS:C4025690 Prenatal maternal abnormality Maternal health problem HP:0002686 Pregnancy history HP:0002686 HP:0032316 Information about close relatives of an individual who is the proband of a study or who is being investigated with the goal of identifying a medical diagnosis. Usually, the family history includes information from three generations of relatives, including children, brothers and sisters, parents, aunts and uncles, nieces and nephews, grandparents, and cousins. 2019-02-14T11:40:50Z This subontology is intended to help record summary information about family members if only a limited amount of information is available or required. Family history HP:0032443 In a medical encounter, the physician generally will interview the patient about his or her current problem, and may perform additional testing. The past medical history (PMH) in contrast records information about the patient's medical, personal and family history that might be relevant to the presenting illness or to provide optimal clinical management. The PMH generally includes (if relevant) other major illnesses, hospitalizations, surgeries, injuries, allergies, gynecologic and obstetric history, family history, personal history including occupational history, alcohol and drug use, etc. 2019-03-03T16:39:26Z This subontology of the HPO is not intended to provide all needed terms to describe the past medical history, but rather to be combined with other ontologies such as MONDO in order to capture information that is often needed to properly assess phenotypic findings related to a presenting medical problem. Past medical history HP:0040406 Perimenopause, or the menopausal transition, encompasses that period of time during which physiologic changes mark progression toward a woman's final menstrual period. This phase begins with the onset of menstrual irregularities and continues until a woman reaches menopause, or one year after amenorrhea has occurred. Perimenopause can last for a variable amount of time, the median of which is four years. 2024-01-02T13:17:13Z Perimenopausal HP:4000112 Information about current or past medications taken by an individual. 2023-01-17T09:25:01Z Medication history A spatiotemporal region encompassing some part of the life cycle of an organism. UBERON:0000105 developmental stage stage human_stages_ontology HsapDv:0000000 life cycle stage HsapDv:0000000 A life cycle stage that starts at sexual maturity of the human adult, and ends before senescence. 60.0 15.0 UBERON:0018241 human_developmental_stage HsapDv:0000226 We start this stage at 15 years to follow the Human Phenotype Ontology defintion of adult onset (HP:0003581), and we ends the stage at 60 years, the start of late onset in HPO (HP:0003584). prime adult stage HsapDv:0000226 Late adult stage that refers to an individu who is over 60 and starts to have some age-related impairments. 60.0 HP:0003584 UBERON:0007222 60+ years human_developmental_stage elderly HsapDv:0000227 Age-related hearing loss (presbycusis) is one of the most common conditions affecting older and elderly adults(see https://www.nidcd.nih.gov/health/age-related-hearing-loss#1). We follow Human Phenotype Ontology (HPO) late onset definition (HP:0003584) to start this stage at 60 years. late adult stage HsapDv:0000227 Human developmental stage that refers to a sexually mature human. 15.0 HP:0003581 UBERON:0000113 mature stage human_developmental_stage HsapDv:0000258 HPO (Human Phenotype Ontology) considers HP:0003581 (adult onset) as 'at the age of 16 years or later', but this adult stage directly follows the pediatric onset (HP:0410280) defined 'as before the age of 15 years' (see https://github.com/obophenotype/human-phenotype-ontology/issues/6099). To be consistent, we consider adult stage as starting at 15 years. adult stage HsapDv:0000258 Human stage that refers to a child who is over 12 months and under 5 years old. 5.0 1.0 HP:0011463 human_developmental_stage childhood stage preschool child HsapDv:0000265 We follow HPO (Human Phenotype Ontology) definition for child period, see HP:0011463 (Childhood onset). child stage (1-4 yo) HsapDv:0000265 A prime adult stage that refers to an adult who is under 40 years old. 40.0 15.0 HP:0011462 human_developmental_stage HsapDv:0000266 young adult stage HsapDv:0000266 Late adulthood that refers to an adult who is over 40 and under 60 years old. 60.0 40.0 HP:0003596 human_developmental_stage HsapDv:0000267 middle aged stage HsapDv:0000267 Pediatric stage that refers to a human who is over 5 and under 15 years old. 15.0 5.0 HP:0003621 UBERON:0034919 human_developmental_stage HsapDv:0000271 juvenile stage (5-14 yo) HsapDv:0000271 IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum MAXO:0000001 A clinically prescribed procedure, therapy, intervention, or recommendation. 2018-11-16T20:07:28Z OGMS:0000096 health care process medical action MAXO:0000465 Therapy occuring in a pool or bath which is a low-impact activity and takes the pressure off your bones, joints, and muscles. 2020-01-08T18:07:42Z aquatic exercise therapy MAXO:0000900 A procedure that displays the electrical activity of the heart. 2021-08-09T19:19:35Z NCIT:C38053 ECG EKG electrocardiogram procedure electrocardiography MAXO:0035091 Electromyography (EMG) is a diagnostic procedure that evaluates the muscle response to electrical impulses from the nerves that control them, called motor neurons. The test is used to help detect neuromuscular abnormalities. It is usually performed after a nerve conduction study. 2023-04-11T12:00:00Z electromyography procedure NCIT:C101234 A medically supervised program to improve the health and well-being of people who have heart problems. This may include exercise training, education on heart healthy living, and/or counseling to reduce stress. (ACC) C101234 Therapeutic or Preventive Procedure Cardiac Rehabilitation Cardiac Rehabilitation C0700431 CPTAC CTRP Cardiac Rehabilitation Cardiac Rehabilitation NCIT:C110943 Damage to the muscles, bones and their supportive structural attachments. C110943 Finding Musculoskeletal Injury CL451681 FDA Any injury to muscle or tendon tissue including strains. IMDRF:E1620 Muscle/Tendon Damage Musculoskeletal Injury Musculoskeletal Injury NCIT:C116517 A clinical tool to evaluate exercise capacity and to assess cardiac function under stress. C116517 Diagnostic Procedure Cardiopulmonary Exercise Testing Cardiopulmonary Exercise Testing C2959886 CTRP CPET CPX Cardiopulmonary Exercise Testing Cardiopulmonary Exercise Testing NCIT:C122028 A scale for a subject to rate their perception of the intensity of their own physical effort. C122028 Intellectual Product Rating of Perceived Exertion C4050303 RPE Rated Perceived Exertion Rating of Perceived Exertion Relative Perceived Exertion Rating of Perceived Exertion NCIT:C122029 A period of lower-intensity activity designed to prepare the body for more vigorous exercise. C122029 Daily or Recreational Activity Warm-Up C2350169 Warm-Up Warm-Up Exercise Warm-Up NCIT:C129778 The amount of glucose present in a sample two hours after a subject has eaten a meal. C129778 Laboratory or Test Result 2-Hour Postprandial Glucose 2-Hour Postprandial Glucose CL512847 CTRP 2 Hour Glucose 2 Hour Postprandial Glucose 2 hr Glucose 2 hr Postprandial Glucose 2-Hour Glucose 2-Hour Postprandial Glucose 2h Glucose 2h Postprandial Glucose 2-Hour Postprandial Glucose NCIT:C132453 The volume exhaled during the first three seconds of a forced expiratory maneuver that is started from the level of total lung capacity. C132453 Diagnostic Procedure Forced Expiratory Volume in 3 Seconds CL520386 CDISC The volume of air that can be forcibly exhaled during the first three seconds following maximal inhalation. FEV3 Forced Expiratory Volume in 3 Seconds Forced Expiratory Volume in 3 Seconds NCIT:C139210 An assessment of hand muscle strength that measures that force with which one holds or grasps. C139210 Conceptual Entity Grip Strength Grip Strength C0429271 CDISC CTRP An assessment of muscle strength that measures that force with which one holds or grasps. GRIPSTR Grip Strength Grip Strength NCIT:C150046 An individual's capacity to undertake physical activities, such as everyday tasks. C150046 Organism Attribute Physical Function CL551885 Physical Function Physical Function NCIT:C150523 Any of various activities and tests designed to assess an individual's physical fitness. C150523 Health Care Activity Physical Performance Testing Physical Performance Testing C4279961 CTRP Physical Fitness Testing Physical Function Testing Physical Performance Testing Physical Performance Testing NCIT:C15302 The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. C15302 Therapeutic or Preventive Procedure Physical Therapy Physical Therapy C0949766 CTRP NICHD OORO The use of exercises and physical activities to help condition muscles and restore strength and movement. For example, physical therapy can be used to restore arm and shoulder movement and build back strength after breast cancer surgery. The use of exercises and physical activity to restore movement, reduce pain, strengthen muscles, and improve balance and posture in order to restore the ability to function. Therapists provide education and suggest activity modification suited to an individual. Physical_Therapy PT Physiatric Procedure Physical Medicine Procedure Physical Therapeutics Physical Therapy Physical Therapy Procedure Physiotherapy Physiotherapy Procedure physical therapy Physical Therapy NCIT:C154219 Physical exercise that uses weight, or other forms of resistance, to induce muscle contraction and build strength, anaerobic endurance, and size of skeletal muscles. Typical exercises include leg and chest press, knee extension, leg curl, row, abdominal crunch, and bicep curl. C154219 Daily or Recreational Activity Resistance Training Resistance Training C0872279 CTRP Resistance Training Strength Training Resistance Training NCIT:C154225 A physical exercise in which a specific muscle or tendon is deliberately flexed or stretched in order to improve the muscle's elasticity. C154225 Daily or Recreational Activity Stretching Stretching C0600080 ACC/AHA CTRP An activity that elongates shortened soft-tissue structures and thereby increases flexibility. Stretching Stretching NCIT:C16268 An age group comprised of individuals 65 years of age and older. C16268 Age Group Elderly C2825054 FDA Elderly Aged 65 and Over ELDERLY Elderly Elderly (Over 65) Senior Citizen Elderly NCIT:C16423 An age group comprised of individuals who are not yet an adult. The specific cut-off age will vary by purpose. C16423 Age Group Child C0008059 FDA NICHD Children CHILD Child Children Children (0-21) Child NCIT:C16567 Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness. C16567 Daily or Recreational Activity Exercise Exercise C0015259 ACC/AHA CTRP Performance of physical exertion for improvement of health or correction of physical deformity. Exercise Exercise Exercise Type Exercise NCIT:C168192 A graded test to measure an individual's heart rate and oxygen intake while undergoing strenuous physical exercise; most often assessed on a treadmill. C168192 Diagnostic Procedure Exercise Cardiac Stress Test C0015260 ACC/AHA A graded test to measure an individual's heart rate and oxygen intake while undergoing strenuous physical exercise, as on a treadmill. ECST Exercise Cardiac Stress Test Exercise Stress Test Exercise Cardiac Stress Test NCIT:C17049 A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. C17049 Population Group Race C0034510 CDISC-GLOSS CTDC DIPG/DMG FDA GDC NICHD OORO PCDC SeroNet An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. (NCI) Race reported by the patient. This is important for research and health care policy using social determinants of health (SDOH). Race Patient Reported Race RACE Race Racial Group race Race NCIT:C172269 A physical activity that consists of moving your feet and body rhythmically, usually in response to music. C172269 Daily or Recreational Activity Dancing C0010963 Dancing Dancing NCIT:C172473 A determination or assessment of the degree or magnitude of an individual's exertion during physical activity. C172473 Quantitative Concept Exercise Intensity C3669170 CDISC A determination or assessment of the degree or magnitude of an individual's exertion during physical activity. EXCINTSY Exercise Intensity Exercise Intensity NCIT:C17357 Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.) C17357 Organism Attribute Gender C0079399 CDISC-GLOSS CTDC DIPG/DMG GDC SeroNet Subject self-identification re: masculine/feminine. [IOM] See also sex. Gender Gender gender Gender NCIT:C17600 An age group comprised of humans who have reached reproductive age. C17600 Age Group Adult C0001675 FDA Adult ADULT Adult Adult Human (21+) Human, Adult Adult NCIT:C17708 Any form of exercise or movement. Physical activity may include planned activity such as walking, running, basketball, or other sports. Physical activity may also include other daily activities such as household chores, yard work, walking the dog, etc. C17708 Daily or Recreational Activity Physical Activity Physical Activity C0026606 CTRP Physical_Activity Physical Activity Physical Activity NCIT:C178017 A measurement of the mass of all skeletal muscle in the body. C178017 Diagnostic Procedure Skeletal Muscle Mass CL1647734 CDISC A measurement of the total mass of the skeletal muscle. SMMASS Skeletal Muscle Mass Skeletal Muscle Mass Measurement Skeletal Muscle Mass NCIT:C180667 The activity of walking for recreation, exercise, or training that is usually strenuous and on unpaved surfaces. C180667 Daily or Recreational Activity Hiking CL586879 Hike Hiking Hiking NCIT:C181501 A measurement of a muscle's ability to perform repetitive contractions against a force. C181501 Conceptual Entity Muscle Endurance Measurement CL1664431 CDISC A measurement of a muscle's ability to perform repetitive contractions against a force. ENDURM Muscle Endurance Muscle Endurance Measurement Muscle Endurance Measurement NCIT:C185297 A type of cardiovascular exercise that alternates short periods of intense anaerobic exercise with less intense recovery periods. C185297 Daily or Recreational Activity High-Intensity Interval Training High-Intensity Interval Training C4277545 CTRP HIIT High-Intensity Interval Training High-Intensity Interval Training NCIT:C192423 A near sitting position in which the body is lowered while the knees and hips are bent and the weight is supported on one's ankles and feet. The chest is up and the thighs are nearly parallel to the floor. C192423 Spatial Concept Squatting CL1912950 OORO Squatting Squatting NCIT:C19796 An indication of a person's current tobacco and nicotine consumption as well as some indication of smoking history. C19796 Organism Attribute Smoking Status C1519386 GDC Smoking_Status Current Tobacco and Nicotine Consumption Status Smoking Status tobacco smoking status tobacco_smoking_status Smoking Status NCIT:C21007 Any physical or mental impairment that interferes with an individual's ability to perform desired activities. C21007 Organism Attribute Disability C0231170 Patient Code (Appendix B) FDA OORO Any physical or mental impairment that interferes with an individual's ability to perform desired activities. High level categorizations of disabilities having an impact on basic functioning. This is important for research and health care policy using social determinants of health (SDOH). Values should be as identified by patient. Disability IMDRF:F1202 DISABILITY Disability Handicap Infirmity Disability NCIT:C21057 An exercise that is performed by exerting force against an immovable object or by holding an object in a static position. C21057 Daily or Recreational Activity Isometric Exercise C0022206 ACC/AHA Grasping one’s hands in the midline and pushing them away from each other with tensed muscles OR leg crossing plus tensing of leg, abdominal, and buttock muscles. Isometric_Exercise Isometric Exercise Isometric countermeasures Isometrics Muscle-Setting Exercise Static Exercise Isometric Exercise NCIT:C21058 An exercise that involves the movement of a constant weight or load through a specified range of motion. C21058 Daily or Recreational Activity Isotonic Exercise C0454287 Isotonic_Exercise This exercise can build strength and endurance. Isotonic Exercise Isotonics Isotonic Exercise NCIT:C21059 An exercise that involves movement at a constant rate with a variable force throughout a specified range of motion. C21059 Daily or Recreational Activity Isokinetic Exercise CL448791 Isokinetic_Exercise The advantage of this exercise is that it stresses the muscle being used throughout the entire range. Isokinetic Exercise Isokinetics Isokinetic Exercise NCIT:C25190 A human being. C25190 Human Person C0027361 BRIDG NICHD A human being. A human being. EXAMPLE(S): OTHER NAME(S): NOTE(S): Person Individual Person Person NCIT:C27954 An age group comprised of juveniles between the onset of puberty and maturity; in the state of development between puberty and maturity. C27954 Age Group Adolescent C0205653 FDA Adolescent ADOLESCENT Adolescent Adolescents Adolescent NCIT:C28220 C28220 Medical Device Sensor C0183210 A device that responds to a stimulus, such as heat, light, or pressure, and generates a signal that can be measured or interpreted. Sensor Sensor sensor Sensor NCIT:C3283 Having a high amount of body fat (body mass index [BMI] of 30 or more). C3283 Sign or Symptom Obesity Obesity C3809449 CPTAC CTRP GDC SeroNet mCode A condition marked by an abnormally high, unhealthy amount of body fat. A disorder characterized by having a high amount of body fat. Obesity Obesity Obesity Obesity, unspecified obesity Obesity NCIT:C34405 An injury sustained while practicing or competing in a sport. C34405 Finding Sports Injury C0004161 Sports_Injury Sports Injury Sports Injury NCIT:C38084 A test of lung function, the FEV1 is the volume exhaled during the first second of a forced expiratory maneuver started from the level of total lung capacity. It is the most frequently used index for assessing bronchoconstriction or bronchodilatation. C38084 Diagnostic Procedure Forced Expiratory Volume in 1 Second C0849974 CDISC PCDC The volume of air that can be forcibly exhaled during the first second following maximal inhalation. Forced_Expiratory_Volume_1_Test FEV1 FEV1%VC Forced Expiratory Volume 1 Test Forced Expiratory Volume in 1 Second PFT/FEV1 Pulmonary Function Test/Forced Expiratory Volume 1 Forced Expiratory Volume in 1 Second NCIT:C39771 20-60 minutes of exercise which elevates your heart rate to 35-60% of your maximum heart rate performed at least 3-4 times per week. C39771 Daily or Recreational Activity Light Exercise C1517883 Light_Exercise Light exercises include housework, gardening, bowling, and slow walking. Maximum heart rate is approximately 220 minus current age in years. Light Activity Light Exercise Light Exercise NCIT:C39772 20-60 minutes of exercise which elevates your heart rate to 60-80% of your maximum heart rate performed at least 3-4 times per week. C39772 Daily or Recreational Activity Moderate Exercise C3833417 Moderate_Exercise Moderate exercises include basketball, singles tennis, downhill skiing, and moderate walking. Maximum heart rate is approximately 220 minus current age in years. Moderate Activity Moderate Exercise Moderate Exercise NCIT:C39773 20-60 minutes of exercise which elevates your heart rate to 80-90% of your maximum heart rate performed at least 3-4 times per week. C39773 Daily or Recreational Activity Strenuous Exercise C1514989 Strenuous_Exercise Strenuous exercises include jogging, swimming, bicycling, and brisk walking. Maximum heart rate is approximately 220 minus current age in years. Strenuous Activity Strenuous Exercise Strenuous Exercise NCIT:C39774 Sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. C39774 Daily or Recreational Activity Aerobic Exercise Aerobic Exercise C0001701 CTRP Physical activity that increases the heart rate and the body's use of oxygen. It helps improve a person's physical fitness. Aerobic_Exercise Examples of aerobic exercise include running, swimming, and cycling. Aerobic Activity Aerobic Exercise aerobic exercise Aerobic Exercise NCIT:C39777 Light exercise for less than 20 minutes, 20-60 minutes of exercise which elevates your heart rate to less than 35% of your maximum heart rate, or light exercise less than 3 times per week. C39777 Daily or Recreational Activity Very Light Exercise Very Light Exercise C1519977 CTRP Very_Light_Exercise Maximum heart rate is approximately 220 minus current age in years. Sedentary Exercise Very Light Activity Very Light Exercise Very Light Exercise NCIT:C40645 Lipid Metabolism involves anabolic and catabolic biochemical changes to the hydrophobic class of biochemicals within a cell as materials needed for important life processes. C40645 Physiologic Function Lipid Metabolism Lipid-Lipoprotein-Membrane_Constituent_Metabolism Cholesterol_Homeostasis Cholesterol_Synthesis_Inhibition Eicosanoid_Modulation Fatty_Acid_Metabolism Phospholipid_Metabolism Triglyceride_Metabolism Biological_Process_Kind Retired_Concept See 'Lipid Metabolism' Lipid Metabolism Lipid Metabolism NCIT:C43545 A method to assess body composition, i.e., the relative percentages of body weight comprised of fat tissue and lean body mass. It is based on the principle that the resistance to an applied electric current is inversely related to the amount of lean body mass within the body. Impedance is greatest in fat tissue, which contains only 10-20% water, while lean body mass, which contains 70-75% water, allows the signal to pass much more easily. C43545 Diagnostic Procedure Bioelectric Impedance Analysis Bioelectric Impedance Analysis C1704746 CTRP Bioelectric_Impedance_Analysis BIA Bioelectric Impedance Bioelectric Impedance Analysis Bioelectric Impedance Test Bioelectrical Impedance Analysis Bioimpedance Analysis Bioelectric Impedance Analysis NCIT:C46109 The cultural, social, psychological, and behavior norms that are associated with being a man. C46109 Qualitative Concept Male Gender C1706180 OORO SeroNet Male_Gender Male Male Gender Male Gender NCIT:C46110 The cultural, social, psychological, and behavior norms that are associated with being a woman. C46110 Qualitative Concept Female Gender CL448708 OORO SeroNet Female_Gender Female Female Gender Female Gender NCIT:C48058 The capacity of a physical system to do work. C48058 Natural Phenomenon or Process Energy C0542479 Energy Energy Energy NCIT:C49157 The act of making necessary corrections or modifications. C49157 Activity Adjustment C0376209 Adjustment Adjusted Adjustment Adjustment NCIT:C49643 An age group comprised of individuals between 28 days to 23 months of age. C49643 Age Group Infant And Toddler C1708505 Infant_and_Toddler Infant And Toddler Infant And Toddler (28 Days to 23 Months) Infant And Toddler NCIT:C49835 Any device that is spherical in shape. C49835 Manufactured Object Ball Device C1706910 FDA Any component that is spherical in shape. Ball_Device_Component IMDRF:G04009 Ball Ball Device Ball Device NCIT:C50750 Traumatic damage of the spinal cord. C50750 Finding Spinal Cord Injury C0037929 Patient Code (Appendix B) FDA NICHD Traumatic damage of the spinal cord. Spinal_Cord_Injury IMDRF:E012401 Spinal Cord Injury Spinal Cord Injury NCIT:C61256 The act of observing something (and sometimes keeping a record of it). C61256 Activity Monitoring Monitoring C1283169 CDISC-GLOSS CTRP MRCT-Ctr Act of overseeing, tracking, observing, evaluating or supervising over time by a person, device or system. See also subject monitoring, medical monitoring, study monitoring, trial monitoring, data monitoring, risk based monitoring. In medicine, to regularly watch and check a person or condition to see if there is any change. Also refers to a device that records and/or displays patient data, such as for an electrocardiogram (EKG). To observe, check or evaluate something in a study over time. (https://mrctcenter.org/glossaryterm/monitor/) Monitoring Monitoring monitor monitoring Monitoring NCIT:C62739 C62739 Therapeutic or Preventive Procedure Exercise Intervention Exercise Intervention C1831738 CTRP Exercise_Intervention Exercise Intervention Exercise Intervention NCIT:C63507 A measure of joint flexibility consisting of flexion, how far it can bend, and extension, how far it can stretch. It is usually measured by the number of degrees from the starting position of a segment to its position at the end of its arc. C63507 Clinical Attribute Range of Motion C2607871 Range_of_Motion Joint Mobility Joint Range of Motion Joint Range of Movement Mobility Range of Motion Range of Motion NCIT:C64896 A form of treatment derived from Complimentary and Alternative Medicine (CAM) that uses various methods of movement in an effort to enhance physical, mental, and emotional health. C64896 Therapeutic or Preventive Procedure CAM Exercise Therapy CAM Exercise Therapy C0452240 CTRP Exercise_Therapy CAM Exercise Therapy Exercise Therapy CAM Exercise Therapy NCIT:C64897 C64897 Therapeutic or Preventive Procedure Yoga Yoga C1883583 CTRP An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems in cancer patients. Yoga_Therapy Yoga Yoga Therapy yoga Yoga NCIT:C69317 An instrument used for non-invasive determination of arterial blood pressure, generally consisting of an inflatable cuff and a pressure readout device, classically, a column of mercury. C69317 Medical Device Sphygmomanometer C0183427 Sphygmomanometer Sphygmomanometer Sphygmomanometer NCIT:C73425 A natural and periodic state of rest during which consciousness of the world is suspended. C73425 Organism Function Sleep C0037313 NICHD Sleep Sleep Sleep NCIT:C73554 The act of traveling by foot. C73554 Daily or Recreational Activity Walking C0080331 Walking Ambulation By Foot On Foot Walk Walking Walking NCIT:C80400 A quantitative measurement of the amount of glucose present in a sample of blood, obtained from a source that has abstained from nutrition, typically at least 8 hours prior to the sample collection time. C80400 Laboratory Procedure Fasting Blood Sugar Measurement C2825162 Fasting_Blood_Sugar_Measurement FBS Fasting Blood Sugar Fasting Blood Sugar Measurement Fasting Blood Sugar Measurement NCIT:C81011 A support consisting of a place to rest the foot while ascending or descending a stairway. C81011 Manufactured Object Stair C2825408 Stair Stair Step Stair NCIT:C85398 Running at a trot as a form of cardiopulmonary exercise. C85398 Daily or Recreational Activity Jogging C0022400 Jog Jogging Jogging NCIT:C85401 Riding a bicycle for transportation or recreation. C85401 Daily or Recreational Activity Bicycling C0005377 Bicycling Bike Bicycling NCIT:C87081 The recurrent, measured movements (rhythm) of a beating heart. C87081 Clinical Attribute Heart Rhythm C0232187 ACC/AHA NICHD Cardiac Rhythm Heart Rhythm Rhythm Heart Rhythm NCIT:C88163 A piece of exercise equipment used to walk or run on, for the purposes of cardiovascular training or testing. C88163 Manufactured Object Treadmill C0184069 Treadmill Treadmill NCIT:C88164 The ability of the heart and lungs to deliver blood and oxygen to the tissues during aerobic activity. It is a general measure of the relative conditioning of the heart and respiratory system. C88164 Classification Cardiorespiratory Fitness C2981722 Cardiorespiratory Fitness Cardiorespiratory Fitness NCIT:C88166 An instrument used for measuring a change in velocity. C88166 Manufactured Object Accelerometer Accelerometer C0178951 CTRP Acceleration Sensor Accelerometer Accelerometer Sensor Accelerometer NCIT:C89729 A mathematic formula used to estimate individual oxygen consumption, and thus energy expenditure, at rest and for various physical activities. C89729 Quantitative Concept Metabolic Equivalent of Task C2983100 MET Metabolic Equivalent of Task Metabolic Equivalent of Task (MET) Metabolic Equivalent of Task NCIT:C89800 The volume of air remaining in the lungs after a normal exhalation. C89800 Diagnostic Procedure Functional Residual Capacity C0016815 CDISC The volume of air remaining in the lungs after a normal exhalation. (NCI) FRC Functional Residual Capacity Functional Residual Capacity NCIT:C93039 C93039 Phenomenon or Process Galvanic Skin Response C0016989 A change in the heat and electricity passed through the skin by nerves and sweat. Skin conduction increases in certain emotional states and during hot flashes that happen with menopause. Galvanic Skin Response electrodermal response galvanic skin response skin conduction Galvanic Skin Response NCIT:C93097 C93097 Therapeutic or Preventive Procedure Mind/body Exercise Mind/body Exercise C2985433 CTRP A form of exercise that combines body movement with mental focus and controlled breathing to improve strength, balance, flexibility, and overall health. Examples of mind/body exercises are yoga, tai chi, and qigong. Mind/body Exercise mind/body exercise Mind/body Exercise NCIT:C93098 C93098 Therapeutic or Preventive Procedure Qigong Qigong C0282077 CTRP A form of traditional Chinese mind/body exercise and meditation that uses slow and precise body movements with controlled breathing and mental focusing to improve balance, flexibility, muscle strength, and overall health. Qigong qigong Qigong NCIT:C93099 C93099 Therapeutic or Preventive Procedure Tai Chi Tai Chi C0376403 CTRP A form of traditional Chinese mind/body exercise and meditation that uses slow sets of body movements and controlled breathing. Tai chi is done to improve balance, flexibility, muscle strength, and overall health. Tai Chi tai chi Tai Chi NCIT:C94250 A condition in which body mass index falls between 25 and 29.9. C94250 Finding Overweight C0497406 Being too heavy for one's height. Excess body weight can come from fat, muscle, bone, and/or water retention. Being overweight does not always mean being obese. Overweight overweight Overweight NCIT:C94738 The act of propelling the body through water by movement of the arms and/or legs. C94738 Daily or Recreational Activity Swimming C0039003 ACC/AHA Propel the body through the water by using the limbs. Swim Swimming Swimming NCIT:C94739 A system of free movements designed to develop muscular tone and promote physical fitness. C94739 Daily or Recreational Activity Calisthenics C0006759 Calisthenics Calisthenics NCIT:C94741 A type of resistance exercise and strength training that involves moving weights by muscle contraction. C94741 Daily or Recreational Activity Weight Lifting C0043095 Weight Lifting Weight Training Weight Lifting NCIT:C94748 The act of tending a yard as a chore or hobby. C94748 Daily or Recreational Activity Yard Work C2986650 Lawn Care Yard Work Yardwork Yard Work OBI:0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider See also OMRSE:00000011 'patient role' GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role OBI:0001000 questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OCCO:00000068 The ability to use short bursts of muscle force to propel oneself (as in jumping or sprinting), or to throw an object. Oliver He Sam Smith https://www.onetonline.org/find/descriptor/browse/1.A/1.A.1/1.A.1.g 1.A.3.a.2 explosive strength OGMS:0000045 A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder OGMS:0000102 A disorder that involves some structural damage that is immediately caused by a catastrophic external force. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015 injury OPMI:0000160 body weight OPMI:0000161 A body weight that is obtained immediately after birth Oliver He, Edison Ong NCIT_C76325 birth weight An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. quality PATO:0000047 biological sex PATO:0000047 A behavioral quality inhering in a bearer by virtue of having physical steadiness. quality PATO:0000185 balance PATO:0000185 A behavioral quality inhering in a bearer by virtue of the bearer's having or lacking skillful and effective interaction of movement. quality PATO:0000188 coordination PATO:0000188 A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. quality PATO:0000383 female PATO:0000383 A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. quality PATO:0000384 male PATO:0000384 A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction. quality PATO:0001028 acceleration PATO:0001028 A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. quality PATO:0001543 flexibility PATO:0001543 An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. quality PATO:0001894 phenotypic sex PATO:0001894 A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. quality PATO:0020000 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, we have XY, XX, though abnormal XXY, X0, XYY, and other combinations are possible. genotypic sex PATO:0020000 A biological sex quality inhering in an individual based upon genotypic composition that confers the capability for an organism to differentiate male gonads. quality PATO:0020001 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, this would be XY, though abnormal XXY and XYY would also result in a male phenotypic outcome. male genotypic sex PATO:0020001 A biological sex quality inhering in an individual or a population based upon genotypic composition that confers the capability for an organism to differentiate female gonads. quality PATO:0020002 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, this would be XX, though abnormal X0 and XXX would also result in a female phenotypic outcome. female genotypic sex PATO:0020002 SCDO:1000755 The temperature of the oral cavity. Sufficient SCDO:1000755 VSO:0000025 Oral Body Temperature Oral Temperature SCDO:1000756 The temperature of the external acoustic tube. Sufficient SCDO:1000756 VSO:0000045 Tympanic (ear) Temperature Tympanic Body Temperature Tympanic Temperature SCDO:1000757 The temperature of the lumen of the rectum. Sufficient SCDO:1000757 VSO:0000033 Rectal Body Temperature Rectal Temperature SCDO:1000758 The temperature of the axillary fossa. Sufficient SCDO:1000758 VSO:0000003 Armpit Temperature Axillary (armpit) Temperature Axillary Temperature Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. Portion of connective tissue that connects bone or cartilage.[TAO] uberon UBERON:0000211 ligament UBERON:0000211 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. uberon UBERON:0001062 anatomical entity UBERON:0001062 Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] uberon UBERON:0001134 skeletal muscle tissue UBERON:0001134 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] uberon UBERON:0002385 muscle tissue UBERON:0002385 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] uberon UBERON:0004288 skeleton UBERON:0004288 example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument Researcher ORCID=0000-0001-6677-8489 Aleix Puig-Barbé Researcher ORCID=0000-0001-6677-8489 Aleix Puig-Barbé Researcher Austin Meier Researcher Austin Meier researcher Shawn Zheng Kai Tan researcher Shawn Zheng Kai Tan researcher Raymund Stefancsik researcher Raymund Stefancsik researcher, metadata, diseases, University of Maryland Lynn Schriml researcher, metadata, diseases, University of Maryland Lynn Schriml researcher William D Duncan researcher William D Duncan data scientist Anne Thessen data scientist Anne Thessen researcher (ORCID 0000-0002-2999-0103) Jie Zheng researcher (ORCID 0000-0002-2999-0103) Jie Zheng researcher Pier Luigi Buttigieg researcher Pier Luigi Buttigieg researcher Christian J Stoeckert researcher Christian J Stoeckert bioinformatics researcher Christopher J. Mungall bioinformatics researcher Christopher J. Mungall researcher David Osumi-Sutherland researcher David Osumi-Sutherland researcher Lauren E. Chan researcher Lauren E. Chan researcher Marie-Angélique Laporte researcher Marie-Angélique Laporte researcher James P. Balhoff researcher James P. Balhoff researcher (ORCID 0000-0002-8844-9165) Damion M Dooley researcher (ORCID 0000-0002-8844-9165) Damion M Dooley researcher Lindsay G Cowell researcher Lindsay G Cowell Canadian biocurator Pascale Gaudet Canadian biocurator Pascale Gaudet researcher Mathias Brochhausen researcher Mathias Brochhausen Researcher ORCID=0000-0003-1909-9269 S. Clint Dowland Researcher ORCID=0000-0003-1909-9269 S. Clint Dowland researcher Anna Maria Masci researcher Anna Maria Masci Researcher ORCID=0000-0003-2620-0345 Asiyah Yu Lin Researcher ORCID=0000-0003-2620-0345 Asiyah Yu Lin software/data engineer Jorrit Poelen software/data engineer Jorrit Poelen American chemist Charles Tapley Hoyt American chemist Charles Tapley Hoyt data item data item data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term 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 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split 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 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 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal 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 defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class 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 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 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 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 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 scheduled for obsoletion on or after ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. out of scope 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 CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms abbreviation A synonym type for describing ambiguous synonyms ambiguous synonym A synonym type for describing dubious synonyms 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 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 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 UK spelling synonym A synonym type for common misspellings misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 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. 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 legal name 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 is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant Bairong Shen Danting Li Hui Zong Jiao Wang Ke Zhang Min Jiang Ting Bao Tong Tang Xingyun Liu Yin Yang A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise. EXMO Exercise Medicine Ontology https://creativecommons.org/licenses/by/4.0/ This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X